16s rrna amplicons Search Results


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  • 90
    Illumina Inc 16s ribosomal rna rrna amplicons
    16s Ribosomal Rna Rrna Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc 16s rrna amplicon
    Relative abundance of bacterial phyla Stacked bar graph of relative abundance of bacterial phyla identified in <t>16S</t> <t>amplicon</t> based analysis (a), read-based analysis of WGS data (b) and contig-based analysis of WGS data (c) in the v2-total, v3-total, v2+v3-total and v2+v3+HiSeq-total datasets. Relative abundance (y-axis) of the dominant bacterial phyla includes Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. The “other phyla” for 16S amplicon analysis contains 19 non-abundant phyla and unclassified bacteria representing
    16s Rrna Amplicon, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 135 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Roche 16s rrna amplicons
    Linear fit analysis to assess the correlation between the <t>16S</t> <t>rRNA</t> and GroEL primers for detection of the same Bifidobacterium species.
    16s Rrna Amplicons, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 81 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    GATC Biotech 16s rrna amplicons
    DGGE profiles of amplified bacterial <t>16S</t> <t>rRNA</t> genes from the on-board mesocosms (days 2, 4 and 6).A. Profiles of days 2, 4 and 6 of all the four mesocosms are shown. The bands in white rectangles were excised and sequenced. BI: no oil (control); BII: 2 L of Arabian Light crude oil; BIII: 5.5 L of Arabian Light crude oil; BIV: 2 L of Arabian Light crude oil and UV treated (killed control).B. MDS plot of the DGGE profiles of the on-board mesocosms. White squares indicate the non-oiled mesocosm (BI), grey squares the less oiled (BII), black squares the most oiled (BIII) and UV treated mesocosm is indicated by an ‘x’.
    16s Rrna Amplicons, supplied by GATC Biotech, used in various techniques. Bioz Stars score: 91/100, based on 73 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Pacific Biosciences 16s rrna amplicons
    Two-step generation of <t>16S</t> <t>amplicons</t> for PacBio sequencing using M13-tagged barcoded primers. The first round of PCR amplifies full-length 16S <t>rRNA</t> fragments using gene-specific primers tailed with universal M13 forward or reverse sequence. In the second step, a unique combination of barcode sequences is added to 16S amplicons from each sample using M13 forward and reverse primers tagged with 16-base PacBio barcodes at their 5′ ends. Barcoded amplicons are subsequently pooled for SMRTbell library construction and multiplexed sequencing.
    16s Rrna Amplicons, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 91/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Macrogen 16s rrna amplicons
    Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length <t>16S</t> <t>rRNA</t> gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.
    16s Rrna Amplicons, supplied by Macrogen, used in various techniques. Bioz Stars score: 91/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    LGC Genomics GmbH 16s rrna amplicons
    Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length <t>16S</t> <t>rRNA</t> gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.
    16s Rrna Amplicons, supplied by LGC Genomics GmbH, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies 16s rrna amplicons
    Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length <t>16S</t> <t>rRNA</t> gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.
    16s Rrna Amplicons, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eurofins 16s rrna amplicons
    Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length <t>16S</t> <t>rRNA</t> gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.
    16s Rrna Amplicons, supplied by Eurofins, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biotechnology Information 16s rrna amplicon
    Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length <t>16S</t> <t>rRNA</t> gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.
    16s Rrna Amplicon, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc v4 16s rrna amplicons
    Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length <t>16S</t> <t>rRNA</t> gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.
    V4 16s Rrna Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/v4 16s rrna amplicons/product/Illumina Inc
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    86
    Thermo Fisher 16s rrna amplicon fragments
    <t>16S</t> <t>rRNA</t> read lengths in MiSeq and Ion Torrent sequence data. (A) Comparison of absolute sequence lengths for assembled paired-end MiSeq reads and unidirectional reads from the Ion Torrent PGM platform derived from a mock-community mixture of 20 bacterial
    16s Rrna Amplicon Fragments, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Roche 16s rrna sequencing 16s rrna amplicon sequencing
    a Sensitivity testing of the Enterobacteriaceae database. Randomly fragmented <t>16S</t> <t>rRNA</t> genes specific to S. enterica were compared to the Enterobacteriaceae database using BLASTn. Fragment sizes ranged from 100 to 500 bp and errors were randomly introduced at rates ranging from 0 to 1 %. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S fragments without a Salmonella best alignment (right axis). b Specificity testing of the Enterobacteriaceae database. 16S rRNA fragments specific to E. coli were randomly fragmented to sizes ranging from 100 to 500 bp and random errors were introduced. Fragments were searched against the Enterobacteriaceae database using BLASTn. c Validation of the Enterobacteriaceae database using BLASTn analysis of raw Illumina MiSeq reads from 105 S. enterica 16S rRNA genes to the EnteroDB. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S rRNA fragments without a Salmonella best alignment (right axis)
    16s Rrna Sequencing 16s Rrna Amplicon Sequencing, supplied by Roche, 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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    90
    Illumina Inc bacterial 16s rrna amplicons
    Principal component analysis of urine, genital swab, and rectal swab microbiota, as determined via <t>16S</t> <t>rRNA</t> amplicon sequencing, colored by sample collection site, from 20 healthy adult dogs ( n = 10 female, 10 male). Plots depict PC1 versus PC2 ( A ), PC1 versus PC3 ( B ), and PC1 versus PC4 ( C ).
    Bacterial 16s Rrna Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Microsynth bacterial 16s rrna amplicons
    Heatmap showing the T-RF found in Bacterial <t>16S</t> <t>rRNA</t> gene T-RFLP fingerprints from different groundwater samples collected from deep aquifers of coal-rich sedimentary basin, coal-rich sediment samples, and the derived enrichment cultures amended with n -hexadecane. The gray scale indicates the relative abundance of each fragment. Only values above 1% are given. *The abundance of this peak equals the maximum abundance for the sample.
    Bacterial 16s Rrna Amplicons, supplied by Microsynth, used in various techniques. Bioz Stars score: 89/100, based on 80 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc 16s rrna amplicon sequencing
    Prevalence of Mycoplasma lineages in Senegalese rodents, by site, and phylogenetic associations between Mycoplasma lineages and rodent species. (A) Comparison of phylogenetic trees based on the <t>16S</t> <t>rRNA</t> V4 sequences of Mycoplasma and on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR) for rodents (the tree was drawn based on data from reference 92 ). Lines link the Mycoplasma lineages detected in the various rodent species (for a minimum site prevalence exceeding 10%). The numbers next to the branches are bootstrap values (shown only if > 70%). (B) Plots of OTU prevalences, with 95% confidence intervals calculated by Sterne’s exact method ( 93 ) according to rodent species and site (see reference 69 for more information about site codes and their geographic locations). The gray bars on the x axis indicate sites from which the rodent species concerned is absent.
    16s Rrna Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 452 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Relative abundance of bacterial phyla Stacked bar graph of relative abundance of bacterial phyla identified in 16S amplicon based analysis (a), read-based analysis of WGS data (b) and contig-based analysis of WGS data (c) in the v2-total, v3-total, v2+v3-total and v2+v3+HiSeq-total datasets. Relative abundance (y-axis) of the dominant bacterial phyla includes Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. The “other phyla” for 16S amplicon analysis contains 19 non-abundant phyla and unclassified bacteria representing

