Structured Review

Roche 16s rrna gene amplicons
Characterization of sulfate-reducing and methanogenic populations using dsrB and <t>16S</t> <t>rRNA</t> gene analyses. (a) Number of bacterial 16S rRNA copies detected in groundwater using quantitative PCR on RNA extracts. (b) Number of dsrB mRNA transcript copies
16s Rrna Gene Amplicons, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 33 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿ †"

Article Title: A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿ †

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.00220-11

Characterization of sulfate-reducing and methanogenic populations using dsrB and 16S rRNA gene analyses. (a) Number of bacterial 16S rRNA copies detected in groundwater using quantitative PCR on RNA extracts. (b) Number of dsrB mRNA transcript copies
Figure Legend Snippet: Characterization of sulfate-reducing and methanogenic populations using dsrB and 16S rRNA gene analyses. (a) Number of bacterial 16S rRNA copies detected in groundwater using quantitative PCR on RNA extracts. (b) Number of dsrB mRNA transcript copies

Techniques Used: Real-time Polymerase Chain Reaction

Comparisons of groundwater archaeal community structures and composition during the EVO experiment. (A) Samples clustered according to abundance-based Sorenson's indices of 16S rRNA gene libraries normalized to 650 reads each. Sample names are the monitoring
Figure Legend Snippet: Comparisons of groundwater archaeal community structures and composition during the EVO experiment. (A) Samples clustered according to abundance-based Sorenson's indices of 16S rRNA gene libraries normalized to 650 reads each. Sample names are the monitoring

Techniques Used:

2) Product Images from "The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization"

Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

Journal: Scientific Reports

doi: 10.1038/s41598-017-11427-2

Comparison of Hypervariable Regions for the Analysis of the Alpha Diversity of Saliva Samples. ( A ) Rarefaction curves of sequencing data obtained using saliva samples for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 27,000 sequences per sample. ( B ) Average Shannon diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection. ( C ) Average Simpson diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection.
Figure Legend Snippet: Comparison of Hypervariable Regions for the Analysis of the Alpha Diversity of Saliva Samples. ( A ) Rarefaction curves of sequencing data obtained using saliva samples for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 27,000 sequences per sample. ( B ) Average Shannon diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection. ( C ) Average Simpson diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection.

Techniques Used: Sequencing

Analysis of Microbial Mock Community HM-783D. ( A ) Rarefaction curves of sequencing data obtained using mock microbial community HM-783D for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 14,000 sequences per sample. ( B ) Shannon and ( C ) Simpson diversity calculated for the mock community using the V1V2 and V4V5 hypervariable regions. ( D ) Theoretical and observed relative abundances of genera detected in HM-783D using the V1V2 and V4V5 hypervariable regions.
Figure Legend Snippet: Analysis of Microbial Mock Community HM-783D. ( A ) Rarefaction curves of sequencing data obtained using mock microbial community HM-783D for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 14,000 sequences per sample. ( B ) Shannon and ( C ) Simpson diversity calculated for the mock community using the V1V2 and V4V5 hypervariable regions. ( D ) Theoretical and observed relative abundances of genera detected in HM-783D using the V1V2 and V4V5 hypervariable regions.

Techniques Used: Sequencing

Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.
Figure Legend Snippet: Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.

Techniques Used: Generated

3) Product Images from "Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes"

Article Title: Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dst052

Phylum-level taxonomic compositions of prokaryotes in the soil metagenome on the basis of the 338F-533R and 342F-806R amplicon pyrosequencing and the 16S rRNA gene fragments from Illumina metagenomic sequencing. The top 18 abundant phyla from the results of Illumina metagenomic sequencing are listed.
Figure Legend Snippet: Phylum-level taxonomic compositions of prokaryotes in the soil metagenome on the basis of the 338F-533R and 342F-806R amplicon pyrosequencing and the 16S rRNA gene fragments from Illumina metagenomic sequencing. The top 18 abundant phyla from the results of Illumina metagenomic sequencing are listed.

