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  • 99
    Thermo Fisher biofilm stain
    Representative fluorescence microscopic images of implants (50x objective) after bacterial infection in vivo. The bar indicates 100 µ m. The red coloured areas in the picture correspond to the locations covered by <t>biofilms</t> of methicillin-resistant Staphylococcus aureus (MRSA). (a) HA coating at 1 day, (b) HA coating at 3 days, (c) HA coating at 7 days, (d) 3% Ag-HA coating at 1 day, (e) 3% Ag-HA coating at 3 days, and (f) 3% Ag-HA coating at 7 days. Calculated BCRs: (a) 16.0%, (b) 26.6%, (c) 30.1%, (d) 8.9%, (e) 14.6%, and (f) 13.7%.
    Biofilm Stain, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Johnson & Johnson biofilms
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Biofilms, supplied by Johnson & Johnson, used in various techniques. Bioz Stars score: 80/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    biofilms - by Bioz Stars, 2020-04
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    89
    Bio-Rad biofilm a
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Biofilm A, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 89/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Rayto Life biofilm
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Biofilm, supplied by Rayto Life, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    MJ Research biofilm a
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Biofilm A, supplied by MJ Research, used in various techniques. Bioz Stars score: 80/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    GraphPad Prism Inc biofilm chemostats
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Biofilm Chemostats, supplied by GraphPad Prism Inc, used in various techniques. Bioz Stars score: 96/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Denville Scientific blue biofilm
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Blue Biofilm, supplied by Denville Scientific, used in various techniques. Bioz Stars score: 93/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Olympus biofilm distribution
    Percentage <t>biofilm</t> formed and inhibited in Staphylococcus aureus. (A) Expression levels of SarA in the bacterial strains taken in this study at the log and late phases of growth. (B) Percentage biofilm formation of SarA mutant ALC637 (ΔsarA::795 Tn917LTV1) on treatment and no treatment with 2-[(Methylamino)methyl]phenol by crystal violet method. (C,D) Percentage biofilm inhibition in clinical S. aureus isolates P1966 and AB459 by 2-[(Methylamino)methyl]phenol. All the assays were done in triplicates and the values were expressed as mean ± SD. ∗ Indicates significantly different ( p ≤ 0.05) when compared to untreated (control) with 2-[(Methylamino)methyl]phenol. NS denotes not significant ( P > 0.05).
    Biofilm Distribution, supplied by Olympus, used in various techniques. Bioz Stars score: 93/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Waters Corporation biofilm formation
    Colonization patterns of P. fluorescens strain SBW25 on non-mycorrhizal Aspen roots. Z-stack reconstruction of root surface topology was performed by SDCM at x100 magnification. SBW25 cells are green and plant tissues are visualized using red auto-fluorescence. Scale is indicated by a white bar. Images are representative of colonization patterns on all the observed plant roots. (A) Long strip (LS) colonization pattern observed 1 week after inoculation, (B) long patch (LP) patterns after 2 weeks, (C) short patch (SP) microcolonies formed after 3 weeks, (D,E) bulge–like structures observed along roots after 4-5 weeks, with enlarged images showing dense <t>biofilm-like</t> structures (DBS) in which cells appear encased in a matrix.
    Biofilm Formation, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 92/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Fisher Scientific biofilm substratum
    The S-layer and type IV pili are required for <t>biofilm</t> formation by Synechocystis . The “attached” data series shows crystal violet binding measured at the OD 600 . The “suspended” data series shows planktonic growth measured at OD 730 . Wza, SD517; Slyr, SD523; PilC, SD519; WT, SD100. Both data series are shown on the same y axis. Error bar corresponds to one standard deviation from the sample mean.
    Biofilm Substratum, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 95/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Innovotech biofilm inoculator
    The S-layer and type IV pili are required for <t>biofilm</t> formation by Synechocystis . The “attached” data series shows crystal violet binding measured at the OD 600 . The “suspended” data series shows planktonic growth measured at OD 730 . Wza, SD517; Slyr, SD523; PilC, SD519; WT, SD100. Both data series are shown on the same y axis. Error bar corresponds to one standard deviation from the sample mean.
    Biofilm Inoculator, supplied by Innovotech, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Innovotech biofilms biofilms
    Persister cells in H. volcanii <t>biofilms.</t> Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p
    Biofilms Biofilms, supplied by Innovotech, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    75
    Bitplane biofilm analysis xtension
    Persister cells in H. volcanii <t>biofilms.</t> Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p
    Biofilm Analysis Xtension, supplied by Bitplane, used in various techniques. Bioz Stars score: 75/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Corning Life Sciences biofilm construction biofilms
    Viable counts of each bacterial species present in the initial inoculum (per well) and in the 3‐day old <t>biofilms</t> ( n = 7). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = Aggregatibacter actinomycetemcomitans . Error bars: standard error
    Biofilm Construction Biofilms, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Becton Dickinson biofilm formation biofilms
    Confocal Laser Scanning Microscopy of <t>biofilm</t> formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static <t>biofilms</t> were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100
    Biofilm Formation Biofilms, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Kodak Corp xar biofilm
    Confocal Laser Scanning Microscopy of <t>biofilm</t> formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static <t>biofilms</t> were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100
    Xar Biofilm, supplied by Kodak Corp, used in various techniques. Bioz Stars score: 92/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Amazon biofilms
    Confocal Laser Scanning Microscopy of <t>biofilm</t> formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static <t>biofilms</t> were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100
    Biofilms, supplied by Amazon, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Amorphous Materials Inc biofilms
    PittGG biofilm formation is stimulated by ampicillin in a narrow concentration range. Crystal violet assay of 1-day PittGG <t>biofilms,</t> formed in the presence of increasing amounts of ampicillin up 300 ng/mL, showed a stimulation of biofilm formation at 170 ng/mL concentration.
    Biofilms, supplied by Amorphous Materials Inc, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Avantor biofilms
    Tracking and quantification of <t>biofilm</t> community structure changes after temperature increase. ( a ) viSNE submaps ( Fig. 2a ) belonging to days 0, 7, 14 and 21 post temperature increase. More colour-intense regions of the submaps depict regions of higher cell density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, five independent microcosms) and time points indicated that the detected changes in community structure were governed by time point and not biological or technical noise ( Supplementary Fig. 10 ). ( b ) Quantification of subpopulations defined in Fig. 2b , pooled from five biological replicates for each time point after temperature increase (all biological replicates are depicted in Supplementary Fig. 11 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 9 .
    Biofilms, supplied by Avantor, used in various techniques. Bioz Stars score: 97/100, based on 121 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    83
    BioSpec biofilms
    Change in thickness of <t>biofilms</t> with time, as measured by confocal microscopy. The depth of the biofilm represents the mean of five randomly chosen sites within each biofilm.
    Biofilms, supplied by BioSpec, used in various techniques. Bioz Stars score: 83/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    BioTek Instruments biofilm
    <t>Biofilm</t> production dynamics after extubation in 9 ETT-MRSA isolates under O 2 or 5% CO 2 Each color-bar represents the biofilm production of each ETT-MRSA isolate compared with the MRSA-in over days 1–8 after extubation. ( A ) Biofilm production dynamics under O 2 . Maximum biofilm production was on day 2. ( B ) Biofilm production dynamics under CO 2 . Maximum biofilm production was on day 1. Since the 5% CO 2 atmosphere better mimics the atmospheric conditions of mechanical ventilation. When ETT-MRSA are rapidly switched from the ETT environment to O 2 alone, they would need a day to adapt their metabolism to the new atmospheric conditions. Black points represent median biofilm production of the 9 isolates each day. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .
    Biofilm, supplied by BioTek Instruments, used in various techniques. Bioz Stars score: 96/100, based on 128 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    98
    Bitplane biofilms
    Tree diagrams showing grouping of values for quantitative parameters of <t>biofilms.</t> These are biovolume ( A ) percentage of surface covered ( B ) roughness ( C ) and maximum thickness ( D ) corresponding to 20 strains of Listeria monocytogenes taken from meat (Euclidean distance, unweighted pair-group average).
    Biofilms, supplied by Bitplane, used in various techniques. Bioz Stars score: 98/100, based on 333 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Carl Zeiss biofilms
    Changes in V. vulnificus biofilm composition in response to a lytic phage. The MO-6/24-Tn and CMCP6 strains were grown in mixed culture on crab shells in 12-well plates for 24 h. The <t>biofilms</t> were then exposed to the MO-6/24-specific lytic phage 152-A10
    Biofilms, supplied by Carl Zeiss, used in various techniques. Bioz Stars score: 99/100, based on 1764 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Eppendorf AG biofilm
    Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the <t>biofilm.</t> Negative depths in the profile represent the distance from the biofilm surface into the wastewater.
    Biofilm, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 94/100, based on 125 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Fisher Scientific biofilms
    Phloxine B staining of C. albicans ) and photographed (Arcturus). Differences in staining are evident during the 6 h of <t>biofilm</t> development. (A) T = 30; (B) T = 90; (C) T = 270. Magnification, ×40.
    Biofilms, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 94/100, based on 171 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Hitachi Ltd biofilm
    The antibacterial effects of Nano-CHX treatment for 24 h on the mixed-species <t>biofilms</t> of S. sobrinus , F. nucleatum and P. gingivalis . Representative scanning electron microscopy images: B vs. A (blank nanoparticles); and confocal laser scanning microscopy images: D vs. C (blank nanoparticles).
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    97
    ibidi biofilms
    Quantitative analysis of macrophage migration within 48 h <t>biofilms</t> prepared from C. albicans strains CAI4, pmr1 Δ, and pmr1 Δ+ PMR1 . The chart shows mean relative macrophage velocity + SD relative to macrophage velocity of J774.1 macrophages added in suspension to CAI4 (wild type biofilms). Migration data over a 30 min period are shown. No statistical significance of mean differences was determined using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests.
    Biofilms, supplied by ibidi, used in various techniques. Bioz Stars score: 97/100, based on 136 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    MatTek biofilms
    Typical light microscopy images of (a) full-thickness tissue after infection with acrylic coupons only (no biofilm), showing no damage to epithelium; (b) full-thickness tissue after infection with bacteria-only biofilm, showing slight tissue damage and clustering of <t>biofilms</t> on the epithelial surface (indicated by arrows); (c) full-thickness tissue after infection with Candida albicans -only biofilm, showing substantial epithelial damage and biofilms clustered on the surface of the epithelium (indicated by arrows); (d) full-thickness tissue after infection with mixed-species biofilm, showing extensive epithelial damage and microbial invasion through the epithelium (indicated by arrows). Stained with haematoxylin and eosin. The scale bar represents 50 µm.
    Biofilms, supplied by MatTek, used in various techniques. Bioz Stars score: 97/100, based on 152 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Merck KGaA biofilm
    <t>Biofilm</t> formation inhibition assay performed on S. epidermidis . Values are mean of three replicates, ± standard error.
    Biofilm, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 94/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore biofilms
    Rapid development of nfxB mutants in a 24-h-old PAO1 flow cell biofilm treated with low-dose CIP. The <t>biofilms</t> of PAO1- mCherry -P CD - gfp + were grown in flow cell chambers with a continuous flow of minimal medium for 24 h at 37°C and then grown for an additional 24 h with 0.2 μg/ml CIP (24 h +CIP for 24 h) or without CIP (24 h −CIP for 24 h). Red shows wild-type cells (elongated or filamentous) due to the constitutive expression of mCherry, and green shows nfxB mutants due to the expression of GFP via the P CD - gfp + reporter. z-stacks were generated by using a Zeiss LSM 710 microscope and processed with Imaris 8.2 software (Bitplane). Top-row images show orthogonal 3D views, and middle and bottom (for treated biofilms only) rows show perspective 3D views of biofilms with an overlay of red and green fluorescence. The images shown are representative of results for two independent flow cell channels.
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    Nikon biofilms
    Mechanics of cell reorientation in modeled <t>biofilms,</t> ( a-b ) Properties of individual cells at the time t r of reorientation, defined as the time of the peak of total force on the cell prior to it becoming vertical. Analyses are shown for all reorientation events among different biofilms simulated for a range of initial cell lengths ℓ 0 ( a ) Distributions of reorientation “surface pressure” p r , defined as the total contact force in the xy plane acting on a cell at time t r , normalized by the cell’s perimeter, versus cell cylinder length ℓ . The white dashed curve shows the average reorientation surface pressure ⟨ p r ⟩ as a function of ℓ . The magenta dashed curve shows the threshold surface pressure p t from linear stability analysis for a modeled cell under uniform pressure, depicted schematically in the inset, ( b ) Distributions of the logarithm of reorientation torque τ r , defined as the magnitude of the torque on a cell due to cell-cell contact forces in the z direction at time t r , for different cell cylinder lengths ℓ . The white dashed curve shows the average values ⟨log τ r ⟩ as a function of ℓ . The orange dashed curve shows the scaling τ t ~ ℓ 2 of the threshold torque for peeling from linear stability analysis for a modeled cell, depicted schematically in the inset, ( c ) Mean reorientation length ⟨ ℓ r ⟩ (red), defined as the average value of cell length at t r , and mean cell cylinder length ⟨ ℓ ⟩ (gray), defined as the average length of all horizontal cells over all times of biofilm growth, averaged over ten simulated biofilms, each with initial cell cylinder length ℓ 0 , plotted versus ℓ 0 . The inset shows the distribution of reorientation lengths (red) and horizontal surface-cell lengths (gray) for ℓ 0 = 1 μm. ( d ) Mean avalanche size ⟨ N ⟩, defined as the average size of a cluster of reorienting cells that are proximal in space and time ( Supplementary Figs. 8 - 10 ), versus initial cell length ℓ 0 for the experimental biofilm (red triangle) and the modeled biofilm (red circles). Open gray triangle and circles indicate the corresponding mean avalanche sizes for a null model. Inset shows a side view of cell configurations in the xy plane at times t r for all reorientation events in a simulated biofilm with ℓ 0 = 2.5 μm. Reorientation events are colored alike if they belong to the same avalanche. Scale bars: 10 μm and 1 hour.
    Biofilms, supplied by Nikon, used in various techniques. Bioz Stars score: 99/100, based on 642 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Olympus biofilm
    Degree of saturation of membrane fatty acids of Sphingomonas sp. LH128 <t>biofilm</t> cells grown in flow chambers without solute stress (control) and with acute or chronic solute stress. The values shown are the average of three biological replicates with the indicated standard deviations. The asterisk indicates a statistically significant difference from the control (*, P
    Biofilm, supplied by Olympus, used in various techniques. Bioz Stars score: 95/100, based on 228 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Representative fluorescence microscopic images of implants (50x objective) after bacterial infection in vivo. The bar indicates 100 µ m. The red coloured areas in the picture correspond to the locations covered by biofilms of methicillin-resistant Staphylococcus aureus (MRSA). (a) HA coating at 1 day, (b) HA coating at 3 days, (c) HA coating at 7 days, (d) 3% Ag-HA coating at 1 day, (e) 3% Ag-HA coating at 3 days, and (f) 3% Ag-HA coating at 7 days. Calculated BCRs: (a) 16.0%, (b) 26.6%, (c) 30.1%, (d) 8.9%, (e) 14.6%, and (f) 13.7%.

    Journal: BioMed Research International

    Article Title: Silver-Containing Hydroxyapatite Coating Reduces Biofilm Formation by Methicillin-Resistant Staphylococcus aureus In Vitro and In Vivo

    doi: 10.1155/2016/8070597

    Figure Lengend Snippet: Representative fluorescence microscopic images of implants (50x objective) after bacterial infection in vivo. The bar indicates 100 µ m. The red coloured areas in the picture correspond to the locations covered by biofilms of methicillin-resistant Staphylococcus aureus (MRSA). (a) HA coating at 1 day, (b) HA coating at 3 days, (c) HA coating at 7 days, (d) 3% Ag-HA coating at 1 day, (e) 3% Ag-HA coating at 3 days, and (f) 3% Ag-HA coating at 7 days. Calculated BCRs: (a) 16.0%, (b) 26.6%, (c) 30.1%, (d) 8.9%, (e) 14.6%, and (f) 13.7%.