    Journal: Biochemical and biophysical research communications

    Article Title: Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

    doi: 10.1016/j.bbrc.2015.12.083

    Figure Lengend Snippet: Relative abundance of bacterial phyla Stacked bar graph of relative abundance of bacterial phyla identified in 16S amplicon based analysis (a), read-based analysis of WGS data (b) and contig-based analysis of WGS data (c) in the v2-total, v3-total, v2+v3-total and v2+v3+HiSeq-total datasets. Relative abundance (y-axis) of the dominant bacterial phyla includes Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. The “other phyla” for 16S amplicon analysis contains 19 non-abundant phyla and unclassified bacteria representing

    Article Snippet: We compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads.

    Techniques: Amplification

    LEfSe analysis identified the most differentially abundant taxa between CA and PA. The taxonomic cladogram was obtained from LEfSe analysis of 16S rRNA sequences; only taxa meeting an LDA significance threshold of 4.0 are shown. Small circles and shading with different colors in the diagram represent the abundance of those taxa in the respective group. Yellow circles represent nonsignificant differences in abundance between CA and PA for that particular taxonomic group. The brightness of each dot is proportional to its effect size. Taxa enriched in PA are shown with a positive LDA score (green) and taxa enriched in CA have a negative score (red). CA means sparging air; PA means culturing C. pyrenoidosa with sparging air

    Journal: Biotechnology for Biofuels

    Article Title: Comprehensive evaluation of a cost-effective method of culturing Chlorella pyrenoidosa with unsterilized piggery wastewater for biofuel production

    doi: 10.1186/s13068-019-1407-x

    Figure Lengend Snippet: LEfSe analysis identified the most differentially abundant taxa between CA and PA. The taxonomic cladogram was obtained from LEfSe analysis of 16S rRNA sequences; only taxa meeting an LDA significance threshold of 4.0 are shown. Small circles and shading with different colors in the diagram represent the abundance of those taxa in the respective group. Yellow circles represent nonsignificant differences in abundance between CA and PA for that particular taxonomic group. The brightness of each dot is proportional to its effect size. Taxa enriched in PA are shown with a positive LDA score (green) and taxa enriched in CA have a negative score (red). CA means sparging air; PA means culturing C. pyrenoidosa with sparging air

    Article Snippet: The high-throughput sequencing of 16S rRNA amplicons was performed on the Illumina MiSeq platform at Novogene Bioinformatics Company (Beijing, China).

    Techniques: Sparging

    LEfSe analysis identified the most differentially abundant taxa between CC and PC. The taxonomic cladogram was obtained from LEfSe analysis of 16S rRNA sequences; only taxa meeting an LDA significance threshold of 4.0 are shown. Small circles and shading with different colors in the diagram represent the abundance of those taxa in the respective group. Yellow circles represent nonsignificant differences in abundance between CC and PC for that particular taxonomic group. The brightness of each dot is proportional to its effect size. Taxa enriched in PC are shown with a positive LDA score (green), and taxa enriched in CC have a negative score (red). CC means sparging simulated flue gas; PC means culturing C. pyrenoidosa with sparging simulated flue gas

    Journal: Biotechnology for Biofuels

    Article Title: Comprehensive evaluation of a cost-effective method of culturing Chlorella pyrenoidosa with unsterilized piggery wastewater for biofuel production

    doi: 10.1186/s13068-019-1407-x

    Figure Lengend Snippet: LEfSe analysis identified the most differentially abundant taxa between CC and PC. The taxonomic cladogram was obtained from LEfSe analysis of 16S rRNA sequences; only taxa meeting an LDA significance threshold of 4.0 are shown. Small circles and shading with different colors in the diagram represent the abundance of those taxa in the respective group. Yellow circles represent nonsignificant differences in abundance between CC and PC for that particular taxonomic group. The brightness of each dot is proportional to its effect size. Taxa enriched in PC are shown with a positive LDA score (green), and taxa enriched in CC have a negative score (red). CC means sparging simulated flue gas; PC means culturing C. pyrenoidosa with sparging simulated flue gas

    Article Snippet: The high-throughput sequencing of 16S rRNA amplicons was performed on the Illumina MiSeq platform at Novogene Bioinformatics Company (Beijing, China).