Techniques Used: Amplification, Sequencing

A partial plot of the consensus sequence in each window and its coverage rate for each phylum from 531 16S rRNA genes of genome-sequenced strains. The number of species in each phylum is indicated in parentheses. The start position of each window is represented according to the corresponding position in the 16S rRNA gene from Escherichia coli . The consensus sequence in each window is represented at the bottom of the figure. Each line indicate the coverage rate for the consensus sequence of each phylum by using the colours of dots: black
Figure Legend Snippet: A partial plot of the consensus sequence in each window and its coverage rate for each phylum from 531 16S rRNA genes of genome-sequenced strains. The number of species in each phylum is indicated in parentheses. The start position of each window is represented according to the corresponding position in the 16S rRNA gene from Escherichia coli . The consensus sequence in each window is represented at the bottom of the figure. Each line indicate the coverage rate for the consensus sequence of each phylum by using the colours of dots: black

Techniques Used: Sequencing

4) Product Images from "Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance"

Article Title: Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dsv023

Phylum- and genus-level taxonomical succession of microbial communities in control and polluted soils. PCR amplicons of V3–V4 regions in the 16S rRNA genes from metagenomic samples were pyrosequenced, and taxonomically assigned by the RDP classifier (see the text for details). (A) Phylum-level succession. (B) Genus-level succession. C and M: metagenomic samples from the control and polluted soils, respectively. The numerals before C and M are the weeks after the pollution. Only the top 15 prokaryotic genera are shown for simplicity. Taxa with asterisks are genera incertae sedis .
Figure Legend Snippet: Phylum- and genus-level taxonomical succession of microbial communities in control and polluted soils. PCR amplicons of V3–V4 regions in the 16S rRNA genes from metagenomic samples were pyrosequenced, and taxonomically assigned by the RDP classifier (see the text for details). (A) Phylum-level succession. (B) Genus-level succession. C and M: metagenomic samples from the control and polluted soils, respectively. The numerals before C and M are the weeks after the pollution. Only the top 15 prokaryotic genera are shown for simplicity. Taxa with asterisks are genera incertae sedis .

Techniques Used: Polymerase Chain Reaction

Hierarchical clustering analysis of taxonomic and functional compositions of 11 soil metagenomic samples. Clustering of (A) taxonomic compositions of 97% OTUs of 16S rRNA gene amplicons, and (B) functional compositions of genes for KEGG KO-assigned proteins was performed by comparison of the Euclidean distances. See the text for details.
Figure Legend Snippet: Hierarchical clustering analysis of taxonomic and functional compositions of 11 soil metagenomic samples. Clustering of (A) taxonomic compositions of 97% OTUs of 16S rRNA gene amplicons, and (B) functional compositions of genes for KEGG KO-assigned proteins was performed by comparison of the Euclidean distances. See the text for details.

Techniques Used: Functional Assay

Time-course changes in taxonomic and functional diversity of metagenomes in control and polluted soils. (A) Taxonomic diversity. (B) Functional diversity. Open and closed circles: control and polluted soils, respectively. The Shannon-Wiener indices (H′) for taxonomic and functional diversities of the metagenomic samples were calculated from the compositions of 97% OTUs of the 16S rRNA gene amplicons and the compositions of genes for KO-assigned proteins, respectively.
Figure Legend Snippet: Time-course changes in taxonomic and functional diversity of metagenomes in control and polluted soils. (A) Taxonomic diversity. (B) Functional diversity. Open and closed circles: control and polluted soils, respectively. The Shannon-Wiener indices (H′) for taxonomic and functional diversities of the metagenomic samples were calculated from the compositions of 97% OTUs of the 16S rRNA gene amplicons and the compositions of genes for KO-assigned proteins, respectively.

Techniques Used: Functional Assay

5) Product Images from "Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence"