    Article Snippet: Calculation of Biofilm Coverage Rates (BCRs) All disks (from in vitro and in vivo experiments) were rinsed twice with 500 μ L of sterile PBS and stained with biofilm stain (FilmTracer calcein red-orange biofilm stain, Thermo Fisher Scientific) for 1 h. After staining, disks were washed twice with 500 μ L of sterile PBS.

    Techniques: Fluorescence, Infection, In Vivo

    Box-and-whisker plots of biofilm coverage rates (BCRs) of implants after bacterial culture for 7 days and 14 days in vitro. In the 7-day experiment, 49 images of HA coating, including 14 images of 0.5% Ag-HA, 14 images of 1% Ag-HA, and 21 images of 3% Ag-HA, were used. In the 14-day experiment, 63 images of HA and 21 images of each group of Ag-HA were used. ∗ denotes significant differences between the BCRs of HA and each concentration of Ag-HA. The significance levels are as follows: 7 days: 0.5% Ag-HA, p = 0.011; 1% Ag-HA, p

    Journal: BioMed Research International

    Article Title: Silver-Containing Hydroxyapatite Coating Reduces Biofilm Formation by Methicillin-Resistant Staphylococcus aureus In Vitro and In Vivo

    doi: 10.1155/2016/8070597

    Figure Lengend Snippet: Box-and-whisker plots of biofilm coverage rates (BCRs) of implants after bacterial culture for 7 days and 14 days in vitro. In the 7-day experiment, 49 images of HA coating, including 14 images of 0.5% Ag-HA, 14 images of 1% Ag-HA, and 21 images of 3% Ag-HA, were used. In the 14-day experiment, 63 images of HA and 21 images of each group of Ag-HA were used. ∗ denotes significant differences between the BCRs of HA and each concentration of Ag-HA. The significance levels are as follows: 7 days: 0.5% Ag-HA, p = 0.011; 1% Ag-HA, p

    Article Snippet: Calculation of Biofilm Coverage Rates (BCRs) All disks (from in vitro and in vivo experiments) were rinsed twice with 500 μ L of sterile PBS and stained with biofilm stain (FilmTracer calcein red-orange biofilm stain, Thermo Fisher Scientific) for 1 h. After staining, disks were washed twice with 500 μ L of sterile PBS.

    Techniques: Whisker Assay, In Vitro, Concentration Assay

    Confocal microscopy images of biofilms stained with Filmtracer (which does not label Nasopore) demonstrating the effect of incubation with naïve rabbit serum (panel a), amoxicillin/clavulanate (panel b), rabbit anti-IHF (panel c) and rabbit anti-IHF

    Journal: The Laryngoscope

    Article Title: Antibodies directed against Integration Host Factor Mediate Biofilm Clearance from Nasopore®

    doi: 10.1002/lary.24183

    Figure Lengend Snippet: Confocal microscopy images of biofilms stained with Filmtracer (which does not label Nasopore) demonstrating the effect of incubation with naïve rabbit serum (panel a), amoxicillin/clavulanate (panel b), rabbit anti-IHF (panel c) and rabbit anti-IHF

    Article Snippet: The remaining wells were stained with 50 uL of Filmtracer Biofilm stain (Life Technologies, Grand Island, NY).

    Techniques: Confocal Microscopy, Staining, Incubation, Immunohistofluorescence

    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The biofilms were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.

    Journal: BMC Microbiology

    Article Title: High-throughput metal susceptibility testing of microbial biofilms

    doi: 10.1186/1471-2180-5-53

    Figure Lengend Snippet: An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The biofilms were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.

    Article Snippet: In general, biofilms formed using a trough have a 5- to 10-fold greater cell density than those formed using the microtiter plate format (J.J. Harrison, H. Ceri and C. Stremick, unpublished data).

    Techniques: High Throughput Screening Assay, Incubation

    Growth of bacterial biofilms in the MBEC assay . (A) Mean cell density of Pseudomonas aeruginosa ATCC 27853 biofilms on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.842 using one-way ANOVA). (B) SEM photomicrograph of a P. aeruginosa biofilm on the peg surface. (C) Mean cell density of Escherichia coli TG1 on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.274 using one-way ANOVA). (D) SEM photomicrograph of an E. coli biofilm on the peg surface. The bar represents 5 μm.

    Journal: BMC Microbiology

    Article Title: High-throughput metal susceptibility testing of microbial biofilms

    doi: 10.1186/1471-2180-5-53

    Figure Lengend Snippet: Growth of bacterial biofilms in the MBEC assay . (A) Mean cell density of Pseudomonas aeruginosa ATCC 27853 biofilms on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.842 using one-way ANOVA). (B) SEM photomicrograph of a P. aeruginosa biofilm on the peg surface. (C) Mean cell density of Escherichia coli TG1 on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.274 using one-way ANOVA). (D) SEM photomicrograph of an E. coli biofilm on the peg surface. The bar represents 5 μm.

    Article Snippet: In general, biofilms formed using a trough have a 5- to 10-fold greater cell density than those formed using the microtiter plate format (J.J. Harrison, H. Ceri and C. Stremick, unpublished data).

    Techniques: Standard Deviation

    Percentage biofilm formed and inhibited in Staphylococcus aureus. (A) Expression levels of SarA in the bacterial strains taken in this study at the log and late phases of growth. (B) Percentage biofilm formation of SarA mutant ALC637 (ΔsarA::795 Tn917LTV1) on treatment and no treatment with 2-[(Methylamino)methyl]phenol by crystal violet method. (C,D) Percentage biofilm inhibition in clinical S. aureus isolates P1966 and AB459 by 2-[(Methylamino)methyl]phenol. All the assays were done in triplicates and the values were expressed as mean ± SD. ∗ Indicates significantly different ( p ≤ 0.05) when compared to untreated (control) with 2-[(Methylamino)methyl]phenol. NS denotes not significant ( P > 0.05).

    Journal: Frontiers in Microbiology

    Article Title: Staphylococcus aureus Quorum Regulator SarA Targeted Compound, 2-[(Methylamino)methyl]phenol Inhibits Biofilm and Down-Regulates Virulence Genes

    doi: 10.3389/fmicb.2017.01290

    Figure Lengend Snippet: Percentage biofilm formed and inhibited in Staphylococcus aureus. (A) Expression levels of SarA in the bacterial strains taken in this study at the log and late phases of growth. (B) Percentage biofilm formation of SarA mutant ALC637 (ΔsarA::795 Tn917LTV1) on treatment and no treatment with 2-[(Methylamino)methyl]phenol by crystal violet method. (C,D) Percentage biofilm inhibition in clinical S. aureus isolates P1966 and AB459 by 2-[(Methylamino)methyl]phenol. All the assays were done in triplicates and the values were expressed as mean ± SD. ∗ Indicates significantly different ( p ≤ 0.05) when compared to untreated (control) with 2-[(Methylamino)methyl]phenol. NS denotes not significant ( P > 0.05).

    Article Snippet: Two and three-dimensional images were captured using a confocal laser scanning microscope with a 40× objective lens to show biofilm distribution (Olympus FLUOVIEW, FV1000).

    Techniques: Expressing, Mutagenesis, Inhibition

    Confocal laser scanning microscopy imaging. Representative images showing the biofilm inhibition effects of 2-[(Methylamino)methyl]phenol at varying concentrations on Staphylococcus aureus P1966 and AB459 during log phase of growth (6 h). The results were in concordance with microtitre plate quantitative assays where biofilm inhibition was more at 1.25 μM. Scale bar in images represents 50 μm.

    Journal: Frontiers in Microbiology

    Article Title: Staphylococcus aureus Quorum Regulator SarA Targeted Compound, 2-[(Methylamino)methyl]phenol Inhibits Biofilm and Down-Regulates Virulence Genes

    doi: 10.3389/fmicb.2017.01290

    Figure Lengend Snippet: Confocal laser scanning microscopy imaging. Representative images showing the biofilm inhibition effects of 2-[(Methylamino)methyl]phenol at varying concentrations on Staphylococcus aureus P1966 and AB459 during log phase of growth (6 h). The results were in concordance with microtitre plate quantitative assays where biofilm inhibition was more at 1.25 μM. Scale bar in images represents 50 μm.

    Article Snippet: Two and three-dimensional images were captured using a confocal laser scanning microscope with a 40× objective lens to show biofilm distribution (Olympus FLUOVIEW, FV1000).

    Techniques: Confocal Laser Scanning Microscopy, Imaging, Inhibition

    Colonization patterns of P. fluorescens strain SBW25 on non-mycorrhizal Aspen roots. Z-stack reconstruction of root surface topology was performed by SDCM at x100 magnification. SBW25 cells are green and plant tissues are visualized using red auto-fluorescence. Scale is indicated by a white bar. Images are representative of colonization patterns on all the observed plant roots. (A) Long strip (LS) colonization pattern observed 1 week after inoculation, (B) long patch (LP) patterns after 2 weeks, (C) short patch (SP) microcolonies formed after 3 weeks, (D,E) bulge–like structures observed along roots after 4-5 weeks, with enlarged images showing dense biofilm-like structures (DBS) in which cells appear encased in a matrix.

    Journal: Frontiers in Microbiology

    Article Title: Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

    doi: 10.3389/fmicb.2018.00853

    Figure Lengend Snippet: Colonization patterns of P. fluorescens strain SBW25 on non-mycorrhizal Aspen roots. Z-stack reconstruction of root surface topology was performed by SDCM at x100 magnification. SBW25 cells are green and plant tissues are visualized using red auto-fluorescence. Scale is indicated by a white bar. Images are representative of colonization patterns on all the observed plant roots. (A) Long strip (LS) colonization pattern observed 1 week after inoculation, (B) long patch (LP) patterns after 2 weeks, (C) short patch (SP) microcolonies formed after 3 weeks, (D,E) bulge–like structures observed along roots after 4-5 weeks, with enlarged images showing dense biofilm-like structures (DBS) in which cells appear encased in a matrix.

    Article Snippet: In many Gram-negative bacteria, quorum sensing (QS) plays a pivotal role in biofilm formation through the production and sensing of small diffusible autoinducer (AI) molecules, such as N-Acyl homoserine lactones (AHLs) that monitor cell density and regulate cell behaviors (Newton and Fray, ; Waters and Bassler, ).

    Techniques: Fluorescence, Stripping Membranes

    Internal architecture of bacterial biofilms on Aspen roots. 3D-volumes of cell structures were unstacked to deploy a panel of 2D-slices revealing the internal colony architecture. (A) Unstacking of a SBW25 macro-colony highlighting void spaces. One slice every 0.5 μm is shown. (B) Unstacking of a z-directional movie. Maximum intensity and Orthogonal projections from a reconstruction from 60 planes (left) and panel of 2D-slices revealing internal canals.

    Journal: Frontiers in Microbiology

    Article Title: Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

    doi: 10.3389/fmicb.2018.00853

    Figure Lengend Snippet: Internal architecture of bacterial biofilms on Aspen roots. 3D-volumes of cell structures were unstacked to deploy a panel of 2D-slices revealing the internal colony architecture. (A) Unstacking of a SBW25 macro-colony highlighting void spaces. One slice every 0.5 μm is shown. (B) Unstacking of a z-directional movie. Maximum intensity and Orthogonal projections from a reconstruction from 60 planes (left) and panel of 2D-slices revealing internal canals.

    Article Snippet: In many Gram-negative bacteria, quorum sensing (QS) plays a pivotal role in biofilm formation through the production and sensing of small diffusible autoinducer (AI) molecules, such as N-Acyl homoserine lactones (AHLs) that monitor cell density and regulate cell behaviors (Newton and Fray, ; Waters and Bassler, ).

    Techniques:

    The S-layer and type IV pili are required for biofilm formation by Synechocystis . The “attached” data series shows crystal violet binding measured at the OD 600 . The “suspended” data series shows planktonic growth measured at OD 730 . Wza, SD517; Slyr, SD523; PilC, SD519; WT, SD100. Both data series are shown on the same y axis. Error bar corresponds to one standard deviation from the sample mean.

    Journal: Applied and Environmental Microbiology

    Article Title: Axenic Biofilm Formation and Aggregation by Synechocystis sp. Strain PCC 6803 Are Induced by Changes in Nutrient Concentration and Require Cell Surface Structures

    doi: 10.1128/AEM.02192-18

    Figure Lengend Snippet: The S-layer and type IV pili are required for biofilm formation by Synechocystis . The “attached” data series shows crystal violet binding measured at the OD 600 . The “suspended” data series shows planktonic growth measured at OD 730 . Wza, SD517; Slyr, SD523; PilC, SD519; WT, SD100. Both data series are shown on the same y axis. Error bar corresponds to one standard deviation from the sample mean.

    Article Snippet: Three milliliters of culture was added to each well of a 12-well plate (Corning Costar, catalog no. 07–200–82; Fisher Scientific) that contained a 22-mm-thick glass coverslip as a biofilm substratum (12–540–B; Fisher Scientific).

    Techniques: Binding Assay, Standard Deviation

    Biofouling of a nonaxenic rooftop photobioreactor during growth of WT Synechocystis . (A) During lag phase, no biofilm growth was evident. (B to G) Images taken every 24 h during rapid growth (approximate doubling every 24 h over a period of 5 days). Biofouling such as in the representative images shown was correlated with using hard tap water to prepare BG11 medium; no biofouling was evident when softened tap water was used. Scale bar, ~2 cm. The glass PBR tubes are ~20 cm in diameter.

    Journal: Applied and Environmental Microbiology

    Article Title: Axenic Biofilm Formation and Aggregation by Synechocystis sp. Strain PCC 6803 Are Induced by Changes in Nutrient Concentration and Require Cell Surface Structures

    doi: 10.1128/AEM.02192-18

    Figure Lengend Snippet: Biofouling of a nonaxenic rooftop photobioreactor during growth of WT Synechocystis . (A) During lag phase, no biofilm growth was evident. (B to G) Images taken every 24 h during rapid growth (approximate doubling every 24 h over a period of 5 days). Biofouling such as in the representative images shown was correlated with using hard tap water to prepare BG11 medium; no biofouling was evident when softened tap water was used. Scale bar, ~2 cm. The glass PBR tubes are ~20 cm in diameter.

    Article Snippet: Three milliliters of culture was added to each well of a 12-well plate (Corning Costar, catalog no. 07–200–82; Fisher Scientific) that contained a 22-mm-thick glass coverslip as a biofilm substratum (12–540–B; Fisher Scientific).

    Techniques:

    Persister cells in H. volcanii biofilms. Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p

    Journal: Frontiers in Microbiology

    Article Title: Archaeal Persisters: Persister Cell Formation as a Stress Response in Haloferax volcanii

    doi: 10.3389/fmicb.2017.01589

    Figure Lengend Snippet: Persister cells in H. volcanii biofilms. Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p

    Article Snippet: Persister Cell Formation in Biofilms Biofilms of H. volcanii were grown using the MBEC device (Innovotech).

