16s rrna gene sequencing Search Results


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  • 93
    ATCC 16s rrna gene sequencing
    16s Rrna Gene Sequencing, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 94 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Macrogen 16s rrna gene sequence
    Phylogenetic tree constructed from the <t>16S</t> <t>rRNA</t> gene sequence of B. thuringiensis ) and related organisms using NCBI
    16s Rrna Gene Sequence, supplied by Macrogen, used in various techniques. Bioz Stars score: 90/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MIDI Inc 16s rrna gene sequencing
    Phylogenetic tree constructed from the <t>16S</t> <t>rRNA</t> gene sequence of B. thuringiensis ) and related organisms using NCBI
    16s Rrna Gene Sequencing, supplied by MIDI Inc, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Macrogen 16s rrna gene
    Phylogenetic tree of the two Egyptian bacterial isolates and the other three P. larvae bacterial strains based on the DNA nucleotide sequences of the <t>16S</t> <t>rRNA</t> gene. The phylogeny was constructed by the Meg4 program (neighbour-joining tree).
    16s Rrna Gene, supplied by Macrogen, used in various techniques. Bioz Stars score: 92/100, based on 178 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GATC Biotech 16s rrna gene
    Molecular phylogeny of thirteen selected bacteria and the most related type strains species using partial <t>16S</t> <t>rRNA</t> sequences. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. Tree topology was constructed using MEGA 4.0. Bootstrap values ( n = 1000 replicates) were indicated at the nodes. Escherichia coli KCTC2441 sequence was added as an out group for this tree.
    16s Rrna Gene, supplied by GATC Biotech, used in various techniques. Bioz Stars score: 92/100, based on 85 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Ylichron 16s rrna gene sequencing
    Phylogenetic tree based on <t>16S</t> <t>rRNA</t> gene sequences of K. oxytoca representatives. K. oxytoca DSM 29614 is reported as koxy
    16s Rrna Gene Sequencing, supplied by Ylichron, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc 16s rrna genes
    Percentage contribution of <t>16S</t> <t>rRNA</t> gene sequences (grouped by class) during acetate enrichment under mesophilic (M) or thermophilic (T) temperature conditions, as determined using Illumina MiSeq sequencing. Chemostats designated M H /T H and M L /T L received medium containing 7.5 and 0.4 g acetate l −1 respectively. The corresponding hydraulic retention time ( HRT ) at the point of sampling is given on the x ‐axis. Yellow, green, blue and red bars represent classes within the phyla Bacteriodetes, Firmicutes, Proteobacteria and Thermotogae respectively. Purple indicates methanogenic archaea. Classes representing
    16s Rrna Genes, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 1543 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Roche 16s rrna genes
    Predominant taxa detected in DNA of control OSPW samples, and in heavy DNA fractions extracted after incubation with 13 C benzene or 13 C naphthalene. Data are relative abundances of taxa within sequenced <t>16S</t> <t>rRNA</t> gene amplicons (only OTUs > 1% of the total reads are shown). The lowest taxonomic level confidently assigned is based on 16S rRNA identity thresholds defined by Yarza et al. ( 2014 ). Phylum, class, order, and either family or genus is indicated. Benzene: heavy-DNA fraction of benzene-amended OSPW incubated for 9 days; Naphthalene: heavy-DNA fraction of naphthalene- amended OSPW incubated for 7 days; OSPW-heavy: heavy fraction of OSPW incubated for the same amount of time as the amended samples; and OSPW-control: complete, unfractionated DNA from OSPW. The bubbles show 6 abundance classes (1–1.75%; 1.76–4.5%; 4.6–9%; 9.1–18.5%; 18.6–37.5%; > 37.6%).
    16s Rrna Genes, supplied by Roche, used in various techniques. Bioz Stars score: 94/100, based on 819 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher 16s rrna gene sequences
    Phylogenetic tree, showing selected archaeal <t>16S</t> <t>rRNA</t> genes from US American, European and South American spacecraft-associated clean rooms. The tree was calculated on the basis of the maximum likelihood methodology, implemented in the ARB software package
    16s Rrna Gene Sequences, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 257 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    SolGent 16s rrna gene sequencing
    Phylogenetic tree, showing selected archaeal <t>16S</t> <t>rRNA</t> genes from US American, European and South American spacecraft-associated clean rooms. The tree was calculated on the basis of the maximum likelihood methodology, implemented in the ARB software package
    16s Rrna Gene Sequencing, supplied by SolGent, used in various techniques. Bioz Stars score: 92/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    LGC Genomics GmbH 16s rrna gene sequencing
    Agar-well Diffusion Test showing the antimicrobial activity of cell-free supernatants collected from cultures of 40 LAB isolated from badgers against M. smegmatis. These 40 isolates were identified by <t>16S</t> <t>rRNA</t> sequencing and named as: (1) Pediococcus acidilactici A5; (2) P. lolii A6; (3) Enterococcus faecalis A7; (4) Weissella cibaria A23; (5) W. paramesenteroides A37; (6) P. pentosaceus B4; (7) P. acidilactici B41; (8) P. lolii B53; (9) E. faecalis C34; (10) Lactobacillus reuterii D4; (11) P. acidilactici E12; (12) P. lolii E23; (13) P. acidilactici E24; (14) P. acidilactici E48; (15) P. lolii F7; (16) P. acidilactici F20; (17) P. acidilactici F24; (18) P. acidilactici F44; (19) E. faecalis F48; (20) P. lolii G23; (21) P. pentosaceus G24; (22) P. acidilactici G41; (23) E. faecalis G42; (24) P. lolii G54; (25) P. acidilactici H33; (26) E. faecalis H34; (27) P. acidilactici I32; (28) E. faecium I47; (29) L. plantarum J2; (30) P. acidilactici J26; (31) P. acidilactici L4; (32) P. acidilactici M16; (33) P. acidilactici M17; (34) W. paramesenteroides N43; (35) E. faecium O44; (36) L. plantarum P5; (37) P. acidilactici Q16; (38) L. plantarum R20; (39) L. plantarum S48; (40) L. plantarum T17. All supernatants showed very acidic pH ranging between 3.6–-4.0 for lactobacilli and pediococci, and 4.2–-4.5 for weissella and enterococci. MRS broth (MRS) and supernatants from cultures of L. lactis NZ9700 (700) and L. lactis NZ9800 (800) were used as controls. Both L. lactis strains reduce pH in MRS but no lower than pH 4.5