    Techniques: Sparging

    The absolute bacterial abundance based on 16S rRNA copies in unsterilized piggery wastewater. CA means sparging air, CC means sparging simulated flue gas, PA means culturing C. pyrenoidosa with sparging air, and PC means culturing C. pyrenoidosa with sparging simulated flue gas. Data are presented as the mean ± standard deviation of the mean. The different letters indicate that there was a significant difference with P

    Journal: Biotechnology for Biofuels

    Article Title: Comprehensive evaluation of a cost-effective method of culturing Chlorella pyrenoidosa with unsterilized piggery wastewater for biofuel production

    doi: 10.1186/s13068-019-1407-x

    Figure Lengend Snippet: The absolute bacterial abundance based on 16S rRNA copies in unsterilized piggery wastewater. CA means sparging air, CC means sparging simulated flue gas, PA means culturing C. pyrenoidosa with sparging air, and PC means culturing C. pyrenoidosa with sparging simulated flue gas. Data are presented as the mean ± standard deviation of the mean. The different letters indicate that there was a significant difference with P

    Article Snippet: The high-throughput sequencing of 16S rRNA amplicons was performed on the Illumina MiSeq platform at Novogene Bioinformatics Company (Beijing, China).

    Techniques: Sparging, Standard Deviation

    Microbial community composition of periodontal pockets as assessed by 16S rRNA gene amplicon sequencing. (A) Abundance of taxonomic classes averaged over all 19 individuals for the four different community profiles analyzed. The error bars show the standard

    Journal: Applied and Environmental Microbiology

    Article Title: High-Resolution Taxonomic Profiling of the Subgingival Microbiome for Biomarker Discovery and Periodontitis Diagnosis

    doi: 10.1128/AEM.03534-14

    Figure Lengend Snippet: Microbial community composition of periodontal pockets as assessed by 16S rRNA gene amplicon sequencing. (A) Abundance of taxonomic classes averaged over all 19 individuals for the four different community profiles analyzed. The error bars show the standard

    Article Snippet: Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences .

    Techniques: Amplification, Sequencing

    16S rRNA gene copy numbers of eubacteria (A, C, E, G, I, and K) and the ratio of genus Bifidobacterium to eubacteria (B, D, F, H, J, and L). Human feces was used to inoculate cultures in the single-batch fermentation system (feces; F37: A and B; F23: C and D; M38: E and F; F35: G and H; M24: I and J; M43: K and L). Samples are labelled according to the prebiotic oligosaccharides [control (no addition), FOS, GOS, IMO, XOS, raffinose, lactulose, and lactosucrose]. Error bars show standard deviation for mean of triplicates. Asterisks indicate values that are significantly different ( p

    Journal: PLoS ONE

    Article Title: A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics

    doi: 10.1371/journal.pone.0160533

    Figure Lengend Snippet: 16S rRNA gene copy numbers of eubacteria (A, C, E, G, I, and K) and the ratio of genus Bifidobacterium to eubacteria (B, D, F, H, J, and L). Human feces was used to inoculate cultures in the single-batch fermentation system (feces; F37: A and B; F23: C and D; M38: E and F; F35: G and H; M24: I and J; M43: K and L). Samples are labelled according to the prebiotic oligosaccharides [control (no addition), FOS, GOS, IMO, XOS, raffinose, lactulose, and lactosucrose]. Error bars show standard deviation for mean of triplicates. Asterisks indicate values that are significantly different ( p

    Article Snippet: 16S rRNA-targeted amplicon reads were taxonomically classified by the GreenGenes taxonomic database (Illumina) using the Ribosomal Database Project (RDP) Classifier as described by Wang et al. [ ].

    Techniques: Standard Deviation

    Phylum-level compositional view of bacteria in three human fecal samples/inocula (–) (F37-1: female, age 37; F37-2: female, age 37; and M54: male, age 54) and corresponding cultures at 6, 9, and 24 h after the initiation of fermentation. A compositional view of bacterial phyla based on the taxonomic assignment of 16S rRNA genes is shown. Bacterial composition of each sample was estimated from the results of the RDP classifier. Eubacterial 16S rRNA gene copy numbers are shown in the right column; units are copies/wet-g-feces (inoculum) or copies/mL-culture (fermentation).

    Journal: PLoS ONE

    Article Title: A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics

    doi: 10.1371/journal.pone.0160533

    Figure Lengend Snippet: Phylum-level compositional view of bacteria in three human fecal samples/inocula (–) (F37-1: female, age 37; F37-2: female, age 37; and M54: male, age 54) and corresponding cultures at 6, 9, and 24 h after the initiation of fermentation. A compositional view of bacterial phyla based on the taxonomic assignment of 16S rRNA genes is shown. Bacterial composition of each sample was estimated from the results of the RDP classifier. Eubacterial 16S rRNA gene copy numbers are shown in the right column; units are copies/wet-g-feces (inoculum) or copies/mL-culture (fermentation).

    Article Snippet: 16S rRNA-targeted amplicon reads were taxonomically classified by the GreenGenes taxonomic database (Illumina) using the Ribosomal Database Project (RDP) Classifier as described by Wang et al. [ ].

    Techniques:

    Linear fit analysis to assess the correlation between the 16S rRNA and GroEL primers for detection of the same Bifidobacterium species.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals

    doi: 10.1073/pnas.1606722113

    Figure Lengend Snippet: Linear fit analysis to assess the correlation between the 16S rRNA and GroEL primers for detection of the same Bifidobacterium species.

    Article Snippet: The 16S rRNA amplicons from the pooled sample were sequenced on a 454 Genome Sequencer FLX Titanium instrument (Roche) in the Microbiome Core Facility of the University of North Carolina at Chapel Hill using GS FLX Titanium XLR70 sequencing reagents and the corresponding protocols.

    Techniques:

    Relative abundance of Bifidobacterium species at day 0 (pretreatment), day 36 (GOS consumption), and day 66 (GOS halted, dairy consumption encouraged) using 16S rRNA-specific ( Left ) and gro EL-specific ( Right ) primers. 16S rRNA-specific primers did not

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals

    doi: 10.1073/pnas.1606722113

    Figure Lengend Snippet: Relative abundance of Bifidobacterium species at day 0 (pretreatment), day 36 (GOS consumption), and day 66 (GOS halted, dairy consumption encouraged) using 16S rRNA-specific ( Left ) and gro EL-specific ( Right ) primers. 16S rRNA-specific primers did not

    Article Snippet: The 16S rRNA amplicons from the pooled sample were sequenced on a 454 Genome Sequencer FLX Titanium instrument (Roche) in the Microbiome Core Facility of the University of North Carolina at Chapel Hill using GS FLX Titanium XLR70 sequencing reagents and the corresponding protocols.

