Journal: Journal of applied microbiology

Article Title: Bacterial inactivation by high-voltage atmospheric cold plasma: influence of process parameters and effects on cell leakage and DNA.

doi: 10.1111/jam.12426

Figure Lengend Snippet: Figure 4 Agarose gel electrophoresis showing genomic DNA and PCR-amplified products of untreated and ACP-treated samples. Voltage: 70 kVRMS; treatment time: 0–30 s; post-treatment storage time: 24 h; gas mix: air. Genomic DNA damage of (a) Escherichia coli ATCC 25922; (b) E. coli NCTC 12900; (c) Listeria monocytogenes NCTC 11994. 16S rRNA PCR results of (d) E. coli ATCC 25922; (e) E. coli NCTC 12900; (f) L. monocytogenes NCTC 11994. Lane 1: Nonplasma treatment control; 2: 5 s directly treated samples; 3: 5 s indirectly treated samples; 4: 30 s directly treated samples; 5: 30 s indirectly treated samples.

Article Snippet: E. coli ATCC 25922 populations were reduced below detection level after 30 s of indirect ACP treatment; however, direct ACP-treated population reduced by 3 4 log cycles.

Techniques: Agarose Gel Electrophoresis, Control

Journal: Food Technology and Biotechnology

Article Title: Autochthonous Human Milk Lactobacillus Strains as Potential Probiotic Starter Cultures

doi: 10.17113/ftb.64.01.26.9074

Figure Lengend Snippet: Antimicrobial activity of lactic acid bacteria (LAB) strains against: a) test microorganisms, and b) related LAB strains tested by the turbidimetric method. Different letters above bars indicate statistically significant difference (p<0.05) between the LAB strains and the same test microorganism, i.e. a related LAB strain

Article Snippet: The antimicrobial activity of the selected LAB isolates from human milk was tested against test microorganisms ( Staphylococcus aureus ATCC ® 25925 TM , Listeria monocytogenes ATCC ® 19111 TM , Escherichia coli ATCC ® 25922 TM and Salmonella Typhimurium FP1) and related LAB strains ( Lactobacillus helveticus M92, L. lactis ssp. lactis LMG 9450 and Enterococcus faecium ATCC ® 9430 TM ) cultured in the appropriate medium until their A 620 nm reached 0.5 and 1.0, respectively.

Techniques: Activity Assay, Bacteria

Journal:

Article Title: Isolation and Characterization of Bacteria Capable of Tolerating the Extreme Conditions of Clean Room Environments ▿

doi: 10.1128/AEM.03007-06

Figure Lengend Snippet: Intracellular ATP content of several microbes that were isolated from spacecraft or other clean environmental surfaces

Article Snippet: No signal above background was obtained. table ft1 table-wrap mode="anchored" t5 TABLE 3. caption a7 Organism Strain a Intracellular ATP content (10 −18 mol/CFU) RLU/CFU or RLU/spore Avg RLU/CFU Gram-negative bacteria 1.34 Acinetobacter radioresistens MO-50v1 1.91 0.98 Escherichia coli ATCC 25922 2.39 1.23 Methylobacterium radiotolerans MSFC 2M5-R1 3.70 1.90 Proteus mirabilis ATCC 29906 2.13 1.10 Pseudomonas aeruginosa ATCC 27853 1.84 0.95 Pseudomonas stutzeri JPL-1 1.44 0.74 Pseudomonas graminis JPL-8 5.45 2.80 Sphingomonas yanoikuyae MSFC 4M9-R1 1.98 1.02 Gram-positive bacteria 4.49 Bacillus subtilis ATCC 9372 8.45 4.34 Bacillus macroides JPL-4 10.27 5.28 Kokuria rhizophila JPL-9 11.99 6.16 Micrococcus luteus IFO 3333 8.28 4.26 Staphylococcus aureus ATCC 25923 5.77 2.97 Staphylococcus capitis JPL-2 8.85 4.55 Staphylococcus epidermidis JPL-7 7.47 3.84 Yeasts 263.50 Candida utilis NISL 3727 677.00 348.07 Saccharomyces cerevisiae NISL 3398 348.00 178.92 Spores 0.0016 Bacillus circulans ATCC 4513 0.0032 0.0016 Bacillus subtilis ATCC 6633 0.0037 0.0019 Lactobacillus buchneri ATCC 11577 0.0022 0.0011 Bacillus subtilis vegetative cells Autoclaved ATCC 6633 No RLU b NG c UV 254 -killed ATCC 6633 No RLU NG H 2 O 2 -sterilized ATCC 6633 No RLU NG Open in a separate window a Abbreviations used in strain designations: MO, Mars Odyssey spacecraft; ATCC, American Type Culture Collection; MSFC, Marshall Space Flight Center; JPL, Jet Propulsion Laboratory; IFO, Institute of Fermentation-Osaka, Japan; NISL, Noda Institute for Scientific Research, Noda, Japan. b When measured for bioluminescence after removing extracellular ATP, no luminescence was recorded. c NG, no growth when grown on TSA or R2A agar.