    16s Rrna Gene Sequencing, supplied by LGC Genomics GmbH, used in various techniques. Bioz Stars score: 92/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BEI Resources 16s rrna gene sequencing
    Agar-well Diffusion Test showing the antimicrobial activity of cell-free supernatants collected from cultures of 40 LAB isolated from badgers against M. smegmatis. These 40 isolates were identified by <t>16S</t> <t>rRNA</t> sequencing and named as: (1) Pediococcus acidilactici A5; (2) P. lolii A6; (3) Enterococcus faecalis A7; (4) Weissella cibaria A23; (5) W. paramesenteroides A37; (6) P. pentosaceus B4; (7) P. acidilactici B41; (8) P. lolii B53; (9) E. faecalis C34; (10) Lactobacillus reuterii D4; (11) P. acidilactici E12; (12) P. lolii E23; (13) P. acidilactici E24; (14) P. acidilactici E48; (15) P. lolii F7; (16) P. acidilactici F20; (17) P. acidilactici F24; (18) P. acidilactici F44; (19) E. faecalis F48; (20) P. lolii G23; (21) P. pentosaceus G24; (22) P. acidilactici G41; (23) E. faecalis G42; (24) P. lolii G54; (25) P. acidilactici H33; (26) E. faecalis H34; (27) P. acidilactici I32; (28) E. faecium I47; (29) L. plantarum J2; (30) P. acidilactici J26; (31) P. acidilactici L4; (32) P. acidilactici M16; (33) P. acidilactici M17; (34) W. paramesenteroides N43; (35) E. faecium O44; (36) L. plantarum P5; (37) P. acidilactici Q16; (38) L. plantarum R20; (39) L. plantarum S48; (40) L. plantarum T17. All supernatants showed very acidic pH ranging between 3.6–-4.0 for lactobacilli and pediococci, and 4.2–-4.5 for weissella and enterococci. MRS broth (MRS) and supernatants from cultures of L. lactis NZ9700 (700) and L. lactis NZ9800 (800) were used as controls. Both L. lactis strains reduce pH in MRS but no lower than pH 4.5
    16s Rrna Gene Sequencing, supplied by BEI Resources, used in various techniques. Bioz Stars score: 90/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc 16s rrna gene sequencing
    Pathway of magmatogene CO 2 , mixing with deep thermal water, paleo-sediment and ground water. Location of sampling sites and relative abundances of phyla determined by Illumina MiSeq sequencing of the <t>16S</t> <t>rRNA</t> gene in different CO 2 affected waters from the Cheb Basin, NW Bohemia. Only phyla with an abundance of at least 2% at a given site are shown. Map provided by © OpenStreetMap-Mitwirkende.
    16s Rrna Gene Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 966 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eurofins rrna gene sequencing
    Pathway of magmatogene CO 2 , mixing with deep thermal water, paleo-sediment and ground water. Location of sampling sites and relative abundances of phyla determined by Illumina MiSeq sequencing of the <t>16S</t> <t>rRNA</t> gene in different CO 2 affected waters from the Cheb Basin, NW Bohemia. Only phyla with an abundance of at least 2% at a given site are shown. Map provided by © OpenStreetMap-Mitwirkende.
    Rrna Gene Sequencing, supplied by Eurofins, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    First BASE Laboratories rrna gene sequencing
    Pathway of magmatogene CO 2 , mixing with deep thermal water, paleo-sediment and ground water. Location of sampling sites and relative abundances of phyla determined by Illumina MiSeq sequencing of the <t>16S</t> <t>rRNA</t> gene in different CO 2 affected waters from the Cheb Basin, NW Bohemia. Only phyla with an abundance of at least 2% at a given site are shown. Map provided by © OpenStreetMap-Mitwirkende.
    Rrna Gene Sequencing, supplied by First BASE Laboratories, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Genewiz complete 16s rrna gene sequences
    Percent representation of bacterial phylum- and subphylum-level groups in <t>16S</t> <t>rRNA</t> gene clone libraries from water column and sediment samples in Smeerenburg Fjord, Svalbard. From left to right, surface water, deep water, surface sediment, and deep sediment
    Complete 16s Rrna Gene Sequences, supplied by Genewiz, used in various techniques. Bioz Stars score: 88/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc 16s rrna gene amplicon sequencing
    Maximum-likelihood tree of <t>16S</t> <t>rRNA</t> gene sequences derived from the metagenome bins analyzed in this study and closely related partial genomes showing their phylogenetic affiliation with the “ Chlorobi lineage 5” (OPB56 clade, “ Ca. Kapabacteria”). Percentage numbers on nodes refer to 100 bootstrap pseudo-replicates conducted. Only values > 50% are shown. Scale bar represents 0.1 changes per nucleotide position.
    16s Rrna Gene Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 396 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rrna gene
    Maximum-likelihood tree of <t>16S</t> <t>rRNA</t> gene sequences derived from the metagenome bins analyzed in this study and closely related partial genomes showing their phylogenetic affiliation with the “ Chlorobi lineage 5” (OPB56 clade, “ Ca. Kapabacteria”). Percentage numbers on nodes refer to 100 bootstrap pseudo-replicates conducted. Only values > 50% are shown. Scale bar represents 0.1 changes per nucleotide position.
    Rrna Gene, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 327 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Phylogenetic tree constructed from the 16S rRNA gene sequence of B. thuringiensis ) and related organisms using NCBI