    Techniques:

    Bacterial communities at genus level in water samples determined by the lowest common ancestor algorithm in MEGAN. (A) Bacterial communities based on the results of a blastn search of 16S rRNA amplicon reads against nucleotide sequences from the NCBI-16SMicrobial-NT database. (B) Bacterial communities based on the results of the blastn search of shotgun sequencing reads against nucleotide sequences from the NCBI-NT database. Colored bars represent the top 20 abundant genera in all samples. Reads from other minor genera are represented in gray, and the reads with unidentified genera are represented in black. The genera ranked in top 20 in both 16S rRNA amplicon and shotgun metagenomic analyses are indicated with asterisks. The results of principal component analysis of the bacterial communities using 16S rRNA reads and shotgun reads are shown in (C,D) , respectively.

    Journal: Frontiers in Microbiology

    Article Title: Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis

    doi: 10.3389/fmicb.2018.01272

    Figure Lengend Snippet: Bacterial communities at genus level in water samples determined by the lowest common ancestor algorithm in MEGAN. (A) Bacterial communities based on the results of a blastn search of 16S rRNA amplicon reads against nucleotide sequences from the NCBI-16SMicrobial-NT database. (B) Bacterial communities based on the results of the blastn search of shotgun sequencing reads against nucleotide sequences from the NCBI-NT database. Colored bars represent the top 20 abundant genera in all samples. Reads from other minor genera are represented in gray, and the reads with unidentified genera are represented in black. The genera ranked in top 20 in both 16S rRNA amplicon and shotgun metagenomic analyses are indicated with asterisks. The results of principal component analysis of the bacterial communities using 16S rRNA reads and shotgun reads are shown in (C,D) , respectively.

    Article Snippet: GS Junior Sequencing for 16S rRNA Amplicon Analysis The GS Junior Titanium System (Roche, Basel, Switzerland) was used for 16S rRNA amplicon analysis.

    Techniques: Amplification, Shotgun Sequencing

    DGGE profiles of amplified bacterial 16S rRNA genes from the on-board mesocosms (days 2, 4 and 6).A. Profiles of days 2, 4 and 6 of all the four mesocosms are shown. The bands in white rectangles were excised and sequenced. BI: no oil (control); BII: 2 L of Arabian Light crude oil; BIII: 5.5 L of Arabian Light crude oil; BIV: 2 L of Arabian Light crude oil and UV treated (killed control).B. MDS plot of the DGGE profiles of the on-board mesocosms. White squares indicate the non-oiled mesocosm (BI), grey squares the less oiled (BII), black squares the most oiled (BIII) and UV treated mesocosm is indicated by an ‘x’.

    Journal: Microbial Biotechnology

    Article Title: Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea

    doi: 10.1111/1751-7915.12176

    Figure Lengend Snippet: DGGE profiles of amplified bacterial 16S rRNA genes from the on-board mesocosms (days 2, 4 and 6).A. Profiles of days 2, 4 and 6 of all the four mesocosms are shown. The bands in white rectangles were excised and sequenced. BI: no oil (control); BII: 2 L of Arabian Light crude oil; BIII: 5.5 L of Arabian Light crude oil; BIV: 2 L of Arabian Light crude oil and UV treated (killed control).B. MDS plot of the DGGE profiles of the on-board mesocosms. White squares indicate the non-oiled mesocosm (BI), grey squares the less oiled (BII), black squares the most oiled (BIII) and UV treated mesocosm is indicated by an ‘x’.

    Article Snippet: The 16S rRNA amplicons of bacterial isolates were sent to GATC Biotech ( http://www.gatc-biotech.com/en/index.html ) for sequencing.

    Techniques: Denaturing Gradient Gel Electrophoresis, Amplification

    DGGE profiles of amplified bacterial 16S rRNA genes from 1.5 m (out) and 3 m (in) below the sea surface during the experimental oil spill (outside and inside the spill respectively) at different times. Refer to the Experimental Procedures for an explanation of the experimental-spill and sampling strategy.

    Journal: Microbial Biotechnology

    Article Title: Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea

    doi: 10.1111/1751-7915.12176

    Figure Lengend Snippet: DGGE profiles of amplified bacterial 16S rRNA genes from 1.5 m (out) and 3 m (in) below the sea surface during the experimental oil spill (outside and inside the spill respectively) at different times. Refer to the Experimental Procedures for an explanation of the experimental-spill and sampling strategy.

    Article Snippet: The 16S rRNA amplicons of bacterial isolates were sent to GATC Biotech ( http://www.gatc-biotech.com/en/index.html ) for sequencing.

    Techniques: Denaturing Gradient Gel Electrophoresis, Amplification, Sampling

    Phylogenetic tree of North Sea isolates based on partial 16S rRNA (500 bp) sequences. Spill-in: inside experimental oil spill; Spill-out: outside experimental spill; Acc-in: inside accidental slicks; Acc-out: outside accidental slicks. On-board mesocosms – BI: no oil (control); BII: 2 L of Arabian Light crude oil; BIII: 5.5 L of Arabian Light crude oil; BIV: 2 L of Arabian Light crude oil and UV treated (killed control). The bar represents the average nucleotide substitution per base. The 16S rRNA gene of H aloferax volcanii NCIMB 2012 (AY425724.1) was used as outgroup.

    Journal: Microbial Biotechnology

    Article Title: Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea

    doi: 10.1111/1751-7915.12176

    Figure Lengend Snippet: Phylogenetic tree of North Sea isolates based on partial 16S rRNA (500 bp) sequences. Spill-in: inside experimental oil spill; Spill-out: outside experimental spill; Acc-in: inside accidental slicks; Acc-out: outside accidental slicks. On-board mesocosms – BI: no oil (control); BII: 2 L of Arabian Light crude oil; BIII: 5.5 L of Arabian Light crude oil; BIV: 2 L of Arabian Light crude oil and UV treated (killed control). The bar represents the average nucleotide substitution per base. The 16S rRNA gene of H aloferax volcanii NCIMB 2012 (AY425724.1) was used as outgroup.