Techniques: Isolation, Bacteria

Journal: Frontiers in Microbiology

Article Title: Systematically Studying the Optimal Amino Acid Distribution Patterns of the Amphiphilic Structure by Using the Ultrashort Amphiphiles

doi: 10.3389/fmicb.2020.569118

Figure Lengend Snippet: (A) Time-kill kinetic curves of W5 (A-1) , L5 (A-2) , and melittin (A-3) at 1× MBC against E. coli ATCC 25922 and S. aureus 29213. (B) Resistance proceedings in the presence of a sub-MBC concentration of the peptides against P. aeruginosa ATCC 27853. The graph was from three independent experiments, and each independent experiment contained three technical replicates.

Article Snippet: Mid-log phase E. coli ATCC 25922 cells (OD 600 = 0.2) were incubated with NPN (10 μM) in 5 mM HEPES buffer (pH 7.4, containing 5 mM glucose) for 30 min.

Techniques: Concentration Assay

Journal: Frontiers in Microbiology

Article Title: Systematically Studying the Optimal Amino Acid Distribution Patterns of the Amphiphilic Structure by Using the Ultrashort Amphiphiles

doi: 10.3389/fmicb.2020.569118

Figure Lengend Snippet: Super-resolution microscopy image analysis of S. aureus 29213 and E. coli ATCC 25922 treated with PI, FITC-labeled W5 and FITC-labeled L5. The green signal is from the FITC peptides, and the red signal is from PI. The FITC peptides mainly cover the surface of the membrane, and PI is a nucleic acid dye that can penetrate broken cells and release red fluorescence.

Article Snippet: Mid-log phase E. coli ATCC 25922 cells (OD 600 = 0.2) were incubated with NPN (10 μM) in 5 mM HEPES buffer (pH 7.4, containing 5 mM glucose) for 30 min.

Techniques: Super-Resolution Microscopy, Labeling, Membrane, Fluorescence

Journal: Frontiers in Microbiology

Article Title: Systematically Studying the Optimal Amino Acid Distribution Patterns of the Amphiphilic Structure by Using the Ultrashort Amphiphiles

doi: 10.3389/fmicb.2020.569118

Figure Lengend Snippet: (A) Peptide binding affinity to LPS from E. coli O111:B4. The fluorescence intensity was monitored at an excitation wavelength of 580 nm and an emission wavelength of 620 nm. (B) The outer membrane permeability induced by W5, L5, and melittin. The uptake of NPN by E. coli in the presence of different concentrations of W5, L5 and melittin was determined using the fluorescent dye (NPN) assay. The NPN uptake was monitored at an excitation wavelength of 350 nm and an emission wavelength of 420 nm. (C) The cytoplasmic membrane potential variation of E. coli treated with different concentrations of W5 (C-1) , L5 (C-2) , or melittin (C-3) , as assessed by the release of the membrane potential-sensitive dye DiSC 3 -5. The fluorescence intensity was monitored at an excitation wavelength of 622 nm and an emission wavelength of 670 nm as a function of time. (D) Inner membrane permeability of the peptides. The hydrolysis of ONPG due to the release of cytoplasmic β-galactosidase by E. coli treated with different concentrations of W5 (D-1) , L5 (D-2) , or melittin (D-3) was measured spectroscopically at an absorbance of 420 nm as a function of time. The graphs were derived from the average of three independent trials.

Article Snippet: Mid-log phase E. coli ATCC 25922 cells (OD 600 = 0.2) were incubated with NPN (10 μM) in 5 mM HEPES buffer (pH 7.4, containing 5 mM glucose) for 30 min.

Techniques: Binding Assay, Fluorescence, Membrane, Permeability, NPN Assay, Derivative Assay

Journal: Frontiers in Microbiology

Article Title: Systematically Studying the Optimal Amino Acid Distribution Patterns of the Amphiphilic Structure by Using the Ultrashort Amphiphiles

doi: 10.3389/fmicb.2020.569118

Figure Lengend Snippet: SEM micrographs of E. coli ATCC 25922 and S. aureus 29213. (A) E. coli -control, (B) E. coli treated with W5 (blebbing), (C) E. coli treated with L5 (hole and wrinkle formation), (D) S. aureus control, (E) S. aureus treated with W5 (content leakage), and (F) S. aureus treated with L5 (hole formation). Scale bar = 2.00 μm (A–E) , 1.00 μm (F) .