Article Title: Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence

Journal: Scientific Reports

doi: 10.1038/s41598-017-07639-1

Distribution of the major bacterial phyla and classes along the toposequence and hierarchical clustering analysis. ( A ) Taxonomic distribution. The relative abundance of the major phyla and classes was calculated as the percentage of sequences belonging to a particular lineage of all 16S rRNA gene sequences recovered from each sample. The Proteobacteria phylum is represented in green and was detailed for the different classes. The Actinobacteria phylum was represented in blue and was detailed for the Actinomycetales and Solirubrobacterales orders. ( B ) Hierarchical clustering analysis. A hierarchical clustering based on Bray-Curtis (BC) distance of the major bacterial phyla and classes was performed. Samples are referred as follow: Calcaric.BS: Calcaric bulk soil; Calcaric.Rh: Calcaric rhizosphere; Eutric.BS: Eutric bulk soil; Eutric.Rh: Eutric rhizosphere; Hyperdystric.BS: Hyperdystric bulk soil; Hyperdystric.Rh: Hyperdystric rhizosphere.
Figure Legend Snippet: Distribution of the major bacterial phyla and classes along the toposequence and hierarchical clustering analysis. ( A ) Taxonomic distribution. The relative abundance of the major phyla and classes was calculated as the percentage of sequences belonging to a particular lineage of all 16S rRNA gene sequences recovered from each sample. The Proteobacteria phylum is represented in green and was detailed for the different classes. The Actinobacteria phylum was represented in blue and was detailed for the Actinomycetales and Solirubrobacterales orders. ( B ) Hierarchical clustering analysis. A hierarchical clustering based on Bray-Curtis (BC) distance of the major bacterial phyla and classes was performed. Samples are referred as follow: Calcaric.BS: Calcaric bulk soil; Calcaric.Rh: Calcaric rhizosphere; Eutric.BS: Eutric bulk soil; Eutric.Rh: Eutric rhizosphere; Hyperdystric.BS: Hyperdystric bulk soil; Hyperdystric.Rh: Hyperdystric rhizosphere.

Techniques Used:

Shift in taxonomic and functional diversity of bulk soil and rhizosphere-associated bacterial communities along the soil toposequence of Montiers. Multivariate analyses were performed at the phylum level for the 16S rRNA gene libraries ( A and B ) and at the subcategory level for the GeoChip microarray ( C and D ). For both approaches, multivariate analyses were conducted separately on bulk soil (BS) and rhizosphere (Rh) samples. The origins of samples are indicated as follows: filled orange squares, bulk soil samples from Calcaric; open orange squares, rhizosphere samples from Calcaric; filled green circles, bulk soil samples from Eutric, open green circles, rhizosphere samples from Eutric; filled blue triangles, bulk soil samples from Hyperdystric; open blue triangles, rhizosphere samples from Hyperdystric. Ellipses correspond to 95% confidence intervals about the mean.
Figure Legend Snippet: Shift in taxonomic and functional diversity of bulk soil and rhizosphere-associated bacterial communities along the soil toposequence of Montiers. Multivariate analyses were performed at the phylum level for the 16S rRNA gene libraries ( A and B ) and at the subcategory level for the GeoChip microarray ( C and D ). For both approaches, multivariate analyses were conducted separately on bulk soil (BS) and rhizosphere (Rh) samples. The origins of samples are indicated as follows: filled orange squares, bulk soil samples from Calcaric; open orange squares, rhizosphere samples from Calcaric; filled green circles, bulk soil samples from Eutric, open green circles, rhizosphere samples from Eutric; filled blue triangles, bulk soil samples from Hyperdystric; open blue triangles, rhizosphere samples from Hyperdystric. Ellipses correspond to 95% confidence intervals about the mean.

Techniques Used: Functional Assay, Microarray

Shift in taxonomic and functional bacterial diversity between bulk soil and rhizosphere compartments in each soil type. Multivariate analyses were performed at the phylum level for the 16S rRNA gene libraries ( A , B and C ) and at the functional subcategory level for the GeoChip dataset ( D , E and F ). For both approaches, multivariate analyses were conducted separately on each soil types to determine a potential rhizosphere effect. The origins of samples are indicated as follows: filled orange squares, bulk soil samples from Calcaric; open orange squares, rhizosphere samples from Calcaric; filled green circles, bulk soil samples from Eutric, open green circles, rhizosphere samples from Eutric; filled blue triangles, bulk soil samples from Hyperdystric; open blue triangles, rhizosphere samples from Hyperdystric. Ellipses correspond to 95% confidence intervals about the mean.
Figure Legend Snippet: Shift in taxonomic and functional bacterial diversity between bulk soil and rhizosphere compartments in each soil type. Multivariate analyses were performed at the phylum level for the 16S rRNA gene libraries ( A , B and C ) and at the functional subcategory level for the GeoChip dataset ( D , E and F ). For both approaches, multivariate analyses were conducted separately on each soil types to determine a potential rhizosphere effect. The origins of samples are indicated as follows: filled orange squares, bulk soil samples from Calcaric; open orange squares, rhizosphere samples from Calcaric; filled green circles, bulk soil samples from Eutric, open green circles, rhizosphere samples from Eutric; filled blue triangles, bulk soil samples from Hyperdystric; open blue triangles, rhizosphere samples from Hyperdystric. Ellipses correspond to 95% confidence intervals about the mean.