    Article Snippet: The 16S rRNA amplicons of bacterial isolates were sent to GATC Biotech ( http://www.gatc-biotech.com/en/index.html ) for sequencing.

    Techniques:

    Changes in alkane concentration in Forties crude oil after cultivation with four different isolates. The values represent percentage remaining of each alkane component relative to the negative control after 12 days of incubation (28 days for strain NS164). Vertical bars show the standard error; n = 3. The asterisk denotes no significant degradation (Tukey's HSD: P > 0.05; Dunnett's two sided: P > 0.05). The four strains are: NS159 (99.6% 16S rRNA sequence identity to H alomonas sp. MAN K33), NS163 (99% 16S rRNA sequence identity to R oseovarius sp. AP6), NS168 (100% 16S rRNA sequence identity to G laciecola sp. MOLA 37) and NS164 (99% 16S rRNA sequence identity to P seudoalteromonas elyakovii ).

    Journal: Microbial Biotechnology

    Article Title: Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea

    doi: 10.1111/1751-7915.12176

    Figure Lengend Snippet: Changes in alkane concentration in Forties crude oil after cultivation with four different isolates. The values represent percentage remaining of each alkane component relative to the negative control after 12 days of incubation (28 days for strain NS164). Vertical bars show the standard error; n = 3. The asterisk denotes no significant degradation (Tukey's HSD: P > 0.05; Dunnett's two sided: P > 0.05). The four strains are: NS159 (99.6% 16S rRNA sequence identity to H alomonas sp. MAN K33), NS163 (99% 16S rRNA sequence identity to R oseovarius sp. AP6), NS168 (100% 16S rRNA sequence identity to G laciecola sp. MOLA 37) and NS164 (99% 16S rRNA sequence identity to P seudoalteromonas elyakovii ).

    Article Snippet: The 16S rRNA amplicons of bacterial isolates were sent to GATC Biotech ( http://www.gatc-biotech.com/en/index.html ) for sequencing.

    Techniques: Concentration Assay, Negative Control, Incubation, Sequencing

    Two-step generation of 16S amplicons for PacBio sequencing using M13-tagged barcoded primers. The first round of PCR amplifies full-length 16S rRNA fragments using gene-specific primers tailed with universal M13 forward or reverse sequence. In the second step, a unique combination of barcode sequences is added to 16S amplicons from each sample using M13 forward and reverse primers tagged with 16-base PacBio barcodes at their 5′ ends. Barcoded amplicons are subsequently pooled for SMRTbell library construction and multiplexed sequencing.

    Journal: Scientific Reports

    Article Title: High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

    doi: 10.1038/s41598-017-03139-4

    Figure Lengend Snippet: Two-step generation of 16S amplicons for PacBio sequencing using M13-tagged barcoded primers. The first round of PCR amplifies full-length 16S rRNA fragments using gene-specific primers tailed with universal M13 forward or reverse sequence. In the second step, a unique combination of barcode sequences is added to 16S amplicons from each sample using M13 forward and reverse primers tagged with 16-base PacBio barcodes at their 5′ ends. Barcoded amplicons are subsequently pooled for SMRTbell library construction and multiplexed sequencing.

    Article Snippet: Conditions used for amplification in the thermocycler were as follows: preincubation at 98 °C for 2 min, followed by 10 cycles of denaturation at 98 °C for 30 s, annealing at 66 °C for 15 s, elongation at 72 °C for 45 s and 10 cycles of denaturation at 98 °C for 30 s, annealing at 68 °C for 15 s, elongation at 72 °C for 45 s and a final extension step at 72 °C for 5 min. A unique combination of forward and reverse barcode sequences was added to 16S rRNA amplicons from each sample through the second round of PCR using M13F and M13R primers tagged with 16-base PacBio barcodes at their 5′ ends.

    Techniques: Sequencing, Polymerase Chain Reaction

    Comparison of species detection between full-length and partial 16S rRNA sequences. A neighbor-joining phylogenetic tree of 20 species identified in coral-associated microbiome generated using MEGA7. Reference type strain sequences were obtained from the RDP database. The clustering of the sequences was tested by a bootstrap approach using 1,000 replications. Orange, green and blue boxes indicate species that are classifiable based on sequence information from full-length, V3-V4 and V5-V6 regions of the 16S rRNA genes, respectively.

    Journal: Scientific Reports

    Article Title: High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

    doi: 10.1038/s41598-017-03139-4

    Figure Lengend Snippet: Comparison of species detection between full-length and partial 16S rRNA sequences. A neighbor-joining phylogenetic tree of 20 species identified in coral-associated microbiome generated using MEGA7. Reference type strain sequences were obtained from the RDP database. The clustering of the sequences was tested by a bootstrap approach using 1,000 replications. Orange, green and blue boxes indicate species that are classifiable based on sequence information from full-length, V3-V4 and V5-V6 regions of the 16S rRNA genes, respectively.

    Article Snippet: Conditions used for amplification in the thermocycler were as follows: preincubation at 98 °C for 2 min, followed by 10 cycles of denaturation at 98 °C for 30 s, annealing at 66 °C for 15 s, elongation at 72 °C for 45 s and 10 cycles of denaturation at 98 °C for 30 s, annealing at 68 °C for 15 s, elongation at 72 °C for 45 s and a final extension step at 72 °C for 5 min. A unique combination of forward and reverse barcode sequences was added to 16S rRNA amplicons from each sample through the second round of PCR using M13F and M13R primers tagged with 16-base PacBio barcodes at their 5′ ends.

    Techniques: Generated, Sequencing

    A histogram illustrating proportions of sequence reads from each sampling site that are classifiable at the species level using full-length (orange) or partial 16S rRNA gene fragments (V3-V4, green; V5-V6, blue).