    Techniques: Incubation

    Cells at the periphery of the biofilm respond to tobramycin

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Cells at the periphery of the biofilm respond to tobramycin

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Ability of the biofilm to limit penetration can be overcome with high concentrations of tobramycin

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Ability of the biofilm to limit penetration can be overcome with high concentrations of tobramycin

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Metal cations facilitate the penetration of tobramycin into biofilms

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Metal cations facilitate the penetration of tobramycin into biofilms

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Limiting penetration of tobramycin protects biofilm cells

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Limiting penetration of tobramycin protects biofilm cells

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Biofilms limit the penetration of tobramycin into the biomass

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Biofilms limit the penetration of tobramycin into the biomass

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Viable counts of each bacterial species present in the initial inoculum (per well) and in the 3‐day old biofilms ( n = 7). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = Aggregatibacter actinomycetemcomitans . Error bars: standard error

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: Viable counts of each bacterial species present in the initial inoculum (per well) and in the 3‐day old biofilms ( n = 7). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = Aggregatibacter actinomycetemcomitans . Error bars: standard error

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques:

    CLSM images of 3‐day old biofilm after antibiotic exposure. Overlapping of images collected from green and red channel. (a) 3‐day‐old biofilm (negative control); (b) 3‐day old biofilm CHX‐treated for 2 hr; (c) 3‐day old biofilm treated with AMX + MET in high concentration for 2 hr; (d) 3‐day old biofilm treated with PV + MET in high concentration for 2 hr. Z‐stacks were taken in xyz projection with 63× objective, oil immersion, at 10 μm from the biofilm bottom. Scale bar: 10 μm

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: CLSM images of 3‐day old biofilm after antibiotic exposure. Overlapping of images collected from green and red channel. (a) 3‐day‐old biofilm (negative control); (b) 3‐day old biofilm CHX‐treated for 2 hr; (c) 3‐day old biofilm treated with AMX + MET in high concentration for 2 hr; (d) 3‐day old biofilm treated with PV + MET in high concentration for 2 hr. Z‐stacks were taken in xyz projection with 63× objective, oil immersion, at 10 μm from the biofilm bottom. Scale bar: 10 μm

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques: Confocal Laser Scanning Microscopy, Negative Control, Concentration Assay

    Viable counts of each bacterial species in the 3‐day old biofilms (negative controls) and subjected to antiseptic or antibiotic treatment ( n = 6). No live CFU were retrieved from biofilms treated with CHX (positive controls). Single green bars: number of live Aggregatibacter actinomycetemcomitans retrieved from biofilms exposed to antibiotic combinations in high (H) or low (L) concentrations. * shows statistical significance between biofilms exposed to PV + MET in high and low concentration ( p = .041, t test). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = A . actinomycetemcomitans . Error bars: standard error

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: Viable counts of each bacterial species in the 3‐day old biofilms (negative controls) and subjected to antiseptic or antibiotic treatment ( n = 6). No live CFU were retrieved from biofilms treated with CHX (positive controls). Single green bars: number of live Aggregatibacter actinomycetemcomitans retrieved from biofilms exposed to antibiotic combinations in high (H) or low (L) concentrations. * shows statistical significance between biofilms exposed to PV + MET in high and low concentration ( p = .041, t test). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = A . actinomycetemcomitans . Error bars: standard error

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques: Concentration Assay

    CLSM image in maximum projection of the series taken in xzy axis of the 3‐day old biofilm. Viable and nonviable bacterial cells are depicted in green and red, respectively. Scale bar: 10 μm

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: CLSM image in maximum projection of the series taken in xzy axis of the 3‐day old biofilm. Viable and nonviable bacterial cells are depicted in green and red, respectively. Scale bar: 10 μm

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques: Confocal Laser Scanning Microscopy

    Effect of farnesol on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to farnesol at 37.5 μM. (c) Biofilm exposed to farnesol at 150 μM. Concanavalin A-Alexa Fluor 647 conjugate (green stain highlighting the Candida cell

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: Effect of farnesol on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to farnesol at 37.5 μM. (c) Biofilm exposed to farnesol at 150 μM. Concanavalin A-Alexa Fluor 647 conjugate (green stain highlighting the Candida cell

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: Staining

    In vitro interaction between farnesol (0.586–300 μM) and micafungin (0.03–2 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: In vitro interaction between farnesol (0.586–300 μM) and micafungin (0.03–2 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: In Vitro

    Effect of farnesol combination treatment on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to fluconazole at 64 mg/L. (c) Biofilm exposed to combination treatment of farnesol at 37.5 μM plus fluconazole at 64 mg/L. (d) Biofilm

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: Effect of farnesol combination treatment on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to fluconazole at 64 mg/L. (c) Biofilm exposed to combination treatment of farnesol at 37.5 μM plus fluconazole at 64 mg/L. (d) Biofilm

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques:

    In vitro interaction between farnesol (0.586–300 μM) and fluconazole (8–512 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: In vitro interaction between farnesol (0.586–300 μM) and fluconazole (8–512 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: In Vitro

    In vitro interaction between farnesol (0.586–300 μM) and amphotericin B (0.5–32 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: In vitro interaction between farnesol (0.586–300 μM) and amphotericin B (0.5–32 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: In Vitro

    Confocal Laser Scanning Microscopy of biofilm formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static biofilms were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Confocal Laser Scanning Microscopy of biofilm formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static biofilms were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Confocal Laser Scanning Microscopy, Flow Cytometry, Staining, Fluorescence

    Kinetic of biofilm formation, through 72 h-incubation, by S. pseudintermedius strain DSM 25713 onto polystyrene. ( a - f ) Representative SEM images of biofilm formation after 1, 4, 8, 24, 48, and 72 h of incubation, respectively. Magnification (x1.000). ( g , h ) Magnification (x20.000) of ( e ) and ( f ), respectively. Cocci are surrounded by EPS appearing as an extensive network of filaments stretched among cells and between these and the substratum. ( i ) Kinetic of biofilm formation as assessed by viable count. Maximum, median, and minimum values are shown in each box (n = 6)

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Kinetic of biofilm formation, through 72 h-incubation, by S. pseudintermedius strain DSM 25713 onto polystyrene. ( a - f ) Representative SEM images of biofilm formation after 1, 4, 8, 24, 48, and 72 h of incubation, respectively. Magnification (x1.000). ( g , h ) Magnification (x20.000) of ( e ) and ( f ), respectively. Cocci are surrounded by EPS appearing as an extensive network of filaments stretched among cells and between these and the substratum. ( i ) Kinetic of biofilm formation as assessed by viable count. Maximum, median, and minimum values are shown in each box (n = 6)

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Incubation

    ESEM images of biofilm formed by S. pseudintermedius strain DSM 25713 onto polystyrene following 72 h-incubation. ( a ) Biofilm exhibited spatially heterogeneous organization, as suggested by the presence of “mushroom-like” structures (as indicated by arrows). Magnification: x3.000. ( b , c ) Multilayered organization with the presence of bacteria under EPS matrix (as indicated by arrows). Magnification: x12.500 and x20.000, respectively

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: ESEM images of biofilm formed by S. pseudintermedius strain DSM 25713 onto polystyrene following 72 h-incubation. ( a ) Biofilm exhibited spatially heterogeneous organization, as suggested by the presence of “mushroom-like” structures (as indicated by arrows). Magnification: x3.000. ( b , c ) Multilayered organization with the presence of bacteria under EPS matrix (as indicated by arrows). Magnification: x12.500 and x20.000, respectively

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Incubation

    Standardization of experimental conditions for biofilm formation by S. pseudintermedius strain DSM 25713 on polystyrene surface. Effect of dynamic (filled squares) or static (filled triangles) incubation, incubation time (24, 48, and 72 h), and inoculum concentration (10 5 , 10 6 , and 10 7 CFU/mL) on biofilm biomass formation, as assessed by spectrophotometric assay. Values are means ± SDs (n = 6). *** p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Standardization of experimental conditions for biofilm formation by S. pseudintermedius strain DSM 25713 on polystyrene surface. Effect of dynamic (filled squares) or static (filled triangles) incubation, incubation time (24, 48, and 72 h), and inoculum concentration (10 5 , 10 6 , and 10 7 CFU/mL) on biofilm biomass formation, as assessed by spectrophotometric assay. Values are means ± SDs (n = 6). *** p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Incubation, Concentration Assay, Spectrophotometric Assay

    Effect of serum and pH on biofilm formation and growth by S. pseudintermedius strain DSM 25713. ( a ) Serum was tested against biofilm formation at various dilutions (1:2, 1:10, and 1:100), as free or adsorbed to polystyrene, under different pH (5.5, 7.1, and 8.7). Control wells contained bacteria but not serum. Biofilm biomass amount was measured by crystal violet assay, then normalized on bacterial growth by calculating the specific biofilm formation (SBF) index (see Materials and Methods). ( b ) The effect of free serum against bacterial growth was assessed by measuring OD 600 of cell grown in broth following 24 h-incubation. Results are means + SDs (n = 9). * p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Effect of serum and pH on biofilm formation and growth by S. pseudintermedius strain DSM 25713. ( a ) Serum was tested against biofilm formation at various dilutions (1:2, 1:10, and 1:100), as free or adsorbed to polystyrene, under different pH (5.5, 7.1, and 8.7). Control wells contained bacteria but not serum. Biofilm biomass amount was measured by crystal violet assay, then normalized on bacterial growth by calculating the specific biofilm formation (SBF) index (see Materials and Methods). ( b ) The effect of free serum against bacterial growth was assessed by measuring OD 600 of cell grown in broth following 24 h-incubation. Results are means + SDs (n = 9). * p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Crystal Violet Assay, Incubation

    In vitro effect of antibiotics against preformed biofilm by S. pseudintermedius strain DSM 25713. Biofilms allowed to form following 48 h-incubation were exposed for further 24 h to each antibiotic at concentrations equal or multiple of MIC. Results are expressed as percentage of biofilm’s viability – as assessed by viable colony count - compared to control (unexposed, 100 % viability) (n = 6). The dotted line indicates a reduction in biofilm viability of at least 20 % vs control ( p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: In vitro effect of antibiotics against preformed biofilm by S. pseudintermedius strain DSM 25713. Biofilms allowed to form following 48 h-incubation were exposed for further 24 h to each antibiotic at concentrations equal or multiple of MIC. Results are expressed as percentage of biofilm’s viability – as assessed by viable colony count - compared to control (unexposed, 100 % viability) (n = 6). The dotted line indicates a reduction in biofilm viability of at least 20 % vs control ( p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: In Vitro, Incubation

    In vitro activity of antibiotics at sub-inhibitory concentrations against biofilm formation by S. pseudintermedius strain DSM 25713. Biofilm biomass formed during 24 h-incubation was measured, using the crystal violet assay, in the presence of antibiotics at concentrations equal to 1/2x, 1/4x, and 1/8xMIC. Results were plotted as percentage of biofilm biomass formed in the presence of antibiotic, compared to controls (not exposed, 100 % biofilm biomass) (n = 6). The dotted line indicates a reduction in biofilm biomass of at least 20 % vs control ( p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: In vitro activity of antibiotics at sub-inhibitory concentrations against biofilm formation by S. pseudintermedius strain DSM 25713. Biofilm biomass formed during 24 h-incubation was measured, using the crystal violet assay, in the presence of antibiotics at concentrations equal to 1/2x, 1/4x, and 1/8xMIC. Results were plotted as percentage of biofilm biomass formed in the presence of antibiotic, compared to controls (not exposed, 100 % biofilm biomass) (n = 6). The dotted line indicates a reduction in biofilm biomass of at least 20 % vs control ( p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: In Vitro, Activity Assay, Incubation, Crystal Violet Assay

    Antimicrobial activity of ColA-43864-His8. Effect of IMAC-purified ColA-43864 on planktonic ( a ) or biofilm ( b ) planktonic bacteria. C. freundii NCTC 9750 (6 × 10 9 and 2 × 10 6 CFU ml −1 for planktonic and biofilm, respectively) were incubated, for 30 min, in the presence of 2–0.02 μg IMAC-purified ColA-43864, PBS control and mock IMAC-purified sample from E. coli S17-pMQ124. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation

    Journal: Archives of microbiology

    Article Title: Isolation and identification of a bacteriocin with antibacterial and antibiofilm activity from Citrobacter freundii

    doi: 10.1007/s00203-012-0793-2

    Figure Lengend Snippet: Antimicrobial activity of ColA-43864-His8. Effect of IMAC-purified ColA-43864 on planktonic ( a ) or biofilm ( b ) planktonic bacteria. C. freundii NCTC 9750 (6 × 10 9 and 2 × 10 6 CFU ml −1 for planktonic and biofilm, respectively) were incubated, for 30 min, in the presence of 2–0.02 μg IMAC-purified ColA-43864, PBS control and mock IMAC-purified sample from E. coli S17-pMQ124. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation

    Article Snippet: Biofilms were formed in a non-tissue culture treated, 96-well polyvinyl chloride microtiter dishes (Becton–Dickinson, Franklin Lakes, NJ, USA) as previously described ( ; ).

    Techniques: Activity Assay, Purification, Incubation, Standard Deviation

    Antimicrobial activity of crude ColA-43864 extract. a Effect of ColA-43864 on planktonic bacteria. Tested bacteria (~10 9 CFU ml −1 ) were incubated for 30 min with PBS ( black bars ), 87 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ), and 37 μg protein isolated from E. coli S17-pMQ348 ( gray bars ). Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. b Effect of ColA-43864 on biofilms. Overnight biofilms (composed of ~10 6 –10 7 CFU ml −1 ) were incubated for 120 min with PBS ( black bars ) and 175 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ). Biofilms were also incubated, for 30 min ( gray bars ) and 120 min ( striped gray bars ), with 75 μg protein isolated from E. coli S17-pMQ348. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. c CLSM micrographs demonstrating the effect of ColA-43864 on biofilms. Overnight biofilms of C. freundii ATCC 8090 were incubated for 60 min with protein (11.6 μg ml −1 final concentration) extracted from empty vector control E. coli S17-pMQ124 or the colicin bearing plasmid E. coli S17-pMQ348. Thereafter, the biofilms were stained with Syto-9 (live) and propidium iodide (dead). A representative image is shown. Images were taken at the same exposures with a 40× magnification objective

    Journal: Archives of microbiology

    Article Title: Isolation and identification of a bacteriocin with antibacterial and antibiofilm activity from Citrobacter freundii

    doi: 10.1007/s00203-012-0793-2

    Figure Lengend Snippet: Antimicrobial activity of crude ColA-43864 extract. a Effect of ColA-43864 on planktonic bacteria. Tested bacteria (~10 9 CFU ml −1 ) were incubated for 30 min with PBS ( black bars ), 87 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ), and 37 μg protein isolated from E. coli S17-pMQ348 ( gray bars ). Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. b Effect of ColA-43864 on biofilms. Overnight biofilms (composed of ~10 6 –10 7 CFU ml −1 ) were incubated for 120 min with PBS ( black bars ) and 175 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ). Biofilms were also incubated, for 30 min ( gray bars ) and 120 min ( striped gray bars ), with 75 μg protein isolated from E. coli S17-pMQ348. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. c CLSM micrographs demonstrating the effect of ColA-43864 on biofilms. Overnight biofilms of C. freundii ATCC 8090 were incubated for 60 min with protein (11.6 μg ml −1 final concentration) extracted from empty vector control E. coli S17-pMQ124 or the colicin bearing plasmid E. coli S17-pMQ348. Thereafter, the biofilms were stained with Syto-9 (live) and propidium iodide (dead). A representative image is shown. Images were taken at the same exposures with a 40× magnification objective

    Article Snippet: Biofilms were formed in a non-tissue culture treated, 96-well polyvinyl chloride microtiter dishes (Becton–Dickinson, Franklin Lakes, NJ, USA) as previously described ( ; ).

    Techniques: Activity Assay, Incubation, Plasmid Preparation, Isolation, Standard Deviation, Confocal Laser Scanning Microscopy, Concentration Assay, Staining

    Biofilm formation by Acinetobacter. Biofilm formation after 24 h at 28°C for the clinically relevant A. baumannii (n = 45), A. gen. sp. 3 (n = 3) and A. gen. sp. 13TU (n = 3) and for the clinically less-relevant A. calcoaceticus (n = 3) and A. junii (n = 7). Data are expressed as mean biofilm mass (in arbitrary units (a.u.)) of three independent experiments; each performed in sixplicate. Outbreak-associated (+) or non-outbreak-associated (−) isolate. European clone I (I), II (II) or III (III) isolate. Multidrug resistant (MDR; +) or susceptible (−) isolate.

    Journal: PLoS ONE

    Article Title: Do Biofilm Formation and Interactions with Human Cells Explain the Clinical Success of Acinetobacter baumannii?

    doi: 10.1371/journal.pone.0010732

    Figure Lengend Snippet: Biofilm formation by Acinetobacter. Biofilm formation after 24 h at 28°C for the clinically relevant A. baumannii (n = 45), A. gen. sp. 3 (n = 3) and A. gen. sp. 13TU (n = 3) and for the clinically less-relevant A. calcoaceticus (n = 3) and A. junii (n = 7). Data are expressed as mean biofilm mass (in arbitrary units (a.u.)) of three independent experiments; each performed in sixplicate. Outbreak-associated (+) or non-outbreak-associated (−) isolate. European clone I (I), II (II) or III (III) isolate. Multidrug resistant (MDR; +) or susceptible (−) isolate.