    Journal: Saudi Journal of Biological Sciences

    Article Title: Biosorption of heavy metals by Bacillus thuringiensis strain OSM29 originating from industrial effluent contaminated north Indian soil

    doi: 10.1016/j.sjbs.2012.11.006

    Figure Lengend Snippet: Phylogenetic tree constructed from the 16S rRNA gene sequence of B. thuringiensis ) and related organisms using NCBI

    Article Snippet: The partial sequencing of 16S rRNA gene sequence of the strain OSM29 was carried out commercially by DNA Sequencing Service, Macrogen Inc., Seoul, South Korea using universal primers, 518F (5′-CCAGCAGCCGCGGTAATACG-3′) and 800R (5’-TACCAGGGTATCTAATCC-3′).

    Techniques: Construct, Sequencing

    Phylogenetic tree of the two Egyptian bacterial isolates and the other three P. larvae bacterial strains based on the DNA nucleotide sequences of the 16S rRNA gene. The phylogeny was constructed by the Meg4 program (neighbour-joining tree).

    Journal: Biotechnology, Biotechnological Equipment

    Article Title: New Paenibacillus larvae bacterial isolates from honey bee colonies infected with American foulbrood disease in Egypt

    doi: 10.1080/13102818.2014.906826

    Figure Lengend Snippet: Phylogenetic tree of the two Egyptian bacterial isolates and the other three P. larvae bacterial strains based on the DNA nucleotide sequences of the 16S rRNA gene. The phylogeny was constructed by the Meg4 program (neighbour-joining tree).

    Article Snippet: DNA sequencing of the amplified 16S rRNA gene The DNA sequence was performed using automated DNA sequencing and terminator dye (Macrogen Company, Korea).

    Techniques: Construct

    Visualization of PCR amplification products (A) and DNA nucleotide sequence (B) of the 16S rRNA gene of the two selected bacterial isolates (SH11 and SH33). Lane M: 1 KBP DNA marker; Lane 1: isolate SH11; Lane 2: isolate SH33.

    Journal: Biotechnology, Biotechnological Equipment

    Article Title: New Paenibacillus larvae bacterial isolates from honey bee colonies infected with American foulbrood disease in Egypt

    doi: 10.1080/13102818.2014.906826

    Figure Lengend Snippet: Visualization of PCR amplification products (A) and DNA nucleotide sequence (B) of the 16S rRNA gene of the two selected bacterial isolates (SH11 and SH33). Lane M: 1 KBP DNA marker; Lane 1: isolate SH11; Lane 2: isolate SH33.

    Article Snippet: DNA sequencing of the amplified 16S rRNA gene The DNA sequence was performed using automated DNA sequencing and terminator dye (Macrogen Company, Korea).

    Techniques: Polymerase Chain Reaction, Amplification, Sequencing, Marker

    Phylogenetic tree of the two bacterial isolates P. larvae (SH33 and SH11) in comparison with 20 bacterial strains Paenibacillus sp. present in the gene bank. The phylogenetic tree was constructed based on the DNA nucleotide sequence of the 16S rRNA genes, using the Meg4 program (neighbour-joining tree).

    Journal: Biotechnology, Biotechnological Equipment

    Article Title: New Paenibacillus larvae bacterial isolates from honey bee colonies infected with American foulbrood disease in Egypt

    doi: 10.1080/13102818.2014.906826

    Figure Lengend Snippet: Phylogenetic tree of the two bacterial isolates P. larvae (SH33 and SH11) in comparison with 20 bacterial strains Paenibacillus sp. present in the gene bank. The phylogenetic tree was constructed based on the DNA nucleotide sequence of the 16S rRNA genes, using the Meg4 program (neighbour-joining tree).

    Article Snippet: DNA sequencing of the amplified 16S rRNA gene The DNA sequence was performed using automated DNA sequencing and terminator dye (Macrogen Company, Korea).

    Techniques: Construct, Sequencing

    Molecular phylogeny of thirteen selected bacteria and the most related type strains species using partial 16S rRNA sequences. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. Tree topology was constructed using MEGA 4.0. Bootstrap values ( n = 1000 replicates) were indicated at the nodes. Escherichia coli KCTC2441 sequence was added as an out group for this tree.