    Journal: Scientific Reports

    Article Title: High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

    doi: 10.1038/s41598-017-03139-4

    Figure Lengend Snippet: A histogram illustrating proportions of sequence reads from each sampling site that are classifiable at the species level using full-length (orange) or partial 16S rRNA gene fragments (V3-V4, green; V5-V6, blue).

    Article Snippet: Conditions used for amplification in the thermocycler were as follows: preincubation at 98 °C for 2 min, followed by 10 cycles of denaturation at 98 °C for 30 s, annealing at 66 °C for 15 s, elongation at 72 °C for 45 s and 10 cycles of denaturation at 98 °C for 30 s, annealing at 68 °C for 15 s, elongation at 72 °C for 45 s and a final extension step at 72 °C for 5 min. A unique combination of forward and reverse barcode sequences was added to 16S rRNA amplicons from each sample through the second round of PCR using M13F and M13R primers tagged with 16-base PacBio barcodes at their 5′ ends.

    Techniques: Sequencing, Sampling

    Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length 16S rRNA gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.

    Journal: PLoS ONE

    Article Title: Evidence of Unique and Generalist Microbes in Distantly Related Sympatric Intertidal Marine Sponges (Porifera: Demospongiae)

    doi: 10.1371/journal.pone.0080653

    Figure Lengend Snippet: Phylogeny and diversity of bacterial isolates from marine sponges H. perlevis (HM), P. penicillus (PL) and O. papilla (OP). ( A ) Maximum-likelihood phylogenetic tree of nearly full length 16S rRNA gene sequences (ca. 1400 bp) using Prochlorococcus marinus as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search ( Table S1 ) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values > 50% are represented. ( B ) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.

    Article Snippet: Purified respective 16S rRNA amplicons were pooled and used as DNA insert for clone library construction using pTOP TA V2 vectors in Macrogen Europe.

    Techniques: Derivative Assay

    Phylogeny and diversity of 16S rRNA gene clone libraries from H. perlevis , O. papilla , P . penicillus and seawater. (A) Maximum-likelihood circular phylogenetic tree constructed using partial 16S rRNA gene sequences bacterial OTUs. (B) Clone library diversity inferred from each source.

    Journal: PLoS ONE

    Article Title: Evidence of Unique and Generalist Microbes in Distantly Related Sympatric Intertidal Marine Sponges (Porifera: Demospongiae)

    doi: 10.1371/journal.pone.0080653

    Figure Lengend Snippet: Phylogeny and diversity of 16S rRNA gene clone libraries from H. perlevis , O. papilla , P . penicillus and seawater. (A) Maximum-likelihood circular phylogenetic tree constructed using partial 16S rRNA gene sequences bacterial OTUs. (B) Clone library diversity inferred from each source.

    Article Snippet: Purified respective 16S rRNA amplicons were pooled and used as DNA insert for clone library construction using pTOP TA V2 vectors in Macrogen Europe.

    Techniques: Construct

    Principal Coordinate Analysis (PCoA) plot based on weighted unifrac distances. 16s rRNA sequences are binned according to sample source using a category mapping file. The percentage variation explained with first two principal components (P1 and P2).

    Journal: PLoS ONE

    Article Title: Evidence of Unique and Generalist Microbes in Distantly Related Sympatric Intertidal Marine Sponges (Porifera: Demospongiae)

    doi: 10.1371/journal.pone.0080653

    Figure Lengend Snippet: Principal Coordinate Analysis (PCoA) plot based on weighted unifrac distances. 16s rRNA sequences are binned according to sample source using a category mapping file. The percentage variation explained with first two principal components (P1 and P2).

    Article Snippet: Purified respective 16S rRNA amplicons were pooled and used as DNA insert for clone library construction using pTOP TA V2 vectors in Macrogen Europe.

    Techniques:

    Rarefaction curve for 16S rRNA gene sequences derived from seawater, H . perlevis , O . papilla and P . penicillus . OTUs are retrieved at a distance of 0.01(99% similarity). Each line represents the respective sponge species and surrounding seawater used.

    Journal: PLoS ONE

    Article Title: Evidence of Unique and Generalist Microbes in Distantly Related Sympatric Intertidal Marine Sponges (Porifera: Demospongiae)

    doi: 10.1371/journal.pone.0080653

    Figure Lengend Snippet: Rarefaction curve for 16S rRNA gene sequences derived from seawater, H . perlevis , O . papilla and P . penicillus . OTUs are retrieved at a distance of 0.01(99% similarity). Each line represents the respective sponge species and surrounding seawater used.

    Article Snippet: Purified respective 16S rRNA amplicons were pooled and used as DNA insert for clone library construction using pTOP TA V2 vectors in Macrogen Europe.

    Techniques: Derivative Assay

    16S rRNA read lengths in MiSeq and Ion Torrent sequence data. (A) Comparison of absolute sequence lengths for assembled paired-end MiSeq reads and unidirectional reads from the Ion Torrent PGM platform derived from a mock-community mixture of 20 bacterial

    Journal: Applied and Environmental Microbiology

    Article Title: Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

    doi: 10.1128/AEM.02206-14

    Figure Lengend Snippet: 16S rRNA read lengths in MiSeq and Ion Torrent sequence data. (A) Comparison of absolute sequence lengths for assembled paired-end MiSeq reads and unidirectional reads from the Ion Torrent PGM platform derived from a mock-community mixture of 20 bacterial

    Article Snippet: Second, it should be recognized that under some conditions, 16S rRNA amplicon fragments of the expected length may not be detectable for some species on the Ion Torrent platform, independently of whether PCR products can be generated from those organisms.