    Article Snippet: Biofilm formation Biofilm formation in 96-wells polyvinylchloride microtiter plates (Falcon, BD, Breda, the Netherlands) was assayed as described .

    Techniques:

    PittGG biofilm formation is stimulated by ampicillin in a narrow concentration range. Crystal violet assay of 1-day PittGG biofilms, formed in the presence of increasing amounts of ampicillin up 300 ng/mL, showed a stimulation of biofilm formation at 170 ng/mL concentration.

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: PittGG biofilm formation is stimulated by ampicillin in a narrow concentration range. Crystal violet assay of 1-day PittGG biofilms, formed in the presence of increasing amounts of ampicillin up 300 ng/mL, showed a stimulation of biofilm formation at 170 ng/mL concentration.

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Concentration Assay, Crystal Violet Assay

    Sub-inhibitory concentrations of ampicillin result in an increase in dead NTHi bacteria in newly formed biofilms. Confocal laser scanning microscopy (cLSM) of biofilms formed by NTHi strains 2019 and PittGG in the absence (− amp) and presence (+ amp) of sub-inhibitory concentrations of ampicillin were stained using the LIVE/DEAD viability assay. 2019 were exposed to 90 ng/mL ampicillin and PittGG to 170 ng/mL ampicillin. Live bacteria were colored green and dead bacteria red. From above, biofilms formed in the absence of ampicillin were mostly green (A C), indicating living (or intact) NTHi bacteria. Clumps of bacteria in both biofilms stained red (A C) indicating the presence of dead, or structurally compromised bacteria. Biofilms formed by 2019 (A) contained fewer aggregates of red bacteria than did PittGG (C) contained more. In the presence of ampicillin (B D) the bacteria in the biofilms were mostly red, indicating a large number of dead bacteria. Green-stained bacteria were still present in both biofilms but appeared more aggregated in the presence of antibiotic (B D). Large amounts of aggregated red bacteria were present in both biofilms, with the aggregates being larger in the PittGG biofilm (Fig. D). Z-stack projections of the biofilms (E–H) showed that all the biofilms were denser at the base of the biofilm, whether exposed to ampicillin or not. In the absence of ampicillin, 2019 (E) and PittGG (G) biofilms comprised green, or intact bacteria. In the presence of ampicillin the biofilm contained mostly structurally compromised bacterial cells, which were colored red or yellow. The 2019 (F) and PittGG (H) biofilms formed in the presence of ampicillin were higher than the comparable biofilms formed without exposure to ampicillin (E G). All images; scale bar (G) = 20 µm.

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: Sub-inhibitory concentrations of ampicillin result in an increase in dead NTHi bacteria in newly formed biofilms. Confocal laser scanning microscopy (cLSM) of biofilms formed by NTHi strains 2019 and PittGG in the absence (− amp) and presence (+ amp) of sub-inhibitory concentrations of ampicillin were stained using the LIVE/DEAD viability assay. 2019 were exposed to 90 ng/mL ampicillin and PittGG to 170 ng/mL ampicillin. Live bacteria were colored green and dead bacteria red. From above, biofilms formed in the absence of ampicillin were mostly green (A C), indicating living (or intact) NTHi bacteria. Clumps of bacteria in both biofilms stained red (A C) indicating the presence of dead, or structurally compromised bacteria. Biofilms formed by 2019 (A) contained fewer aggregates of red bacteria than did PittGG (C) contained more. In the presence of ampicillin (B D) the bacteria in the biofilms were mostly red, indicating a large number of dead bacteria. Green-stained bacteria were still present in both biofilms but appeared more aggregated in the presence of antibiotic (B D). Large amounts of aggregated red bacteria were present in both biofilms, with the aggregates being larger in the PittGG biofilm (Fig. D). Z-stack projections of the biofilms (E–H) showed that all the biofilms were denser at the base of the biofilm, whether exposed to ampicillin or not. In the absence of ampicillin, 2019 (E) and PittGG (G) biofilms comprised green, or intact bacteria. In the presence of ampicillin the biofilm contained mostly structurally compromised bacterial cells, which were colored red or yellow. The 2019 (F) and PittGG (H) biofilms formed in the presence of ampicillin were higher than the comparable biofilms formed without exposure to ampicillin (E G). All images; scale bar (G) = 20 µm.

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Confocal Laser Scanning Microscopy, Staining, Viability Assay

    A sub-inhibitory concentration of ampicillin changes the composition of forming NTHi biofilms. Two strains of NTHi, 2019 and PittGG, exposed to sub-inhibitory concentrations (90 ng/mL: 2019; 170 ng/mL: PittGG) of ampicillin for 24 hr, showed increases in biofilm biomass as measured by dry weight (A. Biomass), and percent protein content (B. Protein Content). In contrast, the presence of the antibiotic during biofilm formation resulted in a decrease in viable (or culturable) bacteria (C. Viable Bacteria). Strain PittGG showed the most noticeable changes in dry weight, protein content and numbers of viable bacteria resulting from exposure to 170 ng/mL ampicillin (t-test p =

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: A sub-inhibitory concentration of ampicillin changes the composition of forming NTHi biofilms. Two strains of NTHi, 2019 and PittGG, exposed to sub-inhibitory concentrations (90 ng/mL: 2019; 170 ng/mL: PittGG) of ampicillin for 24 hr, showed increases in biofilm biomass as measured by dry weight (A. Biomass), and percent protein content (B. Protein Content). In contrast, the presence of the antibiotic during biofilm formation resulted in a decrease in viable (or culturable) bacteria (C. Viable Bacteria). Strain PittGG showed the most noticeable changes in dry weight, protein content and numbers of viable bacteria resulting from exposure to 170 ng/mL ampicillin (t-test p =

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Concentration Assay, T-Test

    Biofilm formation is stimulated by beta-lactam antibiotics. Crystal violet assays of 1-day NTHi biofilms formed in the presence of amoxicillin or amoxicillin. Strains 2019, 9274 and PittEE reacted to inhibitory concentrations of antibiotic (grey vertical bars, Biomass OD 600 ) by producing more crystal violet stainable biofilm (line graph). This stimulatory effect was different for each bacterial strain. PittGG did not react with amoxicillin and produced an ambiguous reaction to ampicillin. PittAA and PittII were not affected by amoxicillin or ampicillin in the concentration ranges studied. Cefuroxime (0–950 ng/mL range) showed a biofilm-stimulatory effect on all the NTHi strains under study. Each strain exhibited biofilm stimulation in different concentrations of antibiotic. Strain 2019 was maximally stimulated at 100 ng/mL cefuroxime, PittGG and PittII at 220 ng/mL, 9274, PittAA at 300 ng/mL and PittEE at 525 ng/mL.

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: Biofilm formation is stimulated by beta-lactam antibiotics. Crystal violet assays of 1-day NTHi biofilms formed in the presence of amoxicillin or amoxicillin. Strains 2019, 9274 and PittEE reacted to inhibitory concentrations of antibiotic (grey vertical bars, Biomass OD 600 ) by producing more crystal violet stainable biofilm (line graph). This stimulatory effect was different for each bacterial strain. PittGG did not react with amoxicillin and produced an ambiguous reaction to ampicillin. PittAA and PittII were not affected by amoxicillin or ampicillin in the concentration ranges studied. Cefuroxime (0–950 ng/mL range) showed a biofilm-stimulatory effect on all the NTHi strains under study. Each strain exhibited biofilm stimulation in different concentrations of antibiotic. Strain 2019 was maximally stimulated at 100 ng/mL cefuroxime, PittGG and PittII at 220 ng/mL, 9274, PittAA at 300 ng/mL and PittEE at 525 ng/mL.

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Produced, Concentration Assay

    Sub-inhibitory concentrations of ampicillin change the ultrastructure of newly formed NTHi biofilms. Scanning electron microscopy (SEM) images comparing NTHi biofilms formed in the absence and presence of ampicillin on Thermanox coverslips. A–C: SEM of 2019 biofilms. A) At low power the 2019 biofilm is seen as a mat covering the Thermanox substrate. Bar = 500 µm. B) higher magnification shows the biofilm to be composed of partitions forming empty spaces, or cells, covered with a film of amorphous material (arrow). Bar = 10 µm. C) the partitions within the biofilm are composed primarily of bacterial cells aggregated into flat sheets. Bar = 5 µm. D–F: SEM of 2019 biofilms formed in 90 ng/mL ampicillin. D) The 2019 biofilm formed with ampicillin covers the substrate. Bar = 500 µm. E) The biofilm is composed of partitions around empty spaces with a flat sheet of amorphous material (arrow) over the top. Bar = 50 µm F) The biofilm partitions are composed of aggregated bacteria embedded in sheets of amorphous material. Bar = 5 µm. G–I: SEM of PittGG biofilms. G) The PittGG bacteria form a biofilm over the Thermanox surface. Bar = 500 µm. H) The biofilm is composed of bacterial cells aggregated into poorly defined partitions and covered with a layer of amorphous material (arrow). Bar = 10 µm. I) The biofilm is composed of bacterial cells aggregated into widely spaced strands, and empty space. Bar = 5 µm. J–L: SEM of PittGG biofilms formed in 170 ng/mL ampicillin. J) In the presence of ampicillin the PittGG bacteria form a biofilm comprised of a thick mat, which appears to be strongly attached to itself but less well attached to the substrate. Bar = 500 µm. K) The biofilm mats appear to be composed mostly of amorphous material, a layer of which covers the biofilm (arrow), and arranged into tightly-packed thin partitions. Bar = 50 µm. L) the biofilm is composed of amorphous material formed into thin partitions. The few bacteria detected were embedded in the thin partitions. Bar = 5 µm.

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: Sub-inhibitory concentrations of ampicillin change the ultrastructure of newly formed NTHi biofilms. Scanning electron microscopy (SEM) images comparing NTHi biofilms formed in the absence and presence of ampicillin on Thermanox coverslips. A–C: SEM of 2019 biofilms. A) At low power the 2019 biofilm is seen as a mat covering the Thermanox substrate. Bar = 500 µm. B) higher magnification shows the biofilm to be composed of partitions forming empty spaces, or cells, covered with a film of amorphous material (arrow). Bar = 10 µm. C) the partitions within the biofilm are composed primarily of bacterial cells aggregated into flat sheets. Bar = 5 µm. D–F: SEM of 2019 biofilms formed in 90 ng/mL ampicillin. D) The 2019 biofilm formed with ampicillin covers the substrate. Bar = 500 µm. E) The biofilm is composed of partitions around empty spaces with a flat sheet of amorphous material (arrow) over the top. Bar = 50 µm F) The biofilm partitions are composed of aggregated bacteria embedded in sheets of amorphous material. Bar = 5 µm. G–I: SEM of PittGG biofilms. G) The PittGG bacteria form a biofilm over the Thermanox surface. Bar = 500 µm. H) The biofilm is composed of bacterial cells aggregated into poorly defined partitions and covered with a layer of amorphous material (arrow). Bar = 10 µm. I) The biofilm is composed of bacterial cells aggregated into widely spaced strands, and empty space. Bar = 5 µm. J–L: SEM of PittGG biofilms formed in 170 ng/mL ampicillin. J) In the presence of ampicillin the PittGG bacteria form a biofilm comprised of a thick mat, which appears to be strongly attached to itself but less well attached to the substrate. Bar = 500 µm. K) The biofilm mats appear to be composed mostly of amorphous material, a layer of which covers the biofilm (arrow), and arranged into tightly-packed thin partitions. Bar = 50 µm. L) the biofilm is composed of amorphous material formed into thin partitions. The few bacteria detected were embedded in the thin partitions. Bar = 5 µm.

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Electron Microscopy

    NTHi biofilms protect against a lethal dose of cefuroxime. Biofilms of NTHi strains 2019 and PittGG were formed overnight in the absence of antibiotic (Untreated), or in the presence of 170 ng/mL ampicillin (AMP), 230 ng/mL amoxicillin (AMOX) or 170 ng/mL cefuroxime (CEF). The amounts of antibiotic were chosen for their ability to stimulate biofilm formation in these two NTHi strains. After washing, the biofilms were exposed to 10 µg/mL of cefuroxime for a further 24 hr. The percentages of viable bacteria present in each biofilm are tabulated here. Not shown: planktonic NTHi bacteria are killed in the presence of 10 µg/mL cefuroxime. Although all of the formed biofilms (in the presence or absence of antibiotic) protected against cefuroxime, the amoxicillin-stimulated biofilm was able to protect bacteria from the lethal effects of the cefuroxime. p-values are documented in Table S3 .

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: NTHi biofilms protect against a lethal dose of cefuroxime. Biofilms of NTHi strains 2019 and PittGG were formed overnight in the absence of antibiotic (Untreated), or in the presence of 170 ng/mL ampicillin (AMP), 230 ng/mL amoxicillin (AMOX) or 170 ng/mL cefuroxime (CEF). The amounts of antibiotic were chosen for their ability to stimulate biofilm formation in these two NTHi strains. After washing, the biofilms were exposed to 10 µg/mL of cefuroxime for a further 24 hr. The percentages of viable bacteria present in each biofilm are tabulated here. Not shown: planktonic NTHi bacteria are killed in the presence of 10 µg/mL cefuroxime. Although all of the formed biofilms (in the presence or absence of antibiotic) protected against cefuroxime, the amoxicillin-stimulated biofilm was able to protect bacteria from the lethal effects of the cefuroxime. p-values are documented in Table S3 .

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques:

    mRNA analysis of PittGG biofilms. A. Principal component analysis of microarray gene expression of the PittGG biofilm bacteria (NTHi) exposed to 170 ng/mL ampicillin. The major variations (PC1, PC2, and PC3) are visualized in 3-dimensions. The three PCs together accounted for about 85% of the variations present in the entire data set. A distinguishable grouping difference can be seen between ampicillin treated (in blue) and non-treated (in red) samples. B. Hierarchical cluster of significantly differentially expressed genes in the PittGG biofilm bacteria (NTHi) treated with 170 ng/mL ampicillin. Heatmap visualization of 59 significantly regulated genes by ampicillin treatment. Results from the 3 replicate experiments (R1, R2 and R3) of ampicillin-treated and untreated biofilms are presented. A hierarchical clustering was analysed on the probe sets representing the 59 genes including 8 up and 51 down regulated gene transcripts with filter criteria of at least 1.5 folds change plus P≤0.05 and FDR less than 0.05. Rows: samples; columns: genes. The up-regulated genes relating to carbohydrate metabolism are indicated.

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: mRNA analysis of PittGG biofilms. A. Principal component analysis of microarray gene expression of the PittGG biofilm bacteria (NTHi) exposed to 170 ng/mL ampicillin. The major variations (PC1, PC2, and PC3) are visualized in 3-dimensions. The three PCs together accounted for about 85% of the variations present in the entire data set. A distinguishable grouping difference can be seen between ampicillin treated (in blue) and non-treated (in red) samples. B. Hierarchical cluster of significantly differentially expressed genes in the PittGG biofilm bacteria (NTHi) treated with 170 ng/mL ampicillin. Heatmap visualization of 59 significantly regulated genes by ampicillin treatment. Results from the 3 replicate experiments (R1, R2 and R3) of ampicillin-treated and untreated biofilms are presented. A hierarchical clustering was analysed on the probe sets representing the 59 genes including 8 up and 51 down regulated gene transcripts with filter criteria of at least 1.5 folds change plus P≤0.05 and FDR less than 0.05. Rows: samples; columns: genes. The up-regulated genes relating to carbohydrate metabolism are indicated.