    Journal: BioMed Research International

    Article Title: Screening for Genes Coding for Putative Antitumor Compounds, Antimicrobial and Enzymatic Activities from Haloalkalitolerant and Haloalkaliphilic Bacteria Strains of Algerian Sahara Soils

    doi: 10.1155/2014/317524

    Figure Lengend Snippet: Molecular phylogeny of thirteen selected bacteria and the most related type strains species using partial 16S rRNA sequences. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. Tree topology was constructed using MEGA 4.0. Bootstrap values ( n = 1000 replicates) were indicated at the nodes. Escherichia coli KCTC2441 sequence was added as an out group for this tree.

    Article Snippet: The nucleotide sequences for the 16S rRNA gene of the different strains were carried out by GATC Biotech (UK).

    Techniques: Construct, Sequencing

    Phylogenetic tree based on 16S rRNA gene sequences of K. oxytoca representatives. K. oxytoca DSM 29614 is reported as koxy

    Journal: BMC Microbiology

    Article Title: Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

    doi: 10.1186/s12866-018-1330-5

    Figure Lengend Snippet: Phylogenetic tree based on 16S rRNA gene sequences of K. oxytoca representatives. K. oxytoca DSM 29614 is reported as koxy

    Article Snippet: The genomic DNA was extracted using the CTAB method [ ] and the authenticity of the genomic DNA was confirmed by 16S rRNA gene sequencing (Ylichron Srl, Italy).

    Techniques:

    Percentage contribution of 16S rRNA gene sequences (grouped by class) during acetate enrichment under mesophilic (M) or thermophilic (T) temperature conditions, as determined using Illumina MiSeq sequencing. Chemostats designated M H /T H and M L /T L received medium containing 7.5 and 0.4 g acetate l −1 respectively. The corresponding hydraulic retention time ( HRT ) at the point of sampling is given on the x ‐axis. Yellow, green, blue and red bars represent classes within the phyla Bacteriodetes, Firmicutes, Proteobacteria and Thermotogae respectively. Purple indicates methanogenic archaea. Classes representing

    Journal: Microbial Biotechnology

    Article Title: Detection of novel syntrophic acetate‐oxidizing bacteria from biogas processes by continuous acetate enrichment approaches

    doi: 10.1111/1751-7915.13035

    Figure Lengend Snippet: Percentage contribution of 16S rRNA gene sequences (grouped by class) during acetate enrichment under mesophilic (M) or thermophilic (T) temperature conditions, as determined using Illumina MiSeq sequencing. Chemostats designated M H /T H and M L /T L received medium containing 7.5 and 0.4 g acetate l −1 respectively. The corresponding hydraulic retention time ( HRT ) at the point of sampling is given on the x ‐axis. Yellow, green, blue and red bars represent classes within the phyla Bacteriodetes, Firmicutes, Proteobacteria and Thermotogae respectively. Purple indicates methanogenic archaea. Classes representing

    Article Snippet: A combination of molecular methods, including Illumina sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T‐RFLP) analysis, was used to identify microbial structure patterns over time and to quantify abundant species.

    Techniques: Sequencing, Sampling

    Different BS11 populations in rumen fluid are associated with different size fractions. Maximum likelihood tree of the reconstructed near full-length BS11 16S rRNA gene OTUs (circles, 97% similarity). Branches are named by corresponding Silva accession number, with Prevotella (EU259391) as the outgroup. Network analyses (right) highlight the distribution of the reconstructed 16S rRNA sequences in the different size fractions (diamonds). Circle size represents the 16S rRNA gene average relative abundance across the detected fractions (detailed in Supplementary Table S2 ). The gray box indicates sequences corresponding to Candidatus Alcium, whereas the white box indicates sequences corresponding to Candidatus Hemicellulyticus. The blue and red stars indicate the EMIRGE 16S sequence that match identically over the V4 region to the enriched BS11 OTUs in Figure 2b (blue and red stars, respectively). In addition, the red starred sequence was also recovered from the Candidatus Alcium genome scaffolds ( Supplementary Text ; Supplementary Figure S11 ).

    Journal: The ISME Journal

    Article Title: New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11

    doi: 10.1038/ismej.2016.150

    Figure Lengend Snippet: Different BS11 populations in rumen fluid are associated with different size fractions. Maximum likelihood tree of the reconstructed near full-length BS11 16S rRNA gene OTUs (circles, 97% similarity). Branches are named by corresponding Silva accession number, with Prevotella (EU259391) as the outgroup. Network analyses (right) highlight the distribution of the reconstructed 16S rRNA sequences in the different size fractions (diamonds). Circle size represents the 16S rRNA gene average relative abundance across the detected fractions (detailed in Supplementary Table S2 ). The gray box indicates sequences corresponding to Candidatus Alcium, whereas the white box indicates sequences corresponding to Candidatus Hemicellulyticus. The blue and red stars indicate the EMIRGE 16S sequence that match identically over the V4 region to the enriched BS11 OTUs in Figure 2b (blue and red stars, respectively). In addition, the red starred sequence was also recovered from the Candidatus Alcium genome scaffolds ( Supplementary Text ; Supplementary Figure S11 ).