    Techniques: Sequencing, Derivative Assay

    a Sensitivity testing of the Enterobacteriaceae database. Randomly fragmented 16S rRNA genes specific to S. enterica were compared to the Enterobacteriaceae database using BLASTn. Fragment sizes ranged from 100 to 500 bp and errors were randomly introduced at rates ranging from 0 to 1 %. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S fragments without a Salmonella best alignment (right axis). b Specificity testing of the Enterobacteriaceae database. 16S rRNA fragments specific to E. coli were randomly fragmented to sizes ranging from 100 to 500 bp and random errors were introduced. Fragments were searched against the Enterobacteriaceae database using BLASTn. c Validation of the Enterobacteriaceae database using BLASTn analysis of raw Illumina MiSeq reads from 105 S. enterica 16S rRNA genes to the EnteroDB. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S rRNA fragments without a Salmonella best alignment (right axis)

    Journal: BMC Microbiology

    Article Title: Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing

    doi: 10.1186/s12866-015-0497-2

    Figure Lengend Snippet: a Sensitivity testing of the Enterobacteriaceae database. Randomly fragmented 16S rRNA genes specific to S. enterica were compared to the Enterobacteriaceae database using BLASTn. Fragment sizes ranged from 100 to 500 bp and errors were randomly introduced at rates ranging from 0 to 1 %. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S fragments without a Salmonella best alignment (right axis). b Specificity testing of the Enterobacteriaceae database. 16S rRNA fragments specific to E. coli were randomly fragmented to sizes ranging from 100 to 500 bp and random errors were introduced. Fragments were searched against the Enterobacteriaceae database using BLASTn. c Validation of the Enterobacteriaceae database using BLASTn analysis of raw Illumina MiSeq reads from 105 S. enterica 16S rRNA genes to the EnteroDB. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S rRNA fragments without a Salmonella best alignment (right axis)

    Article Snippet: 16S rRNA sequencing 16S rRNA amplicon sequencing on the Roche GS FLX Titanium 454 pyrosequencing platform (454 Life Sciences, a Roche company, Branford, CT 06405) was performed on 91 samples.

    Techniques: Diagnostic Assay

    Principal component analysis of urine, genital swab, and rectal swab microbiota, as determined via 16S rRNA amplicon sequencing, colored by sample collection site, from 20 healthy adult dogs ( n = 10 female, 10 male). Plots depict PC1 versus PC2 ( A ), PC1 versus PC3 ( B ), and PC1 versus PC4 ( C ).

    Journal: PLoS ONE

    Article Title: Characterization of the urinary microbiome in healthy dogs

    doi: 10.1371/journal.pone.0177783

    Figure Lengend Snippet: Principal component analysis of urine, genital swab, and rectal swab microbiota, as determined via 16S rRNA amplicon sequencing, colored by sample collection site, from 20 healthy adult dogs ( n = 10 female, 10 male). Plots depict PC1 versus PC2 ( A ), PC1 versus PC3 ( B ), and PC1 versus PC4 ( C ).

    Article Snippet: Bacterial 16S rRNA amplicons were generated via amplification of the V4 hypervariable region of the 16S rRNA gene using single-indexed universal primers (U515F/806R) flanked by Illumina standard adapter sequences and the following parameters: 98° C(3:00) + [98° C(0:15) + 50° C(0:30) + 72° C(0:30) ] × 25 cycles + 72° C(7:00) .

    Techniques: Amplification, Sequencing

    Stacked bar charts showing relative abundance of microbial DNA detected via 16S rRNA amplicon sequencing and annotated to the taxonomic level of family, in samples collected via cystocentesis (urine), vaginal or preputial swab (genital swab), or rectal swab from 20 healthy adult dogs ( n = 10 female, 10 male).

    Journal: PLoS ONE

    Article Title: Characterization of the urinary microbiome in healthy dogs

    doi: 10.1371/journal.pone.0177783

    Figure Lengend Snippet: Stacked bar charts showing relative abundance of microbial DNA detected via 16S rRNA amplicon sequencing and annotated to the taxonomic level of family, in samples collected via cystocentesis (urine), vaginal or preputial swab (genital swab), or rectal swab from 20 healthy adult dogs ( n = 10 female, 10 male).

    Article Snippet: Bacterial 16S rRNA amplicons were generated via amplification of the V4 hypervariable region of the 16S rRNA gene using single-indexed universal primers (U515F/806R) flanked by Illumina standard adapter sequences and the following parameters: 98° C(3:00) + [98° C(0:15) + 50° C(0:30) + 72° C(0:30) ] × 25 cycles + 72° C(7:00) .

    Techniques: Amplification, Sequencing

    Heatmap showing the T-RF found in Bacterial 16S rRNA gene T-RFLP fingerprints from different groundwater samples collected from deep aquifers of coal-rich sedimentary basin, coal-rich sediment samples, and the derived enrichment cultures amended with n -hexadecane. The gray scale indicates the relative abundance of each fragment. Only values above 1% are given. *The abundance of this peak equals the maximum abundance for the sample.

    Journal: Frontiers in Microbiology

    Article Title: Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

    doi: 10.3389/fmicb.2015.00200

    Figure Lengend Snippet: Heatmap showing the T-RF found in Bacterial 16S rRNA gene T-RFLP fingerprints from different groundwater samples collected from deep aquifers of coal-rich sedimentary basin, coal-rich sediment samples, and the derived enrichment cultures amended with n -hexadecane. The gray scale indicates the relative abundance of each fragment. Only values above 1% are given. *The abundance of this peak equals the maximum abundance for the sample.

    Article Snippet: Cloning and sequencing of the archaeal and bacterial 16S rRNA amplicons was performed by Microsynth AG (Switzerland).

    Techniques: Derivative Assay

    Heatmap showing the T-RF found in Archaeal 16S rRNA gene T-RFLP fingerprints from different groundwater samples collected from deep aquifers of coal-rich sedimentary basin, coal-rich sediment samples, and the derived enrichment cultures amended with n -hexadecane. The gray scale indicates the relative abundance of each fragment. Only values above 1% are given.

    Journal: Frontiers in Microbiology

    Article Title: Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

    doi: 10.3389/fmicb.2015.00200

    Figure Lengend Snippet: Heatmap showing the T-RF found in Archaeal 16S rRNA gene T-RFLP fingerprints from different groundwater samples collected from deep aquifers of coal-rich sedimentary basin, coal-rich sediment samples, and the derived enrichment cultures amended with n -hexadecane. The gray scale indicates the relative abundance of each fragment. Only values above 1% are given.