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Microarray, Expressing

    Ultrastructural visualization of glycogen in PittGG biofilms. Resin-embedded thin sections of PittGG biofilms formed in the presence or absence of ampicillin (+/− Am) and treated with a glycogen stain or a no stain control (+/− gly). A–D Biofilms with ampicillin, sections stained for glycogen (periodic acid and sodium chlorite). The glycogen stain reacted with an extracellular granular substance (arrows) that was associated with biofilm bacteria. Exposure to antibiotic resulted in a bacterial size increase with some bacteria (A–C). Extracellular areas that were not in close proximity to bacteria cells (asterisk) did not contain the extracellular granular substance (B–D). E. Biofilm with antibiotic but only treated with sodium chlorite did not reveal extracellular granular substance. Large bacterial cells were present. F. Biofilm with no antibiotic, sections stained for glycogen. No extracellular granular substance was detected and bacterial cells had a normal diameter (approx. 500 nm). Some lysed cells were detected. G. Biofilm with no antibiotic, treated with sodium chlorite (no periodic acid). Bacterial cells appear normal with a few dying cells present (arrowhead). Scale bars = 500 nm.

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: Ultrastructural visualization of glycogen in PittGG biofilms. Resin-embedded thin sections of PittGG biofilms formed in the presence or absence of ampicillin (+/− Am) and treated with a glycogen stain or a no stain control (+/− gly). A–D Biofilms with ampicillin, sections stained for glycogen (periodic acid and sodium chlorite). The glycogen stain reacted with an extracellular granular substance (arrows) that was associated with biofilm bacteria. Exposure to antibiotic resulted in a bacterial size increase with some bacteria (A–C). Extracellular areas that were not in close proximity to bacteria cells (asterisk) did not contain the extracellular granular substance (B–D). E. Biofilm with antibiotic but only treated with sodium chlorite did not reveal extracellular granular substance. Large bacterial cells were present. F. Biofilm with no antibiotic, sections stained for glycogen. No extracellular granular substance was detected and bacterial cells had a normal diameter (approx. 500 nm). Some lysed cells were detected. G. Biofilm with no antibiotic, treated with sodium chlorite (no periodic acid). Bacterial cells appear normal with a few dying cells present (arrowhead). Scale bars = 500 nm.

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Staining

    Biofilm formation is variable between NTHi strains. Biofilm quantification using crystal violet assay showed the variability in biofilm formation between the NTHi strains in this study. Relative Biofilm Quantity was measured as OD 600 of crystal violet in DMSO; higher absorbance indicated more biofilm production. The PittAA and PittEE strains showed the least amount of biofilm attachment to the growth surface while PittII showed the most. The other three strains (2019, 9274 and PittGG) formed intermediate amounts of biofilm material (t-test analysis in Table S2 ).

    Journal: PLoS ONE

    Article Title: Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    doi: 10.1371/journal.pone.0099204

    Figure Lengend Snippet: Biofilm formation is variable between NTHi strains. Biofilm quantification using crystal violet assay showed the variability in biofilm formation between the NTHi strains in this study. Relative Biofilm Quantity was measured as OD 600 of crystal violet in DMSO; higher absorbance indicated more biofilm production. The PittAA and PittEE strains showed the least amount of biofilm attachment to the growth surface while PittII showed the most. The other three strains (2019, 9274 and PittGG) formed intermediate amounts of biofilm material (t-test analysis in Table S2 ).

    Article Snippet: As with the other biofilms, the mats were covered on the top surface with amorphous material ( ) and were composed of partitions and spaces.

    Techniques: Crystal Violet Assay, T-Test

    Tracking and quantification of biofilm community structure changes after temperature increase. ( a ) viSNE submaps ( Fig. 2a ) belonging to days 0, 7, 14 and 21 post temperature increase. More colour-intense regions of the submaps depict regions of higher cell density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, five independent microcosms) and time points indicated that the detected changes in community structure were governed by time point and not biological or technical noise ( Supplementary Fig. 10 ). ( b ) Quantification of subpopulations defined in Fig. 2b , pooled from five biological replicates for each time point after temperature increase (all biological replicates are depicted in Supplementary Fig. 11 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 9 .

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Tracking and quantification of biofilm community structure changes after temperature increase. ( a ) viSNE submaps ( Fig. 2a ) belonging to days 0, 7, 14 and 21 post temperature increase. More colour-intense regions of the submaps depict regions of higher cell density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, five independent microcosms) and time points indicated that the detected changes in community structure were governed by time point and not biological or technical noise ( Supplementary Fig. 10 ). ( b ) Quantification of subpopulations defined in Fig. 2b , pooled from five biological replicates for each time point after temperature increase (all biological replicates are depicted in Supplementary Fig. 11 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 9 .

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques:

    Categorizing subpopulations in temperature-stressed stream biofilms. ( a ) Stream biofilms were assessed by FC directly after transfer to higher temperature, after 1, 2 and 3 weeks and the acquired data was altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell from the biofilms, or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set of wavelengths displayed in Supplementary Fig. 6 ). ( b ) Subpopulations (LA1–LA15) categorized based on the viSNE map, optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 6 ). A fraction of the particles (4.5–5.8%) was not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples allowed for assigning subpopulations to types of organisms and potentially decaying cells ( Supplementary Fig. 8 ).

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Categorizing subpopulations in temperature-stressed stream biofilms. ( a ) Stream biofilms were assessed by FC directly after transfer to higher temperature, after 1, 2 and 3 weeks and the acquired data was altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell from the biofilms, or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set of wavelengths displayed in Supplementary Fig. 6 ). ( b ) Subpopulations (LA1–LA15) categorized based on the viSNE map, optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 6 ). A fraction of the particles (4.5–5.8%) was not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples allowed for assigning subpopulations to types of organisms and potentially decaying cells ( Supplementary Fig. 8 ).

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Fluorescence

    Tracking biofilm community structure changes along a stream. ( a ) viSNE submaps belonging to six sites (A–F) along the stream Mönchaltorfer Aa. More colour-intense regions of the submaps depict regions of higher cell or particle density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, 3 stones per site) and sites indicated that the detected changes in community structure were governed by site and not biological or technical noise ( Supplementary Fig. 17 ). The sites are characterized in Supplementary Tables 4–6 . Site A is at the spring of the stream in the forest, site B is in an unshaded stretch, site C is shaded but in the straightened section of the stream-like sites D–F, which are additionally influenced by waste-water treatment plant effluents, site D being situated immediately downstream a treatment plant. ( b ) Subpopulations are defined in Fig. 4b , pooled from three biological replicates taken from each site (all biological replicates are depicted in Supplementary Fig. 18 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 16 . ( c ) Biplots of the redundancy analysis (RDA) based on the fraction of cells/particles in the subpopulations in Fig. 4b constrained by forward selected field physico-chemical parameters ( Supplementary Tables 4,6 ). Dots/grey tones: specific sampling sites. Dispersion of standard error of the weighted scores of sampling sites are shown as ellipses in the respective grey tone (confidence limit=0.95). Centroids of the subpopulations (MA1a–MA10) are given. Significantly tested model variables are depicted (*** P

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Tracking biofilm community structure changes along a stream. ( a ) viSNE submaps belonging to six sites (A–F) along the stream Mönchaltorfer Aa. More colour-intense regions of the submaps depict regions of higher cell or particle density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, 3 stones per site) and sites indicated that the detected changes in community structure were governed by site and not biological or technical noise ( Supplementary Fig. 17 ). The sites are characterized in Supplementary Tables 4–6 . Site A is at the spring of the stream in the forest, site B is in an unshaded stretch, site C is shaded but in the straightened section of the stream-like sites D–F, which are additionally influenced by waste-water treatment plant effluents, site D being situated immediately downstream a treatment plant. ( b ) Subpopulations are defined in Fig. 4b , pooled from three biological replicates taken from each site (all biological replicates are depicted in Supplementary Fig. 18 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 16 . ( c ) Biplots of the redundancy analysis (RDA) based on the fraction of cells/particles in the subpopulations in Fig. 4b constrained by forward selected field physico-chemical parameters ( Supplementary Tables 4,6 ). Dots/grey tones: specific sampling sites. Dispersion of standard error of the weighted scores of sampling sites are shown as ellipses in the respective grey tone (confidence limit=0.95). Centroids of the subpopulations (MA1a–MA10) are given. Significantly tested model variables are depicted (*** P

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Sampling

    Categorizing subpopulations in stream biofilms sampled in the field. ( a ) Stream biofilms were assessed by FC after sampling at six sites along the stream Mönchaltorfer Aa and altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell or particle from the biofilms or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set displayed in Supplementary Fig. 13 ). ( b ) Subpopulations (MA 1–10) categorized based on the viSNE map and optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 13 ). Some cells (range 2.7–11.2 %) were not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples ( Supplementary Fig. 15 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Categorizing subpopulations in stream biofilms sampled in the field. ( a ) Stream biofilms were assessed by FC after sampling at six sites along the stream Mönchaltorfer Aa and altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell or particle from the biofilms or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set displayed in Supplementary Fig. 13 ). ( b ) Subpopulations (MA 1–10) categorized based on the viSNE map and optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 13 ). Some cells (range 2.7–11.2 %) were not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples ( Supplementary Fig. 15 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Sampling, Fluorescence

    Detection of microplastics in stream biofilms. ( a ) viSNE map shown in Fig. 4a with circled hypothetical microplastic cluster. ( b ) SEM image of a potential microplastic particle isolated from site D. Scale bar, 10 μm. ( c ) SEM image of polystyrene beads isolated from a spiked sample. Scale bar, 50 μm. The squares in the top right corner of the SEM images ( b , c ) with separate scale bars, 1 μm, depict the region scanned for EDS analysis. ( d ) EDS spectrum of a potential microplastic particle isolated from site D. ( e ) EDS spectrum of polystyrene beads isolated from a spiked sample.

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Detection of microplastics in stream biofilms. ( a ) viSNE map shown in Fig. 4a with circled hypothetical microplastic cluster. ( b ) SEM image of a potential microplastic particle isolated from site D. Scale bar, 10 μm. ( c ) SEM image of polystyrene beads isolated from a spiked sample. Scale bar, 50 μm. The squares in the top right corner of the SEM images ( b , c ) with separate scale bars, 1 μm, depict the region scanned for EDS analysis. ( d ) EDS spectrum of a potential microplastic particle isolated from site D. ( e ) EDS spectrum of polystyrene beads isolated from a spiked sample.

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Isolation

    Change in thickness of biofilms with time, as measured by confocal microscopy. The depth of the biofilm represents the mean of five randomly chosen sites within each biofilm.

    Journal: Infection and Immunity

    Article Title: Growth, Development, and Gene Expression in a Persistent Streptococcus gordonii Biofilm

    doi: 10.1128/IAI.71.8.4759-4766.2003

    Figure Lengend Snippet: Change in thickness of biofilms with time, as measured by confocal microscopy. The depth of the biofilm represents the mean of five randomly chosen sites within each biofilm.

    Article Snippet: To enumerate cells in the biofilm phase, the biofilms were dislodged from the substratum by scraping and were transferred to a 2-ml Bead Beater tube (BioSpec Products, Bartlesville, Okla.) containing 0.5 ml of 1-mm-diameter glass beads (BioSpec Products) in 1 ml of PBS.

    Techniques: Confocal Microscopy

    Confocal scanning laser micrographs of the development of S. gordonii Challis DL1 biofilms over 26 days. The biofilms were generated on glass coverslips in 0.5× TY medium supplemented with 10 mM sucrose and were stained immediately prior to microscopy with acridine orange. Numbers indicate the age of the biofilm in days. Magnification, ×63.

    Journal: Infection and Immunity

    Article Title: Growth, Development, and Gene Expression in a Persistent Streptococcus gordonii Biofilm

    doi: 10.1128/IAI.71.8.4759-4766.2003

    Figure Lengend Snippet: Confocal scanning laser micrographs of the development of S. gordonii Challis DL1 biofilms over 26 days. The biofilms were generated on glass coverslips in 0.5× TY medium supplemented with 10 mM sucrose and were stained immediately prior to microscopy with acridine orange. Numbers indicate the age of the biofilm in days. Magnification, ×63.

    Article Snippet: To enumerate cells in the biofilm phase, the biofilms were dislodged from the substratum by scraping and were transferred to a 2-ml Bead Beater tube (BioSpec Products, Bartlesville, Okla.) containing 0.5 ml of 1-mm-diameter glass beads (BioSpec Products) in 1 ml of PBS.

    Techniques: Generated, Staining, Microscopy

    Change in CFU within S. gordonii Challis DL1 biofilms cultured in 0.5× TY medium supplemented with sucrose, which was replaced at 24-h intervals. Cells were enumerated over 30 days of cultivation. Numbers of CFU for biofilms harvested at each time point are expressed as means of triplicate determinations. Error bars represent the standard errors of the means and are not detectable where the error is smaller than the symbol.

    Journal: Infection and Immunity

    Article Title: Growth, Development, and Gene Expression in a Persistent Streptococcus gordonii Biofilm

    doi: 10.1128/IAI.71.8.4759-4766.2003

    Figure Lengend Snippet: Change in CFU within S. gordonii Challis DL1 biofilms cultured in 0.5× TY medium supplemented with sucrose, which was replaced at 24-h intervals. Cells were enumerated over 30 days of cultivation. Numbers of CFU for biofilms harvested at each time point are expressed as means of triplicate determinations. Error bars represent the standard errors of the means and are not detectable where the error is smaller than the symbol.

    Article Snippet: To enumerate cells in the biofilm phase, the biofilms were dislodged from the substratum by scraping and were transferred to a 2-ml Bead Beater tube (BioSpec Products, Bartlesville, Okla.) containing 0.5 ml of 1-mm-diameter glass beads (BioSpec Products) in 1 ml of PBS.

    Techniques: Cell Culture

    Biofilm production dynamics after extubation in 9 ETT-MRSA isolates under O 2 or 5% CO 2 Each color-bar represents the biofilm production of each ETT-MRSA isolate compared with the MRSA-in over days 1–8 after extubation. ( A ) Biofilm production dynamics under O 2 . Maximum biofilm production was on day 2. ( B ) Biofilm production dynamics under CO 2 . Maximum biofilm production was on day 1. Since the 5% CO 2 atmosphere better mimics the atmospheric conditions of mechanical ventilation. When ETT-MRSA are rapidly switched from the ETT environment to O 2 alone, they would need a day to adapt their metabolism to the new atmospheric conditions. Black points represent median biofilm production of the 9 isolates each day. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Biofilm production dynamics after extubation in 9 ETT-MRSA isolates under O 2 or 5% CO 2 Each color-bar represents the biofilm production of each ETT-MRSA isolate compared with the MRSA-in over days 1–8 after extubation. ( A ) Biofilm production dynamics under O 2 . Maximum biofilm production was on day 2. ( B ) Biofilm production dynamics under CO 2 . Maximum biofilm production was on day 1. Since the 5% CO 2 atmosphere better mimics the atmospheric conditions of mechanical ventilation. When ETT-MRSA are rapidly switched from the ETT environment to O 2 alone, they would need a day to adapt their metabolism to the new atmospheric conditions. Black points represent median biofilm production of the 9 isolates each day. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques:

    Representative scanning electron microscopy of in vivo MRSA biofilm ( A ) Isolate 1 showing an in vivo detached biofilm at low magnification. Sometimes the sample processing for scanning electron microscopy released the biofilm cluster from the endotracheal tube surface. At higher magnification ( B ), cocci morphologies can be distinguished. The pig from which we obtained Isolate 1 was treated with vancomycin. ( C ) Isolate 45 (from a placebo treated pig) showing an in vivo biofilm attached to the endotracheal tube at low magnification. ( D ) at higher magnification, a cocci biofilm cluster was found (white arrow). Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Representative scanning electron microscopy of in vivo MRSA biofilm ( A ) Isolate 1 showing an in vivo detached biofilm at low magnification. Sometimes the sample processing for scanning electron microscopy released the biofilm cluster from the endotracheal tube surface. At higher magnification ( B ), cocci morphologies can be distinguished. The pig from which we obtained Isolate 1 was treated with vancomycin. ( C ) Isolate 45 (from a placebo treated pig) showing an in vivo biofilm attached to the endotracheal tube at low magnification. ( D ) at higher magnification, a cocci biofilm cluster was found (white arrow). Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques: Electron Microscopy, In Vivo