    Article Snippet: 16S rRNA gene sequences were reconstructed from the Illumina trimmed unassembled reads using EMIRGE ( ).

    Techniques: Sequencing

    BS11 is a novel family in the Bacteroidales. ( a ) Concatenated ribosomal protein tree of the four BS11 genomes and one BS11 scaffold in comparison to the other 45 known genomic representatives from the order Bacteroidales with the six other families besides BS11 noted (gray box). An additional 18 reference genome sequences from other Bacteroidetes, Chlorobi and Fibrobacteres (outgroup) are also included. The number of genomes in each Bacteroidales family is denoted in parentheses next to the name. The near-complete BS11 sequences are shown in light blue with Candidatus Alcium highlighted with a red star to represent the recovery of a full-length 16S rRNA sequence in these genomic bins. Numbers on the node represent bootstrap support, using 100 bootstraps. The full maximum likelihood tree is provided in Supplementary Figure S8 . ( b ) Glycoside hydrolase (GH) genes in genomes belonging to the order Bacteroidales are reported as the average number of GH genes/per genome for each family. The x -axis denotes the number of GH genes per genome, with specific Pfams clustered into functional category (denoted by color gradient). Gene names in bold were detected in the BS11 genomes. The cluster labeled as ‘other' includes α-amylase, pectinesterase, concanavalin and polyphenol oxidoreductase laccase. The complete dataset from all genomes and accompanying PFAM numbers used to construct Figure 4b is included ( Supplementary Dataset S4 ).

    Journal: The ISME Journal

    Article Title: New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11

    doi: 10.1038/ismej.2016.150

    Figure Lengend Snippet: BS11 is a novel family in the Bacteroidales. ( a ) Concatenated ribosomal protein tree of the four BS11 genomes and one BS11 scaffold in comparison to the other 45 known genomic representatives from the order Bacteroidales with the six other families besides BS11 noted (gray box). An additional 18 reference genome sequences from other Bacteroidetes, Chlorobi and Fibrobacteres (outgroup) are also included. The number of genomes in each Bacteroidales family is denoted in parentheses next to the name. The near-complete BS11 sequences are shown in light blue with Candidatus Alcium highlighted with a red star to represent the recovery of a full-length 16S rRNA sequence in these genomic bins. Numbers on the node represent bootstrap support, using 100 bootstraps. The full maximum likelihood tree is provided in Supplementary Figure S8 . ( b ) Glycoside hydrolase (GH) genes in genomes belonging to the order Bacteroidales are reported as the average number of GH genes/per genome for each family. The x -axis denotes the number of GH genes per genome, with specific Pfams clustered into functional category (denoted by color gradient). Gene names in bold were detected in the BS11 genomes. The cluster labeled as ‘other' includes α-amylase, pectinesterase, concanavalin and polyphenol oxidoreductase laccase. The complete dataset from all genomes and accompanying PFAM numbers used to construct Figure 4b is included ( Supplementary Dataset S4 ).

    Article Snippet: 16S rRNA gene sequences were reconstructed from the Illumina trimmed unassembled reads using EMIRGE ( ).

    Techniques: Sequencing, Functional Assay, Labeling, Construct

    Predominant taxa detected in DNA of control OSPW samples, and in heavy DNA fractions extracted after incubation with 13 C benzene or 13 C naphthalene. Data are relative abundances of taxa within sequenced 16S rRNA gene amplicons (only OTUs > 1% of the total reads are shown). The lowest taxonomic level confidently assigned is based on 16S rRNA identity thresholds defined by Yarza et al. ( 2014 ). Phylum, class, order, and either family or genus is indicated. Benzene: heavy-DNA fraction of benzene-amended OSPW incubated for 9 days; Naphthalene: heavy-DNA fraction of naphthalene- amended OSPW incubated for 7 days; OSPW-heavy: heavy fraction of OSPW incubated for the same amount of time as the amended samples; and OSPW-control: complete, unfractionated DNA from OSPW. The bubbles show 6 abundance classes (1–1.75%; 1.76–4.5%; 4.6–9%; 9.1–18.5%; 18.6–37.5%; > 37.6%).

    Journal: Frontiers in Microbiology

    Article Title: Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond

    doi: 10.3389/fmicb.2017.01845

    Figure Lengend Snippet: Predominant taxa detected in DNA of control OSPW samples, and in heavy DNA fractions extracted after incubation with 13 C benzene or 13 C naphthalene. Data are relative abundances of taxa within sequenced 16S rRNA gene amplicons (only OTUs > 1% of the total reads are shown). The lowest taxonomic level confidently assigned is based on 16S rRNA identity thresholds defined by Yarza et al. ( 2014 ). Phylum, class, order, and either family or genus is indicated. Benzene: heavy-DNA fraction of benzene-amended OSPW incubated for 9 days; Naphthalene: heavy-DNA fraction of naphthalene- amended OSPW incubated for 7 days; OSPW-heavy: heavy fraction of OSPW incubated for the same amount of time as the amended samples; and OSPW-control: complete, unfractionated DNA from OSPW. The bubbles show 6 abundance classes (1–1.75%; 1.76–4.5%; 4.6–9%; 9.1–18.5%; 18.6–37.5%; > 37.6%).

    Article Snippet: Amplification of 16S rRNA genes, sequencing on a Roche 454 GS FLX, and analysis using QIIME were all carried out as described previously (Sharp et al., ).