Article Snippet: Mid-log phase E. coli ATCC 25922 cells (OD 600 = 0.2) were incubated with NPN (10 μM) in 5 mM HEPES buffer (pH 7.4, containing 5 mM glucose) for 30 min.

Techniques: Control

Journal: Frontiers in Microbiology

Article Title: Systematically Studying the Optimal Amino Acid Distribution Patterns of the Amphiphilic Structure by Using the Ultrashort Amphiphiles

doi: 10.3389/fmicb.2020.569118

Figure Lengend Snippet: TEM micrographs of E. coli ATCC 25922 and S. aureus 29213. (A) E. coli control, (B) E. coli treated with W5 (content leakage), (C) E. coli treated with L5 (obviously clear areas), (D) S. aureus control, (E) S. aureus treated with W5 (sparse cytoplasmic distribution), and (F) S. aureus treated with L5 (cytoplasmic membrane and outer membrane separation and hole formation). Scale bar = 500 nm (A,B,D–F) , 1,000 nm (C) .

Article Snippet: Mid-log phase E. coli ATCC 25922 cells (OD 600 = 0.2) were incubated with NPN (10 μM) in 5 mM HEPES buffer (pH 7.4, containing 5 mM glucose) for 30 min.

Techniques: Control, Membrane

Journal: BMC Oral Health

Article Title: Potential of microbial-derived biosurfactants for oral applications–a systematic review

doi: 10.1186/s12903-024-04479-0

Figure Lengend Snippet: Overview of the methods employed and outcomes of studies included in this systematic review

Article Snippet: Farias J.M. et al. [ ] (2019) , Biosurfactant Pseudomonas aeruginosa (PB), Bacillus cereus (BB), Candida bombicola (CB) , C. albicans ATCC 1106 S. aureus ATCC 15,656 E. coli ATCC 25,922 L. acidophilus ATCC 4356 S. salivarius ATCC 25,975 S. mutans ATCC 25,175 , Chitosan (extracted from the cell wall of Mucor javanicus (UCP 69)), Peppermint essential oil (POE) , 1. Characterization of biosurfactants 2. Formulation of mouthwash 3. Determination of antimicrobial activity 4. Analysis of fraction inhibitory concentration 5. Evaluation of toxicity of formulated mouthwashes , 1. The biosurfactants obtained from C. bombicola , B. cereus , and P. aeruginosa (respectively designated as CB, BB, and PB) were capable of reducing the surface tension of water from 70 mN/m to 30, 29, and 26.5 mN/m, respectively. 2. The formulation consists of biosurfactant, peppermint essential oil, and chitosan solution (diluted in 1% acetic acid), the solid components (sodium benzoate and sodium saccharine) in a fine powder, followed by distilled water to complete 100 mL. The pH of the formulation was adjusted to 7.0 with NaOH 1 N. 3. The biosurfactant PB was the most effective against S. aureus , E. coli , and S. salivarius (MIC: 20 μg/mL), while PB and CB had similar effects on S. mutans (MIC: 20 μg/mL). All biosurfactants exhibited uniform effects on C. albicans and L. acidophilus (MIC: 40 μg/mL). Combining biosurfactants with chitosan reduced MIC for all microorganisms. When combined with peppermint essential oils, the MIC for C. albicans either increased (CB + POE and BB + POE: 30 μg/mL) or remained the same (PB + POE: 20 μg/mL). The low MIC combination for L. acidophilus (20 μg/mL) was peppermint essential oil with PB. For S. mutans , only CB + POE maintained the biosurfactant’s MIC, with reductions observed in all other combinations. 4. The combinations of the CB and PB with chitosan demonstrated an additive effect on the majority of microorganisms tested and an indifferent effect on E. coli and C. albicans . The combinations of CB and BB with the peppermint essential oil exhibited an additive effect only on the gram-negative bacterium E. coli and an indifferent effect on the other microorganisms tested. 5. The results demonstrate that the test mouthwashes were classified as non-toxic to the fibroblast line, with cell inhibition rates lower than 20%. However, the mouthwash containing the biosurfactant extracted from C. bombicola + peppermint essential oil + chitosan exhibited moderate toxicity to the macrophage line (66% inhibition)..