    Biofilm production of 52 ETT-MRSA isolates compared with the MRSA-in under ambient air or ambient air with 5% CO 2. Each bar represents the biofilm production of each ETT-MRSA isolate versus the MRSA-in (black bar). ( A ) Biofilm production O 2 on day 2 after extubation (peak production); 50% of ETT-MRSA isolates increased biofilm production more than double that of MRSA-in. ( B ) Biofilm production under 5% CO 2 on day 1 after extubation (peak production); 40% of ETT-MRSA isolates increased more than twice MRSA-in biofilm production. The highest biofilm producers ETT-MRSA isolates (n = 9), in dark gray, under both O 2 and 5% CO 2 were selected to undergo the biofilm production dynamics post-extubation. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Biofilm production of 52 ETT-MRSA isolates compared with the MRSA-in under ambient air or ambient air with 5% CO 2. Each bar represents the biofilm production of each ETT-MRSA isolate versus the MRSA-in (black bar). ( A ) Biofilm production O 2 on day 2 after extubation (peak production); 50% of ETT-MRSA isolates increased biofilm production more than double that of MRSA-in. ( B ) Biofilm production under 5% CO 2 on day 1 after extubation (peak production); 40% of ETT-MRSA isolates increased more than twice MRSA-in biofilm production. The highest biofilm producers ETT-MRSA isolates (n = 9), in dark gray, under both O 2 and 5% CO 2 were selected to undergo the biofilm production dynamics post-extubation. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques:

    Representative confocal laser scanning microscopy of in vivo MRSA biofilm Biofilm clusters (white arrows) were stained with the LIVE/DEAD BacLight kit (INVITROGEN, Barcelona, Spain). Viable bacteria (stained green by SYTO 9) are visible, but dead bacteria (stained red by propidium iodide) were infrequently detected. The nuclei and cytoplasm of eukaryotic cells from the pig were also stained nonspecifically by propidium iodide and SYTO 9 (large red and green blotches, respectively). ( A , B ) correspond to the in vivo biofilms of Isolate 39 and Isolate 45 obtained from pigs treated with vancomycin and placebo, respectively. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Representative confocal laser scanning microscopy of in vivo MRSA biofilm Biofilm clusters (white arrows) were stained with the LIVE/DEAD BacLight kit (INVITROGEN, Barcelona, Spain). Viable bacteria (stained green by SYTO 9) are visible, but dead bacteria (stained red by propidium iodide) were infrequently detected. The nuclei and cytoplasm of eukaryotic cells from the pig were also stained nonspecifically by propidium iodide and SYTO 9 (large red and green blotches, respectively). ( A , B ) correspond to the in vivo biofilms of Isolate 39 and Isolate 45 obtained from pigs treated with vancomycin and placebo, respectively. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques: Confocal Laser Scanning Microscopy, In Vivo, Staining

    Effect of systemic antibiotic treatment on biofilm production in the 52 ETT-MRSA isolates under O 2 or 5% CO 2 conditions Median (interquartile range) values for biofilm production of the 52 ETT-MRSA compared with the MRSA-in under O 2 ( A ) and 5% CO 2 ( B ). Time of assessment: day of peak production. Biofilm production was not influenced by systemic treatment with placebo (n = 19), linezolid (n = 11), or vancomycin (n = 22) under either O 2 (1.96 [0.61–3.02], 2.30 [0.64–3.83], and 1.49 [0.63–2.67], respectively; p = 0.92) or 5% CO 2 (2.02 [1.16–2.34], 1.36 [0.48–2.75], and 1.09 [0.34–2.38], respectively; p = 0.62). Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Effect of systemic antibiotic treatment on biofilm production in the 52 ETT-MRSA isolates under O 2 or 5% CO 2 conditions Median (interquartile range) values for biofilm production of the 52 ETT-MRSA compared with the MRSA-in under O 2 ( A ) and 5% CO 2 ( B ). Time of assessment: day of peak production. Biofilm production was not influenced by systemic treatment with placebo (n = 19), linezolid (n = 11), or vancomycin (n = 22) under either O 2 (1.96 [0.61–3.02], 2.30 [0.64–3.83], and 1.49 [0.63–2.67], respectively; p = 0.92) or 5% CO 2 (2.02 [1.16–2.34], 1.36 [0.48–2.75], and 1.09 [0.34–2.38], respectively; p = 0.62). Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques:

    Tree diagrams showing grouping of values for quantitative parameters of biofilms. These are biovolume ( A ) percentage of surface covered ( B ) roughness ( C ) and maximum thickness ( D ) corresponding to 20 strains of Listeria monocytogenes taken from meat (Euclidean distance, unweighted pair-group average).

    Journal: Microorganisms

    Article Title: Prevalence, Molecular Typing, and Determination of the Biofilm-Forming Ability of Listeria monocytogenes Serotypes from Poultry Meat and Poultry Preparations in Spain

    doi: 10.3390/microorganisms7110529

    Figure Lengend Snippet: Tree diagrams showing grouping of values for quantitative parameters of biofilms. These are biovolume ( A ) percentage of surface covered ( B ) roughness ( C ) and maximum thickness ( D ) corresponding to 20 strains of Listeria monocytogenes taken from meat (Euclidean distance, unweighted pair-group average).

    Article Snippet: Three-dimensional images of the biofilms were reconstructed by means of the IMARIS 9.1 program (Bitplane AG, Zurich, Switzerland) and quantitative structural parameters (biovolume, percentage surface coverage, roughness, maximum thickness) were calculated.

    Techniques:

    Three-dimensional projections of structures of biofilms obtained from one-micron optical sections on the z -axis acquired through confocal laser scanning microscopy. These images represent an overhead view of the biofilms formed by 20 strains of Listeria monocytogenes , with virtual projection of shadows to the right. Each square represented had length of side of 119 μm. Strains: 1 (serotype 1/2a), 2 (1/2a), 3 (1/2b), 4 (1/2b), 5 (1/2c), 6 (1/2c), 7 (3a), 8 (3b), 9 (3b), 10 (3c), 11 (3c), 12 (4a), 13 (4a), 14 (4b), 15 (4b), 16 (4b), 17 (4b), 18 (4c), 19 (4d), 20 (4d).

    Journal: Microorganisms

    Article Title: Prevalence, Molecular Typing, and Determination of the Biofilm-Forming Ability of Listeria monocytogenes Serotypes from Poultry Meat and Poultry Preparations in Spain

    doi: 10.3390/microorganisms7110529

    Figure Lengend Snippet: Three-dimensional projections of structures of biofilms obtained from one-micron optical sections on the z -axis acquired through confocal laser scanning microscopy. These images represent an overhead view of the biofilms formed by 20 strains of Listeria monocytogenes , with virtual projection of shadows to the right. Each square represented had length of side of 119 μm. Strains: 1 (serotype 1/2a), 2 (1/2a), 3 (1/2b), 4 (1/2b), 5 (1/2c), 6 (1/2c), 7 (3a), 8 (3b), 9 (3b), 10 (3c), 11 (3c), 12 (4a), 13 (4a), 14 (4b), 15 (4b), 16 (4b), 17 (4b), 18 (4c), 19 (4d), 20 (4d).

    Article Snippet: Three-dimensional images of the biofilms were reconstructed by means of the IMARIS 9.1 program (Bitplane AG, Zurich, Switzerland) and quantitative structural parameters (biovolume, percentage surface coverage, roughness, maximum thickness) were calculated.

    Techniques: Confocal Laser Scanning Microscopy

    Changes in V. vulnificus biofilm composition in response to a lytic phage. The MO-6/24-Tn and CMCP6 strains were grown in mixed culture on crab shells in 12-well plates for 24 h. The biofilms were then exposed to the MO-6/24-specific lytic phage 152-A10

    Journal: Infection and Immunity

    Article Title: Chitin-Induced Carbotype Conversion in Vibrio vulnificus ▿ ▿ †

    doi: 10.1128/IAI.00158-11

    Figure Lengend Snippet: Changes in V. vulnificus biofilm composition in response to a lytic phage. The MO-6/24-Tn and CMCP6 strains were grown in mixed culture on crab shells in 12-well plates for 24 h. The biofilms were then exposed to the MO-6/24-specific lytic phage 152-A10

    Article Snippet: Biofilms were washed three times with 3 ml of VPBS, and image stacks were captured with a Zeiss LSM 510 Axioplan 2 confocal laser scanning microscope (CLSM) fitted with a W-plan Apochromat 40× objective.

    Techniques:

    Composition of V. vulnificus biofilms grown on crab shells. The 27562 and CMCP6 strains were grown in mixed culture on crab shells in 12-well plates for 24 h. The structure and composition of the biofilms were examined by CSLM. (A) GFP-tagged cells; (B)

    Journal: Infection and Immunity

    Article Title: Chitin-Induced Carbotype Conversion in Vibrio vulnificus ▿ ▿ †

    doi: 10.1128/IAI.00158-11

    Figure Lengend Snippet: Composition of V. vulnificus biofilms grown on crab shells. The 27562 and CMCP6 strains were grown in mixed culture on crab shells in 12-well plates for 24 h. The structure and composition of the biofilms were examined by CSLM. (A) GFP-tagged cells; (B)

    Article Snippet: Biofilms were washed three times with 3 ml of VPBS, and image stacks were captured with a Zeiss LSM 510 Axioplan 2 confocal laser scanning microscope (CLSM) fitted with a W-plan Apochromat 40× objective.

    Techniques:

    Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the biofilm. Negative depths in the profile represent the distance from the biofilm surface into the wastewater.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the biofilm. Negative depths in the profile represent the distance from the biofilm surface into the wastewater.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques:

    Model-predicted sulfate and soluble biodegradable COD profiles in the biofilm.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Model-predicted sulfate and soluble biodegradable COD profiles in the biofilm.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques:

    The SRB (A) and MA (B) proportions of total microorganisms (bacteria and archaea) detected by FISH within the sewer biofilms. C. Methanomethylophilus , “ Candidatus Methanomethylophilus.”

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: The SRB (A) and MA (B) proportions of total microorganisms (bacteria and archaea) detected by FISH within the sewer biofilms. C. Methanomethylophilus , “ Candidatus Methanomethylophilus.”

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Sulforhodamine B Assay, Fluorescence In Situ Hybridization

    FISH images of different sections of the sewer reactor biofilm. (A and B) Images of the biofilm sections cut perpendicularly to the substratum, with SRB in white (A) and MA in purple (B). Arrows indicate the biofilm surface. (C and D) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with SRB in white, archaea in red, and other bacteria in green, blue, and yellow. (E and F) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with MA in purple, other archaea in red, and bacteria in green. Scale bars, 50 μm.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: FISH images of different sections of the sewer reactor biofilm. (A and B) Images of the biofilm sections cut perpendicularly to the substratum, with SRB in white (A) and MA in purple (B). Arrows indicate the biofilm surface. (C and D) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with SRB in white, archaea in red, and other bacteria in green, blue, and yellow. (E and F) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with MA in purple, other archaea in red, and bacteria in green. Scale bars, 50 μm.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Fluorescence In Situ Hybridization, Sulforhodamine B Assay

    Schematic of the laboratory-scale anaerobic, annular biofilm reactor.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Schematic of the laboratory-scale anaerobic, annular biofilm reactor.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques:

    Comparison of model-predicted results with the experimentally measured data. (A) Relative abundances of SRB and MA. (B) Sulfide concentration profiles in the biofilm.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Comparison of model-predicted results with the experimentally measured data. (A) Relative abundances of SRB and MA. (B) Sulfide concentration profiles in the biofilm.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Sulforhodamine B Assay, Concentration Assay

    Heat map displaying the distribution of the predominant SRB (A) and MA (B) in different biofilm layers from the biofilm surface to the bottom (Layer 1 to Layer 5).

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Heat map displaying the distribution of the predominant SRB (A) and MA (B) in different biofilm layers from the biofilm surface to the bottom (Layer 1 to Layer 5).

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Sulforhodamine B Assay

    Phloxine B staining of C. albicans ) and photographed (Arcturus). Differences in staining are evident during the 6 h of biofilm development. (A) T = 30; (B) T = 90; (C) T = 270. Magnification, ×40.

    Journal: Eukaryotic Cell

    Article Title: Genome-Wide Transcription Profiling of the Early Phase of Biofilm Formation by Candida albicans †

    doi: 10.1128/EC.4.9.1562-1573.2005

    Figure Lengend Snippet: Phloxine B staining of C. albicans ) and photographed (Arcturus). Differences in staining are evident during the 6 h of biofilm development. (A) T = 30; (B) T = 90; (C) T = 270. Magnification, ×40.

    Article Snippet: For each time point, biofilms were formed in polystyrene petri dishes (100 mm by 15 mm [Fisher Scientific, Pittsburgh, PA]) using 107 cell/ml of inoculum in fresh F-12 medium (10-ml final volume per plate).

    Techniques: Staining

    ). The scan rates were about 1 Hz with scan sizes between 15 and 60 μm. (A) Cell adhesion ( T = 30); (B to E) biofilm development ( T = 60 to T = 390). Bar: 10 μm (A and B) and 30 μm (C to E).

    Journal: Eukaryotic Cell

    Article Title: Genome-Wide Transcription Profiling of the Early Phase of Biofilm Formation by Candida albicans †

    doi: 10.1128/EC.4.9.1562-1573.2005

    Figure Lengend Snippet: ). The scan rates were about 1 Hz with scan sizes between 15 and 60 μm. (A) Cell adhesion ( T = 30); (B to E) biofilm development ( T = 60 to T = 390). Bar: 10 μm (A and B) and 30 μm (C to E).

    Article Snippet: For each time point, biofilms were formed in polystyrene petri dishes (100 mm by 15 mm [Fisher Scientific, Pittsburgh, PA]) using 107 cell/ml of inoculum in fresh F-12 medium (10-ml final volume per plate).

    Techniques:

    The antibacterial effects of Nano-CHX treatment for 24 h on the mixed-species biofilms of S. sobrinus , F. nucleatum and P. gingivalis . Representative scanning electron microscopy images: B vs. A (blank nanoparticles); and confocal laser scanning microscopy images: D vs. C (blank nanoparticles).

    Journal: PLoS ONE

    Article Title: Nanoparticle-Encapsulated Chlorhexidine against Oral Bacterial Biofilms

    doi: 10.1371/journal.pone.0103234

    Figure Lengend Snippet: The antibacterial effects of Nano-CHX treatment for 24 h on the mixed-species biofilms of S. sobrinus , F. nucleatum and P. gingivalis . Representative scanning electron microscopy images: B vs. A (blank nanoparticles); and confocal laser scanning microscopy images: D vs. C (blank nanoparticles).

    Article Snippet: The topographic features of each biofilm were visualized with a SEM (Hitachi S-3400N SEM at EM Unit, HKU) in high vacuum mode at 10 kV.

    Techniques: Electron Microscopy, Confocal Laser Scanning Microscopy

    Quantitative analysis of macrophage migration within 48 h biofilms prepared from C. albicans strains CAI4, pmr1 Δ, and pmr1 Δ+ PMR1 . The chart shows mean relative macrophage velocity + SD relative to macrophage velocity of J774.1 macrophages added in suspension to CAI4 (wild type biofilms). Migration data over a 30 min period are shown. No statistical significance of mean differences was determined using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests.

    Journal: Journal of Fungi

    Article Title: Macrophage Migration Is Impaired within Candida albicans Biofilms

    doi: 10.3390/jof3030031

    Figure Lengend Snippet: Quantitative analysis of macrophage migration within 48 h biofilms prepared from C. albicans strains CAI4, pmr1 Δ, and pmr1 Δ+ PMR1 . The chart shows mean relative macrophage velocity + SD relative to macrophage velocity of J774.1 macrophages added in suspension to CAI4 (wild type biofilms). Migration data over a 30 min period are shown. No statistical significance of mean differences was determined using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests.