    Techniques: Incubation

    Phylogenetic tree, showing selected archaeal 16S rRNA genes from US American, European and South American spacecraft-associated clean rooms. The tree was calculated on the basis of the maximum likelihood methodology, implemented in the ARB software package

    Journal: The ISME journal

    Article Title: Archaea in artificial environments: Their presence in global spacecraft clean rooms and impact on planetary protection

    doi: 10.1038/ismej.2010.124

    Figure Lengend Snippet: Phylogenetic tree, showing selected archaeal 16S rRNA genes from US American, European and South American spacecraft-associated clean rooms. The tree was calculated on the basis of the maximum likelihood methodology, implemented in the ARB software package

    Article Snippet: Sequencing of the 16S rRNA gene sequences was carried out by the companies Geneart or Entelechon (Regensburg, Germany).

    Techniques: Software

    Comparison of H. pylori. detection methods. (A) Frequency of Helicobacter pylori detection in the same patients by three different detection methods: microscopic identification with Giemsa stain (according to Sydney Scale), PCR detection of urease gene in bioptates, 16S rRNA sequencing in bioptates, grey- H. pylori not detected in the sample (negative), red- H. pylori detected in the sample (positive); (B) assessment by Sydney System parameters (0–3). Numbers of individual samples are in accordance to relevant numbers of samples in Biobank of RSH and to raw data uploaded with this manuscript as Supplemental Information .

    Journal: PeerJ

    Article Title: Application of 16S rRNA gene sequencing in Helicobacter pylori detection

    doi: 10.7717/peerj.9099

    Figure Lengend Snippet: Comparison of H. pylori. detection methods. (A) Frequency of Helicobacter pylori detection in the same patients by three different detection methods: microscopic identification with Giemsa stain (according to Sydney Scale), PCR detection of urease gene in bioptates, 16S rRNA sequencing in bioptates, grey- H. pylori not detected in the sample (negative), red- H. pylori detected in the sample (positive); (B) assessment by Sydney System parameters (0–3). Numbers of individual samples are in accordance to relevant numbers of samples in Biobank of RSH and to raw data uploaded with this manuscript as Supplemental Information .

    Article Snippet: Kit used in this experiment contains primers covering V2, V4, V8, V3-6, V7-9 hypervariable regions of 16S rRNA gene (sequences of the primers have not been revealed by the manufacturer ThermoFisher Scientific).

    Techniques: Giemsa Stain, Polymerase Chain Reaction, Sequencing

    Agar-well Diffusion Test showing the antimicrobial activity of cell-free supernatants collected from cultures of 40 LAB isolated from badgers against M. smegmatis. These 40 isolates were identified by 16S rRNA sequencing and named as: (1) Pediococcus acidilactici A5; (2) P. lolii A6; (3) Enterococcus faecalis A7; (4) Weissella cibaria A23; (5) W. paramesenteroides A37; (6) P. pentosaceus B4; (7) P. acidilactici B41; (8) P. lolii B53; (9) E. faecalis C34; (10) Lactobacillus reuterii D4; (11) P. acidilactici E12; (12) P. lolii E23; (13) P. acidilactici E24; (14) P. acidilactici E48; (15) P. lolii F7; (16) P. acidilactici F20; (17) P. acidilactici F24; (18) P. acidilactici F44; (19) E. faecalis F48; (20) P. lolii G23; (21) P. pentosaceus G24; (22) P. acidilactici G41; (23) E. faecalis G42; (24) P. lolii G54; (25) P. acidilactici H33; (26) E. faecalis H34; (27) P. acidilactici I32; (28) E. faecium I47; (29) L. plantarum J2; (30) P. acidilactici J26; (31) P. acidilactici L4; (32) P. acidilactici M16; (33) P. acidilactici M17; (34) W. paramesenteroides N43; (35) E. faecium O44; (36) L. plantarum P5; (37) P. acidilactici Q16; (38) L. plantarum R20; (39) L. plantarum S48; (40) L. plantarum T17. All supernatants showed very acidic pH ranging between 3.6–-4.0 for lactobacilli and pediococci, and 4.2–-4.5 for weissella and enterococci. MRS broth (MRS) and supernatants from cultures of L. lactis NZ9700 (700) and L. lactis NZ9800 (800) were used as controls. Both L. lactis strains reduce pH in MRS but no lower than pH 4.5

    Journal: BMC Microbiology

    Article Title: Lactic acid Bacteria isolated from European badgers (Meles meles) reduce the viability and survival of Bacillus Calmette-Guerin (BCG) vaccine and influence the immune response to BCG in a human macrophage model