Techniques: Extraction, Purification, Concentration Assay, Activity Assay, Inhibition, Produced, Bacteria, Formulation, Calcium Carbonate, Foaming, Diffusion-based Assay, Disruption, In Vitro, Antibiofilm Assay, Gene Expression, Real-time Polymerase Chain Reaction, High Performance Liquid Chromatography, Fluorescence, Expressing, Mass Spectrometry, Cell Culture, Cytotoxicity Assay

Journal: ACS Infectious Diseases

Article Title: Insights into the Spectrum of Activity and Mechanism of Action of MGB-BP-3

doi: 10.1021/acsinfecdis.2c00445

Figure Lengend Snippet: Thermal melt curves of gDNA (salmon) and gDNA:MGB-BP-3 Complex. (A) Exemplar melt curve from one experimental repeat, visually representing the different melt curves of gDNA and the gDNA:MGB-BP-3 Complex. Data has been fitted with a Boltzmann distribution. (B) Melting temperatures of gDNA and gDNA:MGB-BP-3 Complex calculated from fitted Boltzmann distributions using OriginPro 2021. All values are an average for n = 4 experimental repeats with an error of ±1 °C.

Article Snippet: Bacterial genomic DNA (ATCC 43300, DSM 13661; ATCC 27853, DSM1117; ATCC 700603, DSM 26371; ATCC 25922, DSM 1103; ATCC 19606, DSM 30007; ATCC 51299, DSM 12956; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH) or salmon genomic DNA (deoxyribonucleic acid sodium salt from salmon testes, D1626, Merck) dissolved in 1 mM phosphate buffer pH 7.4 (containing 0.27 mM potassium chloride, 13.7 mM sodium chloride) to a concentration of 100 μg/mL in SybrSafe (SYBR Safe DNA Gel Stain, ×10,000 in DMSO, S33102 Invitrogen) was used as supplied by the manufacturer in DMSO, and MGB-BP-3 was prepared as 10 mM stock in DMSO.

Techniques:

Journal: ACS Infectious Diseases

Article Title: Insights into the Spectrum of Activity and Mechanism of Action of MGB-BP-3

doi: 10.1021/acsinfecdis.2c00445

Figure Lengend Snippet: Remaining Fluorescence (%) of SybrSafe Probe upon Addition of MGB-BP-3 to gDNA a

Article Snippet: Bacterial genomic DNA (ATCC 43300, DSM 13661; ATCC 27853, DSM1117; ATCC 700603, DSM 26371; ATCC 25922, DSM 1103; ATCC 19606, DSM 30007; ATCC 51299, DSM 12956; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH) or salmon genomic DNA (deoxyribonucleic acid sodium salt from salmon testes, D1626, Merck) dissolved in 1 mM phosphate buffer pH 7.4 (containing 0.27 mM potassium chloride, 13.7 mM sodium chloride) to a concentration of 100 μg/mL in SybrSafe (SYBR Safe DNA Gel Stain, ×10,000 in DMSO, S33102 Invitrogen) was used as supplied by the manufacturer in DMSO, and MGB-BP-3 was prepared as 10 mM stock in DMSO.

Techniques: Fluorescence

Journal: Nature communications

Article Title: Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks.

doi: 10.1038/s41467-021-27280-x

Figure Lengend Snippet: Fig. 4 Hypothesis-free identification of surfaceome signaling interactions in prokaryotic systems. a Schematic of coupling the peptidomimetic antibiotic Thanatin to the singlet oxygen generator (SOG) thiorhodamine. b Volcano plot showing relative abundance changes of LUX-MS quantified proteins from Thanatin-SOG treated Escherichia coli illuminated for 5 min with and without Thanatin competition, tested using a two-sided Student’s t test. Blue dots represent significantly enriched proteins and red dots represent the direct binding targets of Thanatin previously found by photo-crosslinking experiments. The main targets and selected surfaceome interactors are highlighted. c Schematic representation outlining the molecular mechanism of action of Thanatin in E. coli cells with spatial context. Source data are provided as a Source Data file and interactive volcano plots (Supplementary Data 4).

Article Snippet: E. coli cells (Migula) Castellani and Chalmers (ATCC: 25922) were incubated with 3 μM Thanatin-SOG in the presence or absence of 30 μM unconjugated Thanatin derivative for 30min at 37 °C in the dark to minimize background light-induced oxidation.