    Article Snippet: Biofilms were prepared by seeding µ-Slide 8-well chambers (ibidi GmbH, Munich, Germany) with 3 × 105 Leicestershire live C. albicans yeast in Dulbecco’s Modified Eagle Medium (DMEM; Lonza, Slough, UK), supplemented with 10% (v /v ) heat-inactivated FCS (Biosera, Ringmer, UK), 200 U/mL penicillin/streptomycin antibiotics (Invitrogen, Paisley, UK), and 2 mM L-glutamine (Invitrogen, Paisley, UK), at 37 °C for 48 h. There were two assay designs, with planktonic yeast added to either imaging dishes containing macrophages, or to fungal biofilms with macrophages added in.

    Techniques: Migration

    Representative single time point images acquired using Volocity software, showing J774.1 macrophages stained with LysoTracker Red (LTR; red), and C. albicans stained with Calcofluor White (CFW; blue). Macrophages were added in suspension to ( a ) planktonic yeast (40× objective), or ( b ) and ( c ) 48 h biofilms (20× objective); presented with ( a ) and ( b ) opacity 3D rendering, and ( c ) x , y and z at 20 μm depth. White grid unit or bar represents ( a ) 18.05 μm, ( b ) 36.17 μm, and ( c ) 40 μm.

    Journal: Journal of Fungi

    Article Title: Macrophage Migration Is Impaired within Candida albicans Biofilms

    doi: 10.3390/jof3030031

    Figure Lengend Snippet: Representative single time point images acquired using Volocity software, showing J774.1 macrophages stained with LysoTracker Red (LTR; red), and C. albicans stained with Calcofluor White (CFW; blue). Macrophages were added in suspension to ( a ) planktonic yeast (40× objective), or ( b ) and ( c ) 48 h biofilms (20× objective); presented with ( a ) and ( b ) opacity 3D rendering, and ( c ) x , y and z at 20 μm depth. White grid unit or bar represents ( a ) 18.05 μm, ( b ) 36.17 μm, and ( c ) 40 μm.

    Article Snippet: Biofilms were prepared by seeding µ-Slide 8-well chambers (ibidi GmbH, Munich, Germany) with 3 × 105 Leicestershire live C. albicans yeast in Dulbecco’s Modified Eagle Medium (DMEM; Lonza, Slough, UK), supplemented with 10% (v /v ) heat-inactivated FCS (Biosera, Ringmer, UK), 200 U/mL penicillin/streptomycin antibiotics (Invitrogen, Paisley, UK), and 2 mM L-glutamine (Invitrogen, Paisley, UK), at 37 °C for 48 h. There were two assay designs, with planktonic yeast added to either imaging dishes containing macrophages, or to fungal biofilms with macrophages added in.

    Techniques: Software, Staining

    Quantitative analysis of macrophage migration in the presence of different wildtype C. albicans . This chart shows mean relative macrophage velocity + SD, relative to macrophage velocity of pre-adhered J774.1 (Adh-macs) responding to planktonic yeast. Relative velocities of J774.1 macrophages added in suspension (Susp-macs) to either yeast or a 48 h biofilm over a 30 min period are shown. Statistical significance was evaluated using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests. ** p

    Journal: Journal of Fungi

    Article Title: Macrophage Migration Is Impaired within Candida albicans Biofilms

    doi: 10.3390/jof3030031

    Figure Lengend Snippet: Quantitative analysis of macrophage migration in the presence of different wildtype C. albicans . This chart shows mean relative macrophage velocity + SD, relative to macrophage velocity of pre-adhered J774.1 (Adh-macs) responding to planktonic yeast. Relative velocities of J774.1 macrophages added in suspension (Susp-macs) to either yeast or a 48 h biofilm over a 30 min period are shown. Statistical significance was evaluated using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests. ** p

    Article Snippet: Biofilms were prepared by seeding µ-Slide 8-well chambers (ibidi GmbH, Munich, Germany) with 3 × 105 Leicestershire live C. albicans yeast in Dulbecco’s Modified Eagle Medium (DMEM; Lonza, Slough, UK), supplemented with 10% (v /v ) heat-inactivated FCS (Biosera, Ringmer, UK), 200 U/mL penicillin/streptomycin antibiotics (Invitrogen, Paisley, UK), and 2 mM L-glutamine (Invitrogen, Paisley, UK), at 37 °C for 48 h. There were two assay designs, with planktonic yeast added to either imaging dishes containing macrophages, or to fungal biofilms with macrophages added in.

    Techniques: Migration, Magnetic Cell Separation

    Typical light microscopy images of (a) full-thickness tissue after infection with acrylic coupons only (no biofilm), showing no damage to epithelium; (b) full-thickness tissue after infection with bacteria-only biofilm, showing slight tissue damage and clustering of biofilms on the epithelial surface (indicated by arrows); (c) full-thickness tissue after infection with Candida albicans -only biofilm, showing substantial epithelial damage and biofilms clustered on the surface of the epithelium (indicated by arrows); (d) full-thickness tissue after infection with mixed-species biofilm, showing extensive epithelial damage and microbial invasion through the epithelium (indicated by arrows). Stained with haematoxylin and eosin. The scale bar represents 50 µm.

    Journal: Journal of Medical Microbiology

    Article Title: Denture-associated biofilm infection in three-dimensional oral mucosal tissue models

    doi: 10.1099/jmm.0.000677

    Figure Lengend Snippet: Typical light microscopy images of (a) full-thickness tissue after infection with acrylic coupons only (no biofilm), showing no damage to epithelium; (b) full-thickness tissue after infection with bacteria-only biofilm, showing slight tissue damage and clustering of biofilms on the epithelial surface (indicated by arrows); (c) full-thickness tissue after infection with Candida albicans -only biofilm, showing substantial epithelial damage and biofilms clustered on the surface of the epithelium (indicated by arrows); (d) full-thickness tissue after infection with mixed-species biofilm, showing extensive epithelial damage and microbial invasion through the epithelium (indicated by arrows). Stained with haematoxylin and eosin. The scale bar represents 50 µm.

    Article Snippet: In order to establish whether there were differences between the commercial and in-house tissues with regard to the infecting biofilms, comparisons were again made of tissue models of the same type; namely SkinEthic RHOE versus in vitro keratinocyte-only tissues, and MatTek EpiOral versus in vitro full-thickness tissues.

    Techniques: Light Microscopy, Infection, Staining

    Expression of putative Candida albicans virulence genes of mixed-species biofilms post-tissue infection. The results are expressed as the fold change of samples relative to the housekeeping gene ACT1 against a normalised C. albicans -only biofilm control. No significant differences in C albicans gene expression were observed between tissue models of the same type (e.g. SkinEthic RHOE versus in vitro keratinocyte only, or MatTek EpiOral full-thickness versus in vitro full-thickness tissues) with the exception of full-thickness tissues for the ALS1 gene.

    Journal: Journal of Medical Microbiology

    Article Title: Denture-associated biofilm infection in three-dimensional oral mucosal tissue models

    doi: 10.1099/jmm.0.000677

    Figure Lengend Snippet: Expression of putative Candida albicans virulence genes of mixed-species biofilms post-tissue infection. The results are expressed as the fold change of samples relative to the housekeeping gene ACT1 against a normalised C. albicans -only biofilm control. No significant differences in C albicans gene expression were observed between tissue models of the same type (e.g. SkinEthic RHOE versus in vitro keratinocyte only, or MatTek EpiOral full-thickness versus in vitro full-thickness tissues) with the exception of full-thickness tissues for the ALS1 gene.

    Article Snippet: In order to establish whether there were differences between the commercial and in-house tissues with regard to the infecting biofilms, comparisons were again made of tissue models of the same type; namely SkinEthic RHOE versus in vitro keratinocyte-only tissues, and MatTek EpiOral versus in vitro full-thickness tissues.

    Techniques: Expressing, Infection, In Vitro

    Representative light microscope image of the mixed-species biofilm infection of MatTek full-thickness tissues, demonstrating tissue damage caused by invading Candida albicans and bacteria as a result of biofilm infection. Stained with haematoxylin and eosin. The scale bar represents 50 µm.

    Journal: Journal of Medical Microbiology

    Article Title: Denture-associated biofilm infection in three-dimensional oral mucosal tissue models

    doi: 10.1099/jmm.0.000677

    Figure Lengend Snippet: Representative light microscope image of the mixed-species biofilm infection of MatTek full-thickness tissues, demonstrating tissue damage caused by invading Candida albicans and bacteria as a result of biofilm infection. Stained with haematoxylin and eosin. The scale bar represents 50 µm.

    Article Snippet: In order to establish whether there were differences between the commercial and in-house tissues with regard to the infecting biofilms, comparisons were again made of tissue models of the same type; namely SkinEthic RHOE versus in vitro keratinocyte-only tissues, and MatTek EpiOral versus in vitro full-thickness tissues.

    Techniques: Light Microscopy, Infection, Staining

    Biofilm-induced tissue damage as measured by the lactate dehydrogenase activity assay of infections. The results are expressed as fold change, normalised against an acrylic-only (no biofilm) control. (a) SkinEthic RHOE, (b) in vitro keratinocyte-only tissue, (c) MatTek EpiOral full-thickness tissue and (d) in vitro full-thickness tissue. All of the tissues show a similar pattern of damage; the largest increase in tissue damage is induced by mixed-species biofilms, compared to single-species and uninfected control acrylic coupons.

    Journal: Journal of Medical Microbiology

    Article Title: Denture-associated biofilm infection in three-dimensional oral mucosal tissue models

    doi: 10.1099/jmm.0.000677

    Figure Lengend Snippet: Biofilm-induced tissue damage as measured by the lactate dehydrogenase activity assay of infections. The results are expressed as fold change, normalised against an acrylic-only (no biofilm) control. (a) SkinEthic RHOE, (b) in vitro keratinocyte-only tissue, (c) MatTek EpiOral full-thickness tissue and (d) in vitro full-thickness tissue. All of the tissues show a similar pattern of damage; the largest increase in tissue damage is induced by mixed-species biofilms, compared to single-species and uninfected control acrylic coupons.

    Article Snippet: In order to establish whether there were differences between the commercial and in-house tissues with regard to the infecting biofilms, comparisons were again made of tissue models of the same type; namely SkinEthic RHOE versus in vitro keratinocyte-only tissues, and MatTek EpiOral versus in vitro full-thickness tissues.

    Techniques: Activity Assay, In Vitro

    Typical light microscopy images of (a) MatTek full-thickness tissue after infection with acrylic coupons only (no biofilm), showing no damage to epithelium; (b) MatTek full-thickness tissue after infection with bacteria-only biofilm, showing very slight tissue damage and clustering of biofilms on the epithelial surface (indicated by arrows); (c) MatTek full-thickness tissue after infection with Candida albicans -only biofilm, showing slight epithelial damage and biofilms clustered on the surface of the epithelium (indicated by arrows); (d) MatTek full-thickness tissue after infection with mixed-species biofilm, showing slight epithelial damage and biofilms clustered on the surface of the epithelium (indicated by arrows). Stained with haematoxylin and eosin. The scale bar represents 50 µm.

    Journal: Journal of Medical Microbiology

    Article Title: Denture-associated biofilm infection in three-dimensional oral mucosal tissue models

    doi: 10.1099/jmm.0.000677

    Figure Lengend Snippet: Typical light microscopy images of (a) MatTek full-thickness tissue after infection with acrylic coupons only (no biofilm), showing no damage to epithelium; (b) MatTek full-thickness tissue after infection with bacteria-only biofilm, showing very slight tissue damage and clustering of biofilms on the epithelial surface (indicated by arrows); (c) MatTek full-thickness tissue after infection with Candida albicans -only biofilm, showing slight epithelial damage and biofilms clustered on the surface of the epithelium (indicated by arrows); (d) MatTek full-thickness tissue after infection with mixed-species biofilm, showing slight epithelial damage and biofilms clustered on the surface of the epithelium (indicated by arrows). Stained with haematoxylin and eosin. The scale bar represents 50 µm.

    Article Snippet: In order to establish whether there were differences between the commercial and in-house tissues with regard to the infecting biofilms, comparisons were again made of tissue models of the same type; namely SkinEthic RHOE versus in vitro keratinocyte-only tissues, and MatTek EpiOral versus in vitro full-thickness tissues.

    Techniques: Light Microscopy, Infection, Staining

    Biofilm formation inhibition assay performed on S. epidermidis . Values are mean of three replicates, ± standard error.

    Journal: Marine Drugs

    Article Title: Characterization of Rhamnolipids Produced by an Arctic Marine Bacterium from the Pseudomonas fluorescence Group

    doi: 10.3390/md16050163

    Figure Lengend Snippet: Biofilm formation inhibition assay performed on S. epidermidis . Values are mean of three replicates, ± standard error.

    Article Snippet: The biofilm was fixed at 65 °C for 1 h before 70 µL 0.1% crystal violet (115940, Merck Millipore) was added to the wells for 10 min of incubation.

    Techniques: Inhibition

    Rapid development of nfxB mutants in a 24-h-old PAO1 flow cell biofilm treated with low-dose CIP. The biofilms of PAO1- mCherry -P CD - gfp + were grown in flow cell chambers with a continuous flow of minimal medium for 24 h at 37°C and then grown for an additional 24 h with 0.2 μg/ml CIP (24 h +CIP for 24 h) or without CIP (24 h −CIP for 24 h). Red shows wild-type cells (elongated or filamentous) due to the constitutive expression of mCherry, and green shows nfxB mutants due to the expression of GFP via the P CD - gfp + reporter. z-stacks were generated by using a Zeiss LSM 710 microscope and processed with Imaris 8.2 software (Bitplane). Top-row images show orthogonal 3D views, and middle and bottom (for treated biofilms only) rows show perspective 3D views of biofilms with an overlay of red and green fluorescence. The images shown are representative of results for two independent flow cell channels.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Real-Time Monitoring of nfxB Mutant Occurrence and Dynamics in Pseudomonas aeruginosa Biofilm Exposed to Subinhibitory Concentrations of Ciprofloxacin

    doi: 10.1128/AAC.02292-16

    Figure Lengend Snippet: Rapid development of nfxB mutants in a 24-h-old PAO1 flow cell biofilm treated with low-dose CIP. The biofilms of PAO1- mCherry -P CD - gfp + were grown in flow cell chambers with a continuous flow of minimal medium for 24 h at 37°C and then grown for an additional 24 h with 0.2 μg/ml CIP (24 h +CIP for 24 h) or without CIP (24 h −CIP for 24 h). Red shows wild-type cells (elongated or filamentous) due to the constitutive expression of mCherry, and green shows nfxB mutants due to the expression of GFP via the P CD - gfp + reporter. z-stacks were generated by using a Zeiss LSM 710 microscope and processed with Imaris 8.2 software (Bitplane). Top-row images show orthogonal 3D views, and middle and bottom (for treated biofilms only) rows show perspective 3D views of biofilms with an overlay of red and green fluorescence. The images shown are representative of results for two independent flow cell channels.

    Article Snippet: To isolate nfxB mutants for further characterization, PAO1- mCherry -PCD - gfp + biofilms were harvested by pumping 1 to 1.5 ml of a glass bead (212 to 300 μm; Sigma)-saline suspension through the flow cell channels and collected into sterile Eppendorf tubes.

    Techniques: Flow Cytometry, Expressing, Generated, Microscopy, Software, Fluorescence

    Development of nfxB mutants in a 72-h-old PAO1 flow cell biofilm during treatment with low-dose CIP. The biofilms of PAO1- mCherry -P CD - gfp + were grown in three independent channels of flow cell chambers with a continuous flow of minimal medium for 72 h and then treated with 0.2 μg/ml CIP for a total of 96 h. Imaging by CLSM was done every 24 h. At least 3 images were taken per channel at every time point. Red represents wild-type cells due to the constitutive expression of mCherry, and green shows nfxB mutants due to the expression of GFP+ via the P CD - gfp + reporter. z-stacks were generated by using a Zeiss LSM 710 microscope and processed with Imaris 8.2 software (Bitplane). The images show orthogonal 3D biofilm views (left) or a perspective view (right) with an overlay of red and green channel fluorescence.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Real-Time Monitoring of nfxB Mutant Occurrence and Dynamics in Pseudomonas aeruginosa Biofilm Exposed to Subinhibitory Concentrations of Ciprofloxacin

    doi: 10.1128/AAC.02292-16

    Figure Lengend Snippet: Development of nfxB mutants in a 72-h-old PAO1 flow cell biofilm during treatment with low-dose CIP. The biofilms of PAO1- mCherry -P CD - gfp + were grown in three independent channels of flow cell chambers with a continuous flow of minimal medium for 72 h and then treated with 0.2 μg/ml CIP for a total of 96 h. Imaging by CLSM was done every 24 h. At least 3 images were taken per channel at every time point. Red represents wild-type cells due to the constitutive expression of mCherry, and green shows nfxB mutants due to the expression of GFP+ via the P CD - gfp + reporter. z-stacks were generated by using a Zeiss LSM 710 microscope and processed with Imaris 8.2 software (Bitplane). The images show orthogonal 3D biofilm views (left) or a perspective view (right) with an overlay of red and green channel fluorescence.