Techniques Used: Functional Assay

6) Product Images from "Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon"

Article Title: Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon

Journal: PLoS ONE

doi: 10.1371/journal.pone.0073140

Rarefaction analysis of 16S libraries from non-ICR and post-ICR samples by location and time point. 2,210 16S rRNA gene sequences were randomly selected from each sample. Species were based on an Operational Taxonomic Unit (OTU) definition of 97% sequence identity.
Figure Legend Snippet: Rarefaction analysis of 16S libraries from non-ICR and post-ICR samples by location and time point. 2,210 16S rRNA gene sequences were randomly selected from each sample. Species were based on an Operational Taxonomic Unit (OTU) definition of 97% sequence identity.

Techniques Used: Sequencing

7) Product Images from "Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia"

Article Title: Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.01301

Distribution and taxonomic assignments of 16S rRNA bacterial sequences in chimneys and fluids of interdidal and submarine sites of PHF . Relative phylogenetic abundance was based on frequencies of the 16S rRNA gene sequences (with respect to the total number of sequences obtained by pyrosequencing) affiliated to major phylogenetic phyla or class in the bacterial communities of the “Bain des Japonais” (BdJ), “Rivière des Kaoris” (RK), and the “Aiguille de Prony” (ST07). The suffix “C” in sample names corresponds to “chimney” and the suffix “F” corresponds to “fluid.” The abbreviations of phyla and the former names of candidate phyla are indicated in parentheses.
Figure Legend Snippet: Distribution and taxonomic assignments of 16S rRNA bacterial sequences in chimneys and fluids of interdidal and submarine sites of PHF . Relative phylogenetic abundance was based on frequencies of the 16S rRNA gene sequences (with respect to the total number of sequences obtained by pyrosequencing) affiliated to major phylogenetic phyla or class in the bacterial communities of the “Bain des Japonais” (BdJ), “Rivière des Kaoris” (RK), and the “Aiguille de Prony” (ST07). The suffix “C” in sample names corresponds to “chimney” and the suffix “F” corresponds to “fluid.” The abbreviations of phyla and the former names of candidate phyla are indicated in parentheses.

Techniques Used:

Hydrogen-producing cultures obtained from hydrothermal chimneys of the Prony bay: performances and identification of bacterial isolates . (A) Hydrogen-producing cultures were attempted using several dilutions of chimney subsamples from three Prony sites: “Bain des Japonais” (BdJ), “Rivière des Kaoris” (RK), and the “Aiguille de Prony” (ST07). The suffix “C” in sample names stands for “chimney.” Subcultures were also performed from the first round of positive enrichment cultures. Values are mean of biological replicates ± standard deviation (errors bars). (B) Maximum-likelihood tree based on 16S rRNA gene sequences showing the phylogenetic position of Firmicutes strains 3b, PROH2, and BJ2, isolated from hydrogen-producing cultures of Prony hydrothermal Field (PHF). Representative sequences in the tree were obtained from GenBank (accession number in the brackets). Other bacterial species isolated from PHF are indicated by asterisks. Bootstrap values > 70% are indicated at nodes.
Figure Legend Snippet: Hydrogen-producing cultures obtained from hydrothermal chimneys of the Prony bay: performances and identification of bacterial isolates . (A) Hydrogen-producing cultures were attempted using several dilutions of chimney subsamples from three Prony sites: “Bain des Japonais” (BdJ), “Rivière des Kaoris” (RK), and the “Aiguille de Prony” (ST07). The suffix “C” in sample names stands for “chimney.” Subcultures were also performed from the first round of positive enrichment cultures. Values are mean of biological replicates ± standard deviation (errors bars). (B) Maximum-likelihood tree based on 16S rRNA gene sequences showing the phylogenetic position of Firmicutes strains 3b, PROH2, and BJ2, isolated from hydrogen-producing cultures of Prony hydrothermal Field (PHF). Representative sequences in the tree were obtained from GenBank (accession number in the brackets). Other bacterial species isolated from PHF are indicated by asterisks. Bootstrap values > 70% are indicated at nodes.