    doi: 10.1186/s12866-018-1210-z

    Figure Lengend Snippet: Agar-well Diffusion Test showing the antimicrobial activity of cell-free supernatants collected from cultures of 40 LAB isolated from badgers against M. smegmatis. These 40 isolates were identified by 16S rRNA sequencing and named as: (1) Pediococcus acidilactici A5; (2) P. lolii A6; (3) Enterococcus faecalis A7; (4) Weissella cibaria A23; (5) W. paramesenteroides A37; (6) P. pentosaceus B4; (7) P. acidilactici B41; (8) P. lolii B53; (9) E. faecalis C34; (10) Lactobacillus reuterii D4; (11) P. acidilactici E12; (12) P. lolii E23; (13) P. acidilactici E24; (14) P. acidilactici E48; (15) P. lolii F7; (16) P. acidilactici F20; (17) P. acidilactici F24; (18) P. acidilactici F44; (19) E. faecalis F48; (20) P. lolii G23; (21) P. pentosaceus G24; (22) P. acidilactici G41; (23) E. faecalis G42; (24) P. lolii G54; (25) P. acidilactici H33; (26) E. faecalis H34; (27) P. acidilactici I32; (28) E. faecium I47; (29) L. plantarum J2; (30) P. acidilactici J26; (31) P. acidilactici L4; (32) P. acidilactici M16; (33) P. acidilactici M17; (34) W. paramesenteroides N43; (35) E. faecium O44; (36) L. plantarum P5; (37) P. acidilactici Q16; (38) L. plantarum R20; (39) L. plantarum S48; (40) L. plantarum T17. All supernatants showed very acidic pH ranging between 3.6–-4.0 for lactobacilli and pediococci, and 4.2–-4.5 for weissella and enterococci. MRS broth (MRS) and supernatants from cultures of L. lactis NZ9700 (700) and L. lactis NZ9800 (800) were used as controls. Both L. lactis strains reduce pH in MRS but no lower than pH 4.5

    Article Snippet: Further identification was carried out by 16S rRNA gene sequencing (LGC Genomics) before a final selection of the 12 most representative LAB species comprising different bacterial species isolated from different animals but also different strains representing the most predominant bacterial species found.

    Techniques: Diffusion-based Assay, Activity Assay, Isolation, Sequencing

    Pathway of magmatogene CO 2 , mixing with deep thermal water, paleo-sediment and ground water. Location of sampling sites and relative abundances of phyla determined by Illumina MiSeq sequencing of the 16S rRNA gene in different CO 2 affected waters from the Cheb Basin, NW Bohemia. Only phyla with an abundance of at least 2% at a given site are shown. Map provided by © OpenStreetMap-Mitwirkende.

    Journal: Frontiers in Microbiology

    Article Title: Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic

    doi: 10.3389/fmicb.2017.02446

    Figure Lengend Snippet: Pathway of magmatogene CO 2 , mixing with deep thermal water, paleo-sediment and ground water. Location of sampling sites and relative abundances of phyla determined by Illumina MiSeq sequencing of the 16S rRNA gene in different CO 2 affected waters from the Cheb Basin, NW Bohemia. Only phyla with an abundance of at least 2% at a given site are shown. Map provided by © OpenStreetMap-Mitwirkende.

    Article Snippet: Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing.

    Techniques: Sampling, Sequencing

    Overview of metabologenomic analysis workflow. Steps used for evaluation of metabolome profiles are summarized in the top row (yellow shading). This process starts with measurement of the amount of fecal metabolites to obtain profiles for the 100–200 metabolites. These metabolome profiles then are compared using Principal Component Analysis (PCA), discriminant analysis, and pathway analysis. Steps used for evaluation of microbiome profiles are summarized in the bottom row (pink shading). This process starts with the sequencing of the community’s 16S rRNA-encoding genes to clarify the relative abundance of operational taxonomic units (OTUs). Microbial memberships and structures are compared using UniFrac principal coordinate analysis (PCoA) and discriminant analysis. Additionally, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) is used to predict metagenomic profiles. Steps for metabologenomic analysis are summarized in the central part of the figure (middle row; orange shading). The PCoA and/or PCA plots are used for Procrustes analyses. The relative abundances of microbial taxonomy and/or metagenome profiles and amounts of metabolites then are used for correlation analysis and network analysis.

    Journal: International Journal of Molecular Sciences

    Article Title: A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet

    doi: 10.3390/ijms19124079

    Figure Lengend Snippet: Overview of metabologenomic analysis workflow. Steps used for evaluation of metabolome profiles are summarized in the top row (yellow shading). This process starts with measurement of the amount of fecal metabolites to obtain profiles for the 100–200 metabolites. These metabolome profiles then are compared using Principal Component Analysis (PCA), discriminant analysis, and pathway analysis. Steps used for evaluation of microbiome profiles are summarized in the bottom row (pink shading). This process starts with the sequencing of the community’s 16S rRNA-encoding genes to clarify the relative abundance of operational taxonomic units (OTUs). Microbial memberships and structures are compared using UniFrac principal coordinate analysis (PCoA) and discriminant analysis. Additionally, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) is used to predict metagenomic profiles. Steps for metabologenomic analysis are summarized in the central part of the figure (middle row; orange shading). The PCoA and/or PCA plots are used for Procrustes analyses. The relative abundances of microbial taxonomy and/or metagenome profiles and amounts of metabolites then are used for correlation analysis and network analysis.

    Article Snippet: 16S rRNA Gene Sequencing 16S rRNA genes in the fecal DNA samples were analyzed using a MiSeq sequencer (Illumina).

    Techniques: Sequencing

    16S rRNA gene sequencing data from the Ni-ISA biodegrading, Fe(III)-reducing enrichment experiment. Diagram shows phylogenetic Classes at selected time points. Notation of Shannon H biodiversity index on top of columns as a measure of microbial community diversity.