    Article Snippet: To isolate nfxB mutants for further characterization, PAO1- mCherry -PCD - gfp + biofilms were harvested by pumping 1 to 1.5 ml of a glass bead (212 to 300 μm; Sigma)-saline suspension through the flow cell channels and collected into sterile Eppendorf tubes.

    Techniques: Flow Cytometry, Imaging, Confocal Laser Scanning Microscopy, Expressing, Generated, Microscopy, Software, Fluorescence

    Mechanics of cell reorientation in modeled biofilms, ( a-b ) Properties of individual cells at the time t r of reorientation, defined as the time of the peak of total force on the cell prior to it becoming vertical. Analyses are shown for all reorientation events among different biofilms simulated for a range of initial cell lengths ℓ 0 ( a ) Distributions of reorientation “surface pressure” p r , defined as the total contact force in the xy plane acting on a cell at time t r , normalized by the cell’s perimeter, versus cell cylinder length ℓ . The white dashed curve shows the average reorientation surface pressure ⟨ p r ⟩ as a function of ℓ . The magenta dashed curve shows the threshold surface pressure p t from linear stability analysis for a modeled cell under uniform pressure, depicted schematically in the inset, ( b ) Distributions of the logarithm of reorientation torque τ r , defined as the magnitude of the torque on a cell due to cell-cell contact forces in the z direction at time t r , for different cell cylinder lengths ℓ . The white dashed curve shows the average values ⟨log τ r ⟩ as a function of ℓ . The orange dashed curve shows the scaling τ t ~ ℓ 2 of the threshold torque for peeling from linear stability analysis for a modeled cell, depicted schematically in the inset, ( c ) Mean reorientation length ⟨ ℓ r ⟩ (red), defined as the average value of cell length at t r , and mean cell cylinder length ⟨ ℓ ⟩ (gray), defined as the average length of all horizontal cells over all times of biofilm growth, averaged over ten simulated biofilms, each with initial cell cylinder length ℓ 0 , plotted versus ℓ 0 . The inset shows the distribution of reorientation lengths (red) and horizontal surface-cell lengths (gray) for ℓ 0 = 1 μm. ( d ) Mean avalanche size ⟨ N ⟩, defined as the average size of a cluster of reorienting cells that are proximal in space and time ( Supplementary Figs. 8 - 10 ), versus initial cell length ℓ 0 for the experimental biofilm (red triangle) and the modeled biofilm (red circles). Open gray triangle and circles indicate the corresponding mean avalanche sizes for a null model. Inset shows a side view of cell configurations in the xy plane at times t r for all reorientation events in a simulated biofilm with ℓ 0 = 2.5 μm. Reorientation events are colored alike if they belong to the same avalanche. Scale bars: 10 μm and 1 hour.

    Journal: Nature physics

    Article Title: Verticalization of bacterial biofilms

    doi: 10.1038/s41567-018-0170-4

    Figure Lengend Snippet: Mechanics of cell reorientation in modeled biofilms, ( a-b ) Properties of individual cells at the time t r of reorientation, defined as the time of the peak of total force on the cell prior to it becoming vertical. Analyses are shown for all reorientation events among different biofilms simulated for a range of initial cell lengths ℓ 0 ( a ) Distributions of reorientation “surface pressure” p r , defined as the total contact force in the xy plane acting on a cell at time t r , normalized by the cell’s perimeter, versus cell cylinder length ℓ . The white dashed curve shows the average reorientation surface pressure ⟨ p r ⟩ as a function of ℓ . The magenta dashed curve shows the threshold surface pressure p t from linear stability analysis for a modeled cell under uniform pressure, depicted schematically in the inset, ( b ) Distributions of the logarithm of reorientation torque τ r , defined as the magnitude of the torque on a cell due to cell-cell contact forces in the z direction at time t r , for different cell cylinder lengths ℓ . The white dashed curve shows the average values ⟨log τ r ⟩ as a function of ℓ . The orange dashed curve shows the scaling τ t ~ ℓ 2 of the threshold torque for peeling from linear stability analysis for a modeled cell, depicted schematically in the inset, ( c ) Mean reorientation length ⟨ ℓ r ⟩ (red), defined as the average value of cell length at t r , and mean cell cylinder length ⟨ ℓ ⟩ (gray), defined as the average length of all horizontal cells over all times of biofilm growth, averaged over ten simulated biofilms, each with initial cell cylinder length ℓ 0 , plotted versus ℓ 0 . The inset shows the distribution of reorientation lengths (red) and horizontal surface-cell lengths (gray) for ℓ 0 = 1 μm. ( d ) Mean avalanche size ⟨ N ⟩, defined as the average size of a cluster of reorienting cells that are proximal in space and time ( Supplementary Figs. 8 - 10 ), versus initial cell length ℓ 0 for the experimental biofilm (red triangle) and the modeled biofilm (red circles). Open gray triangle and circles indicate the corresponding mean avalanche sizes for a null model. Inset shows a side view of cell configurations in the xy plane at times t r for all reorientation events in a simulated biofilm with ℓ 0 = 2.5 μm. Reorientation events are colored alike if they belong to the same avalanche. Scale bars: 10 μm and 1 hour.

    Article Snippet: For biofilm clusters grown in the presence of A22 or Cefalexin, cell lengths were manually measured in the bottom cell layers of the biofilms using the Nikon Element software.

    Techniques:

    Development of experimental and modeled biofilms. ( a , b ) Top-down and perspective visualizations of the surface layer of ( a ) experimental and ( b ) modeled biofilms, showing positions and orientations of horizontal (blue) and vertical (red) surface-adhered cells as spherocylinders of radius R = 0.8 μm, with the surface shown at height z = 0 μm (brown). Cells with n z

    Journal: Nature physics

    Article Title: Verticalization of bacterial biofilms

    doi: 10.1038/s41567-018-0170-4

    Figure Lengend Snippet: Development of experimental and modeled biofilms. ( a , b ) Top-down and perspective visualizations of the surface layer of ( a ) experimental and ( b ) modeled biofilms, showing positions and orientations of horizontal (blue) and vertical (red) surface-adhered cells as spherocylinders of radius R = 0.8 μm, with the surface shown at height z = 0 μm (brown). Cells with n z

    Article Snippet: For biofilm clusters grown in the presence of A22 or Cefalexin, cell lengths were manually measured in the bottom cell layers of the biofilms using the Nikon Element software.

    Techniques:

    Two-component fluid model for verticalizing cells in biofilms. ( a ) Schematic illustration of the two-component continuum model. Horizontal cells (blue) and vertical cells (red) are modeled, respectively, by densities ρ h and ρ v in two spatial dimensions. The total cell density ρ ~ tot is defined as ρ h + ξρ ν , where ξ is the ratio of vertical to horizontal cell footprints. ( b ) Radial densities ρ of vertical cells ( ρ v , red), horizontal cells ( ρ h , blue), and total density ( ρ ~ tot , black), versus shifted radial coordinate r ~ , defined as the radial position relative to the boundary between the mixed interior and the horizontal cell periphery. Results are shown for the continuum model (left; radial cell density in units of μm −2 ), the experimental biofilm (middle; radial cell density in each μm-sized bin averaged over an observation window of 50 minutes), and the agent-based model biofilm (right; radial cell density in each μm-sized bin averaged for ten biofilms over an observation window of 6 minutes). For the continuum model and the agent-based model biofilms the parameters were chosen to match those obtained from the experiment ( Supplementary Figs. 12 - 13 ). Inset in the left-most panel shows the fraction of vertical cells in the continuum model at a given radius from the biofilm center (gray regions contain no cells, color scale is the same as in Fig. 1 ).

    Journal: Nature physics

    Article Title: Verticalization of bacterial biofilms

    doi: 10.1038/s41567-018-0170-4

    Figure Lengend Snippet: Two-component fluid model for verticalizing cells in biofilms. ( a ) Schematic illustration of the two-component continuum model. Horizontal cells (blue) and vertical cells (red) are modeled, respectively, by densities ρ h and ρ v in two spatial dimensions. The total cell density ρ ~ tot is defined as ρ h + ξρ ν , where ξ is the ratio of vertical to horizontal cell footprints. ( b ) Radial densities ρ of vertical cells ( ρ v , red), horizontal cells ( ρ h , blue), and total density ( ρ ~ tot , black), versus shifted radial coordinate r ~ , defined as the radial position relative to the boundary between the mixed interior and the horizontal cell periphery. Results are shown for the continuum model (left; radial cell density in units of μm −2 ), the experimental biofilm (middle; radial cell density in each μm-sized bin averaged over an observation window of 50 minutes), and the agent-based model biofilm (right; radial cell density in each μm-sized bin averaged for ten biofilms over an observation window of 6 minutes). For the continuum model and the agent-based model biofilms the parameters were chosen to match those obtained from the experiment ( Supplementary Figs. 12 - 13 ). Inset in the left-most panel shows the fraction of vertical cells in the continuum model at a given radius from the biofilm center (gray regions contain no cells, color scale is the same as in Fig. 1 ).

    Article Snippet: For biofilm clusters grown in the presence of A22 or Cefalexin, cell lengths were manually measured in the bottom cell layers of the biofilms using the Nikon Element software.

    Techniques:

    Global morphological properties of experimental and modeled biofilms, ( a ) Top-down (upper row) and side views (lower row) of experimental biofilms grown with 0.4 μg/mL A22 (magenta), without treatment (yellow), and with 4 μg/mL Cefalexin (cyan), following overnight growth (upper row) and 7 hours after inoculation (lower row). Scale bar: 10 μm. Insets show magnifications of 10 μm 2 -sized regions of top-down views taken from the peripheries of biofilms. ( b ) Expansion speed c *, defined as the speed of the biofilm edge along the surface, versus the initial cell cylinder length ℓ 0 for experimental biofilms (A22, magenta; no treatment, yellow; Cefalexin, cyan), agent-based model biofilms (black circles), and continuum model (dashed black curve). Expansion velocities were determined from a linear fit of the basal radius R B of the biofilm versus time, where R B is defined at each time point as the radius of a circle with area equal to that of the biofilm base. For experimental biofilms, the boundary was extracted from the normalized fluorescence data (see Methods for details). For each treatment, the vertical error bars show the standard error of the mean of the expansion speed and the horizontal error bars bound the measured initial cell cylinder length ( Supplementary Fig. 1 ). Inset: model cells with lengths and radii corresponding to the averages for different treatments, ( c ) Biofilm aspect ratio H/R B for experimental biofilms grown under different treatments, where the biofilm height is defined as H = 3 V ∕ 2 R B 2 , the height of a semi-ellipsoid with a circular base of radius R B and volume V equal to that of the biofilm. Error bars show the standard error of the mean. Inset: overlay of biofilm outlines from bottom row of panel ( a ). Color designations and treatments same as in panel ( a ).

    Journal: Nature physics

    Article Title: Verticalization of bacterial biofilms

    doi: 10.1038/s41567-018-0170-4

    Figure Lengend Snippet: Global morphological properties of experimental and modeled biofilms, ( a ) Top-down (upper row) and side views (lower row) of experimental biofilms grown with 0.4 μg/mL A22 (magenta), without treatment (yellow), and with 4 μg/mL Cefalexin (cyan), following overnight growth (upper row) and 7 hours after inoculation (lower row). Scale bar: 10 μm. Insets show magnifications of 10 μm 2 -sized regions of top-down views taken from the peripheries of biofilms. ( b ) Expansion speed c *, defined as the speed of the biofilm edge along the surface, versus the initial cell cylinder length ℓ 0 for experimental biofilms (A22, magenta; no treatment, yellow; Cefalexin, cyan), agent-based model biofilms (black circles), and continuum model (dashed black curve). Expansion velocities were determined from a linear fit of the basal radius R B of the biofilm versus time, where R B is defined at each time point as the radius of a circle with area equal to that of the biofilm base. For experimental biofilms, the boundary was extracted from the normalized fluorescence data (see Methods for details). For each treatment, the vertical error bars show the standard error of the mean of the expansion speed and the horizontal error bars bound the measured initial cell cylinder length ( Supplementary Fig. 1 ). Inset: model cells with lengths and radii corresponding to the averages for different treatments, ( c ) Biofilm aspect ratio H/R B for experimental biofilms grown under different treatments, where the biofilm height is defined as H = 3 V ∕ 2 R B 2 , the height of a semi-ellipsoid with a circular base of radius R B and volume V equal to that of the biofilm. Error bars show the standard error of the mean. Inset: overlay of biofilm outlines from bottom row of panel ( a ). Color designations and treatments same as in panel ( a ).

    Article Snippet: For biofilm clusters grown in the presence of A22 or Cefalexin, cell lengths were manually measured in the bottom cell layers of the biofilms using the Nikon Element software.

    Techniques: Fluorescence

    Degree of saturation of membrane fatty acids of Sphingomonas sp. LH128 biofilm cells grown in flow chambers without solute stress (control) and with acute or chronic solute stress. The values shown are the average of three biological replicates with the indicated standard deviations. The asterisk indicates a statistically significant difference from the control (*, P

    Journal: Applied and Environmental Microbiology

    Article Title: Exposure to Solute Stress Affects Genome-Wide Expression but Not the Polycyclic Aromatic Hydrocarbon-Degrading Activity of Sphingomonas sp. Strain LH128 in Biofilms

    doi: 10.1128/AEM.02516-12

    Figure Lengend Snippet: Degree of saturation of membrane fatty acids of Sphingomonas sp. LH128 biofilm cells grown in flow chambers without solute stress (control) and with acute or chronic solute stress. The values shown are the average of three biological replicates with the indicated standard deviations. The asterisk indicates a statistically significant difference from the control (*, P

    Article Snippet: For each condition, the biofilm present in each of the three replicate flow chambers was analyzed on an Olympus IX81 inverted microscope equipped with a Fluoview FV1000 confocal scanning unit and two lasers.

    Techniques: Flow Cytometry

    Oxygen concentrations in the influent and effluent of flow chambers colonized by Sphingomonas sp. LH128 biofilms and of noninoculated systems for comparison. The oxygen concentration was measured in the influent (black bars) and effluent (gray bars) before (A) and after (B) the application of solute stress in the inoculated systems. Values shown are the average of three biological replicates with the indicated standard deviations.

    Journal: Applied and Environmental Microbiology

    Article Title: Exposure to Solute Stress Affects Genome-Wide Expression but Not the Polycyclic Aromatic Hydrocarbon-Degrading Activity of Sphingomonas sp. Strain LH128 in Biofilms

    doi: 10.1128/AEM.02516-12

    Figure Lengend Snippet: Oxygen concentrations in the influent and effluent of flow chambers colonized by Sphingomonas sp. LH128 biofilms and of noninoculated systems for comparison. The oxygen concentration was measured in the influent (black bars) and effluent (gray bars) before (A) and after (B) the application of solute stress in the inoculated systems. Values shown are the average of three biological replicates with the indicated standard deviations.

    Article Snippet: For each condition, the biofilm present in each of the three replicate flow chambers was analyzed on an Olympus IX81 inverted microscope equipped with a Fluoview FV1000 confocal scanning unit and two lasers.

    Techniques: Flow Cytometry, Concentration Assay