Techniques Used: Standard Deviation, Isolation

8) Product Images from "More Than Meets the Eye: Associations of Vaginal Bacteria with Gram Stain Morphotypes Using Molecular Phylogenetic Analysis"

Article Title: More Than Meets the Eye: Associations of Vaginal Bacteria with Gram Stain Morphotypes Using Molecular Phylogenetic Analysis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0078633

Fluorescence micrographs and Gram stain images of vaginal fluid smears. Vaginal fluid smears from two representative study participants are shown. 4+ curved rods were documented by Gram stain (A C) for both participants who had BV (Nugent score 10). Panels A (Gram stain) and B (FISH) are vaginal fluid smears from a representative participant with low concentrations of Mobiluncus DNA (2·5×10 5 copies 16S-rRNA gene/swab) and high concentrations of BVAB1 DNA (2·4×10 9 16S rRNA gene copies/swab). Panel B shows a field of bacteria hybridizing with probes for BVAB1 (green) while no hybridization was observed with Mobiluncus probe (red). Mean quantity of BVAB1 cells was 661 versus
Figure Legend Snippet: Fluorescence micrographs and Gram stain images of vaginal fluid smears. Vaginal fluid smears from two representative study participants are shown. 4+ curved rods were documented by Gram stain (A C) for both participants who had BV (Nugent score 10). Panels A (Gram stain) and B (FISH) are vaginal fluid smears from a representative participant with low concentrations of Mobiluncus DNA (2·5×10 5 copies 16S-rRNA gene/swab) and high concentrations of BVAB1 DNA (2·4×10 9 16S rRNA gene copies/swab). Panel B shows a field of bacteria hybridizing with probes for BVAB1 (green) while no hybridization was observed with Mobiluncus probe (red). Mean quantity of BVAB1 cells was 661 versus

Techniques Used: Fluorescence, Staining, Fluorescence In Situ Hybridization, Hybridization

9) Product Images from "Identification and characterisation of isoprene‐degrading bacteria in an estuarine environment"

Article Title: Identification and characterisation of isoprene‐degrading bacteria in an estuarine environment

Journal: Environmental Microbiology

doi: 10.1111/1462-2920.13842

A. Phylogeny, based on 16S rRNA gene sequences, of known isoprene‐degraders (shown in bold), together with closely related non‐isoprene‐degrading strains. The tree was constructed in MEGA6 (Tamura et al ., 2013 ) using the Neighbour‐joining method. All positions containing gaps and missing data were eliminated, and there were a total of 535 positions in the final dataset. B. Phylogenetic relationship of known isoprene‐degrading strains based on isoA sequences, together with alkene monooxygenase ( xamoA ) from Xanthobacter autotrophicus Py2 (Zhou et al ., 1999 ). The tree was drawn in MEGA6 using the Maximum Likelihood method based on an alignment of isoA sequences. All positions containing gaps and missing data were eliminated and there were a total of 1010 nt in the final dataset. Scale bars indicate nucleotide substitutions per site. Bootstrap values (1000 replications) are shown at the nodes.
Figure Legend Snippet: A. Phylogeny, based on 16S rRNA gene sequences, of known isoprene‐degraders (shown in bold), together with closely related non‐isoprene‐degrading strains. The tree was constructed in MEGA6 (Tamura et al ., 2013 ) using the Neighbour‐joining method. All positions containing gaps and missing data were eliminated, and there were a total of 535 positions in the final dataset. B. Phylogenetic relationship of known isoprene‐degrading strains based on isoA sequences, together with alkene monooxygenase ( xamoA ) from Xanthobacter autotrophicus Py2 (Zhou et al ., 1999 ). The tree was drawn in MEGA6 using the Maximum Likelihood method based on an alignment of isoA sequences. All positions containing gaps and missing data were eliminated and there were a total of 1010 nt in the final dataset. Scale bars indicate nucleotide substitutions per site. Bootstrap values (1000 replications) are shown at the nodes.

Techniques Used: Construct

10) Product Images from "Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation ▿Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation ▿ †"

Article Title: Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation ▿Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation ▿ †

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.02317-10

Taxonomic distribution of the 16S rRNA gene V6 amplicons.
Figure Legend Snippet: Taxonomic distribution of the 16S rRNA gene V6 amplicons.