    Journal: Scientific Reports

    Article Title: The biogeochemical fate of nickel during microbial ISA degradation; implications for nuclear waste disposal

    doi: 10.1038/s41598-018-26963-8

    Figure Lengend Snippet: 16S rRNA gene sequencing data from the Ni-ISA biodegrading, Fe(III)-reducing enrichment experiment. Diagram shows phylogenetic Classes at selected time points. Notation of Shannon H biodiversity index on top of columns as a measure of microbial community diversity.

    Article Snippet: 16S rRNA gene sequencing 16S rRNA gene sequencing was performed with the Illumina MiSeq platform (Illumina, San Diego, CA, USA) using a Roche ‘Fast Start High Fidelity PCR System’ (Roche Diagnostics Ltd, Burgess Hill, UK).

    Techniques: Sequencing

    Percent representation of bacterial phylum- and subphylum-level groups in 16S rRNA gene clone libraries from water column and sediment samples in Smeerenburg Fjord, Svalbard. From left to right, surface water, deep water, surface sediment, and deep sediment

    Journal: Applied and Environmental Microbiology

    Article Title: Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿ †

    doi: 10.1128/AEM.01507-10

    Figure Lengend Snippet: Percent representation of bacterial phylum- and subphylum-level groups in 16S rRNA gene clone libraries from water column and sediment samples in Smeerenburg Fjord, Svalbard. From left to right, surface water, deep water, surface sediment, and deep sediment

    Article Snippet: Nearly complete 16S rRNA gene sequences were obtained from Genewiz, Inc.

    Techniques:

    Neighbor-joining phylogeny of Smeerenburg Fjord Bacteroides phylotypes, based on an ∼1,200-bp alignment of bacterial 16S rRNA sequences. The Svalbard phylotypes are labeled with the habitat indicator (water_surface, water_deep, sediment_surface,

    Journal: Applied and Environmental Microbiology

    Article Title: Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿ †

    doi: 10.1128/AEM.01507-10

    Figure Lengend Snippet: Neighbor-joining phylogeny of Smeerenburg Fjord Bacteroides phylotypes, based on an ∼1,200-bp alignment of bacterial 16S rRNA sequences. The Svalbard phylotypes are labeled with the habitat indicator (water_surface, water_deep, sediment_surface,

    Article Snippet: Nearly complete 16S rRNA gene sequences were obtained from Genewiz, Inc.

    Techniques: Labeling

    Neighbor-joining phylogeny of Smeerenburg Fjord alpha- and deltaproteobacterial phylotypes, based on an ∼1,200-bp alignment of bacterial 16S rRNA sequences. The Svalbard phylotypes are labeled with the habitat indicator (water_surface, water_deep,

    Journal: Applied and Environmental Microbiology

    Article Title: Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿ †

    doi: 10.1128/AEM.01507-10

    Figure Lengend Snippet: Neighbor-joining phylogeny of Smeerenburg Fjord alpha- and deltaproteobacterial phylotypes, based on an ∼1,200-bp alignment of bacterial 16S rRNA sequences. The Svalbard phylotypes are labeled with the habitat indicator (water_surface, water_deep,

    Article Snippet: Nearly complete 16S rRNA gene sequences were obtained from Genewiz, Inc.

    Techniques: Labeling

    Neighbor-joining phylogeny of Smeerenburg Fjord beta- and gammaproteobacterial phylotypes, based on an ∼1,200-bp alignment of bacterial 16S rRNA sequences. The Svalbard phylotypes are labeled with the habitat indicator (water_surface, water_deep,

    Journal: Applied and Environmental Microbiology

    Article Title: Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard ▿ †

    doi: 10.1128/AEM.01507-10

    Figure Lengend Snippet: Neighbor-joining phylogeny of Smeerenburg Fjord beta- and gammaproteobacterial phylotypes, based on an ∼1,200-bp alignment of bacterial 16S rRNA sequences. The Svalbard phylotypes are labeled with the habitat indicator (water_surface, water_deep,

    Article Snippet: Nearly complete 16S rRNA gene sequences were obtained from Genewiz, Inc.

    Techniques: Labeling

    Maximum-likelihood tree of 16S rRNA gene sequences derived from the metagenome bins analyzed in this study and closely related partial genomes showing their phylogenetic affiliation with the “ Chlorobi lineage 5” (OPB56 clade, “ Ca. Kapabacteria”). Percentage numbers on nodes refer to 100 bootstrap pseudo-replicates conducted. Only values > 50% are shown. Scale bar represents 0.1 changes per nucleotide position.

    Journal: Frontiers in Microbiology

    Article Title: “Candidatus Thermonerobacter thiotrophicus,” A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities

    doi: 10.3389/fmicb.2018.03159

    Figure Lengend Snippet: Maximum-likelihood tree of 16S rRNA gene sequences derived from the metagenome bins analyzed in this study and closely related partial genomes showing their phylogenetic affiliation with the “ Chlorobi lineage 5” (OPB56 clade, “ Ca. Kapabacteria”). Percentage numbers on nodes refer to 100 bootstrap pseudo-replicates conducted. Only values > 50% are shown. Scale bar represents 0.1 changes per nucleotide position.

    Article Snippet: Metagenome and 16S rRNA gene amplicon sequencing was conducted on Illumina HiSeq and MiSeq instruments, respectively, as described previously ( , ).

    Techniques: Derivative Assay