    Article Snippet: Cloning and sequencing of the archaeal and bacterial 16S rRNA amplicons was performed by Microsynth AG (Switzerland).

    Techniques: Derivative Assay

    Prevalence of Mycoplasma lineages in Senegalese rodents, by site, and phylogenetic associations between Mycoplasma lineages and rodent species. (A) Comparison of phylogenetic trees based on the 16S rRNA V4 sequences of Mycoplasma and on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR) for rodents (the tree was drawn based on data from reference 92 ). Lines link the Mycoplasma lineages detected in the various rodent species (for a minimum site prevalence exceeding 10%). The numbers next to the branches are bootstrap values (shown only if > 70%). (B) Plots of OTU prevalences, with 95% confidence intervals calculated by Sterne’s exact method ( 93 ) according to rodent species and site (see reference 69 for more information about site codes and their geographic locations). The gray bars on the x axis indicate sites from which the rodent species concerned is absent.

    Journal: mSystems

    Article Title: 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

    doi: 10.1128/mSystems.00032-16

    Figure Lengend Snippet: Prevalence of Mycoplasma lineages in Senegalese rodents, by site, and phylogenetic associations between Mycoplasma lineages and rodent species. (A) Comparison of phylogenetic trees based on the 16S rRNA V4 sequences of Mycoplasma and on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR) for rodents (the tree was drawn based on data from reference 92 ). Lines link the Mycoplasma lineages detected in the various rodent species (for a minimum site prevalence exceeding 10%). The numbers next to the branches are bootstrap values (shown only if > 70%). (B) Plots of OTU prevalences, with 95% confidence intervals calculated by Sterne’s exact method ( 93 ) according to rodent species and site (see reference 69 for more information about site codes and their geographic locations). The gray bars on the x axis indicate sites from which the rodent species concerned is absent.

    Article Snippet: Such HTS microbial identification approaches are based on the sequencing of all (WGS [whole-genome sequencing]) or some (RNA-seq [whole-RNA sequencing] or 16S rRNA amplicon sequencing) of the bacterial DNA or RNA in a sample, followed by comparison to a reference sequence database ( ).

    Techniques:

    Taxonomic assignment of the V4 16S rRNA sequences in wild rodents and in negative controls for extraction and PCR. The histograms show the percentages of sequences for the most abundant bacterial genera in the two MiSeq runs combined. Notice the presence in the controls of several bacterial genera, which was likely due to the inherent contamination of laboratory reagents by bacterial DNA (termed “contaminant genera”). These contaminant genera are also present (to a lesser extent) in the rodent samples. The insertions represent the proportion of sequences from rodent samples which were incorrectly assigned to the controls. See Fig. S1 for separate histograms for the two MiSeq runs.

    Journal: mSystems

    Article Title: 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

    doi: 10.1128/mSystems.00032-16

    Figure Lengend Snippet: Taxonomic assignment of the V4 16S rRNA sequences in wild rodents and in negative controls for extraction and PCR. The histograms show the percentages of sequences for the most abundant bacterial genera in the two MiSeq runs combined. Notice the presence in the controls of several bacterial genera, which was likely due to the inherent contamination of laboratory reagents by bacterial DNA (termed “contaminant genera”). These contaminant genera are also present (to a lesser extent) in the rodent samples. The insertions represent the proportion of sequences from rodent samples which were incorrectly assigned to the controls. See Fig. S1 for separate histograms for the two MiSeq runs.

    Article Snippet: Such HTS microbial identification approaches are based on the sequencing of all (WGS [whole-genome sequencing]) or some (RNA-seq [whole-RNA sequencing] or 16S rRNA amplicon sequencing) of the bacterial DNA or RNA in a sample, followed by comparison to a reference sequence database ( ).

    Techniques: Polymerase Chain Reaction

    Workflow of the wet laboratory, bioinformatics, and data filtering procedures in the process of data filtering for 16S rRNA amplicon sequencing. Reagent contaminants were detected by analyzing the sequences in the NC ext and NC PCR controls. Sequence number thresholds for correcting for cross-contamination (T CC ) are OTU and run dependent and were estimated by analyzing the sequences in the NC mus , NC ext , NC PCR , and PC index controls. Sequence number thresholds for correcting for false-index-pairing (T FA ) values are OTU and run dependent and were estimated by analyzing the sequences in the NC index and PC alien controls. A result was considered positive if the number of sequences was > T CC and > T FA . Samples were considered positive if a positive result was obtained for both PCR replicates. *, see Kozich et al. ( 18 ) for details on the sequencing.

    Journal: mSystems

    Article Title: 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

    doi: 10.1128/mSystems.00032-16

    Figure Lengend Snippet: Workflow of the wet laboratory, bioinformatics, and data filtering procedures in the process of data filtering for 16S rRNA amplicon sequencing. Reagent contaminants were detected by analyzing the sequences in the NC ext and NC PCR controls. Sequence number thresholds for correcting for cross-contamination (T CC ) are OTU and run dependent and were estimated by analyzing the sequences in the NC mus , NC ext , NC PCR , and PC index controls. Sequence number thresholds for correcting for false-index-pairing (T FA ) values are OTU and run dependent and were estimated by analyzing the sequences in the NC index and PC alien controls. A result was considered positive if the number of sequences was > T CC and > T FA . Samples were considered positive if a positive result was obtained for both PCR replicates. *, see Kozich et al. ( 18 ) for details on the sequencing.

    Article Snippet: Such HTS microbial identification approaches are based on the sequencing of all (WGS [whole-genome sequencing]) or some (RNA-seq [whole-RNA sequencing] or 16S rRNA amplicon sequencing) of the bacterial DNA or RNA in a sample, followed by comparison to a reference sequence database ( ).

    Techniques: Amplification, Sequencing, Polymerase Chain Reaction