Techniques: Binding Assay

Journal: mSystems

Article Title: Clostridium difficile Modulates the Gut Microbiota by Inducing the Production of Indole, an Interkingdom Signaling and Antimicrobial Molecule

doi: 10.1128/mSystems.00346-18

Figure Lengend Snippet: C. difficile induces indole production in enterotoxigenic E. coli . (A) E. coli strains H10407 and 25922 were cocultured anaerobically for 24 h at 37°C with either C. difficile R20291 or 630 strain. Mann-Whitney U test showed the amount of indole produced was significant between E. coli cultured alone versus E. coli cocultured with C. difficile ( P < 0.0001). The amount of indole induced was not significant between the different C. difficile strains ( P = 0.2756). (B) E. coli strains were cultured aerobically for 5 h in brain heart infusion (BHI) medium containing 50% C. difficile R20291 culture supernatant collected at different growth periods, namely, 6 h (mid-log phase), 12 h (early stationary phase), and 24 h (late stationary phase), and indole levels were tested. One-way ANOVA indicated significant differences in amounts of indole induced by the supernatants collected from different growth stages of C. difficile ( P < 0.0001). (C) E. coli strains were cultured either aerobically or anaerobically for 5 h at 37°C in BHI medium containing different amounts of the C. difficile R20291 supernatant and indole levels were tested. One-way ANOVA indicated significant differences in the amounts of indole induced by the different supernatant amounts ( P < 0.0001). (D) E. coli strains were cultured aerobically for 5 h at 37°C in BHI medium containing either boiled or unboiled supernatants from C. difficile strains R20291 or 630. Mann-Whitney U test showed no significant difference ( P = 0.8515) in the amounts of indole induced between boiled and unboiled supernatants. Indole concentration was determined in triplicates using the hydroxylamine indole assay . The error bars represent the standard deviations from three replicate experiments.

Article Snippet: All of the bacteria stocks used in the study, including E. coli H10407 (ATCC 35401) and 25922 (ATCC 25922) were either purchased from the American Type Culture Collection (Manassas, VA) or frozen stocks of clinical isolates stored in our laboratory.

Techniques: MANN-WHITNEY, Produced, Cell Culture, Concentration Assay

Journal: mSystems

Article Title: Clostridium difficile Modulates the Gut Microbiota by Inducing the Production of Indole, an Interkingdom Signaling and Antimicrobial Molecule

doi: 10.1128/mSystems.00346-18

Figure Lengend Snippet: C. difficile induces tnaA overexpression in enterotoxigenic E. coli . (A) E. coli strains H10407 and 25922 were incubated anaerobically for 6 h at 37°C in fresh BHI medium containing 25% 0.2-µm-filtered cell-free C. difficile R20291 supernatant and 5 mM l -tryptophan. Total RNA was isolated using an RNeasy kit (Qiagen), and this was followed by cDNA synthesis by reverse transcription using a ProtoScript AMV First Strand cDNA synthesis kit (New England BioLabs) with 1 µg of the isolated total RNA. Quantitative PCR was performed using primers specific for tnaA and rpoB genes (control). Known quantities of tnaA DNA were used as standards. Mann-Whitney U test showed a significant difference ( P > 0.001) in the tnaA transcript levels detected in both E. coli strains cultured in the presence and absence of the C. difficile but no significant difference ( P = 0.401) between the two E. coli strains. Samples of the RNA preparation processed without the reverse transcription step uniformly yielded no detectable SYBR green signal. Error bars represent the standard deviations from three independent experiments. (B) Effect of the C. difficile Agr1 quorum signaling system on indole production in E. coli . (I) E. coli H10407 cells were cocultured with and without C. difficile wild-type R20291, agr1 mutant ( agr1 Mut), and the complemented agr1 mutant (Comp agr1 Mut) for 24 h anaerobically. (II) E. coli H10407 cells were cocultured with and without purified Agr1 quorum signaling autoinducing peptide (TI signal) for 6 h aerobically at 37°C. The culture supernatants were tested for indole using the hydroxylamine indole assay . (C) Effect of indole on growth of anaerobes. The anaerobes were cultured anaerobically for 24 h at 37°C in the presence of different indole amounts (0 to 6 mM). Concentration of indole that completely inhibited bacterial growth was recorded. Data shown represent three independent replicates.

Article Snippet: All of the bacteria stocks used in the study, including E. coli H10407 (ATCC 35401) and 25922 (ATCC 25922) were either purchased from the American Type Culture Collection (Manassas, VA) or frozen stocks of clinical isolates stored in our laboratory.

Techniques: Over Expression, Incubation, Isolation, cDNA Synthesis, Reverse Transcription, Real-time Polymerase Chain Reaction, Control, MANN-WHITNEY, Cell Culture, SYBR Green Assay, Mutagenesis, Purification, Concentration Assay