Techniques Used:

11) Product Images from "Microbial communities associated with ferromanganese nodules and the surrounding sediments"

Article Title: Microbial communities associated with ferromanganese nodules and the surrounding sediments

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2013.00161

Maximum likelihood phylogenetic tree constructed using 16S rRNA gene sequences (289 bp) covering the V4 hypervariable region from representatives of each OTU putatively assigned as belonging to the Thaumarchaea MG-1 group (Sequence ID OTU No.|No. of total sequences assigned to OTU), sequences from Durbin and Teske ( 2010 ) (Accession No.), and sequenced members of the Phylum. Colored circles correspond to the samples represented by the OTU (at least one subsample must have > 0.5% abundance). In fixed order: sediment, purple; SPG2, red; SPG9, green; SPG10, blue. Scale bar: 0.02 changes per site. Bootstraps: 1000.
Figure Legend Snippet: Maximum likelihood phylogenetic tree constructed using 16S rRNA gene sequences (289 bp) covering the V4 hypervariable region from representatives of each OTU putatively assigned as belonging to the Thaumarchaea MG-1 group (Sequence ID OTU No.|No. of total sequences assigned to OTU), sequences from Durbin and Teske ( 2010 ) (Accession No.), and sequenced members of the Phylum. Colored circles correspond to the samples represented by the OTU (at least one subsample must have > 0.5% abundance). In fixed order: sediment, purple; SPG2, red; SPG9, green; SPG10, blue. Scale bar: 0.02 changes per site. Bootstraps: 1000.

Techniques Used: Construct, Sequencing

12) Product Images from "Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes"

Article Title: Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dst052

Phylum-level taxonomic compositions of prokaryotes in the soil metagenome on the basis of the 338F-533R and 342F-806R amplicon pyrosequencing and the 16S rRNA gene fragments from Illumina metagenomic sequencing. The top 18 abundant phyla from the results of Illumina metagenomic sequencing are listed.
Figure Legend Snippet: Phylum-level taxonomic compositions of prokaryotes in the soil metagenome on the basis of the 338F-533R and 342F-806R amplicon pyrosequencing and the 16S rRNA gene fragments from Illumina metagenomic sequencing. The top 18 abundant phyla from the results of Illumina metagenomic sequencing are listed.

Techniques Used: Amplification, Sequencing

A partial plot of the consensus sequence in each window and its coverage rate for each phylum from 531 16S rRNA genes of genome-sequenced strains. The number of species in each phylum is indicated in parentheses. The start position of each window is represented according to the corresponding position in the 16S rRNA gene from Escherichia coli . The consensus sequence in each window is represented at the bottom of the figure. Each line indicate the coverage rate for the consensus sequence of each phylum by using the colours of dots: black
Figure Legend Snippet: A partial plot of the consensus sequence in each window and its coverage rate for each phylum from 531 16S rRNA genes of genome-sequenced strains. The number of species in each phylum is indicated in parentheses. The start position of each window is represented according to the corresponding position in the 16S rRNA gene from Escherichia coli . The consensus sequence in each window is represented at the bottom of the figure. Each line indicate the coverage rate for the consensus sequence of each phylum by using the colours of dots: black

Techniques Used: Sequencing

13) Product Images from "Patterns of bacterial biodiversity in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica"

Article Title: Patterns of bacterial biodiversity in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica

Journal: FEMS Microbiology Ecology

doi: 10.1093/femsec/fiw148

Stacked bar graphs of the OTUs derived from 16S rRNA gene sequences at the phylum level for all bacterial sequences ( A ), the order level for chemotrophic bacteria ( B ), and the genus level for Cyanobacteria/chloroplasts ( C ). The samples are averaged by the identified K-means clusters and are organized by mat/sediment type (black = black mat, green = green mat, orange = orange mat, red = red mat, and brown = sediment). See Fig. S1 for the taxonomic distribution of OTUs for individual samples.
Figure Legend Snippet: Stacked bar graphs of the OTUs derived from 16S rRNA gene sequences at the phylum level for all bacterial sequences ( A ), the order level for chemotrophic bacteria ( B ), and the genus level for Cyanobacteria/chloroplasts ( C ). The samples are averaged by the identified K-means clusters and are organized by mat/sediment type (black = black mat, green = green mat, orange = orange mat, red = red mat, and brown = sediment). See Fig. S1 for the taxonomic distribution of OTUs for individual samples.

Techniques Used: Derivative Assay

14) Product Images from "Cigarette smoking and the oral microbiome in a large study of American adults"

Article Title: Cigarette smoking and the oral microbiome in a large study of American adults

Journal: The ISME Journal

doi: 10.1038/ismej.2016.37

Bacterial taxa associated with smoking status are related to several gene functional pathways. Bacterial gene functions were predicted from 16S rRNA gene-based microbial compositions using the PICRUSt algorithm to make inferences from KEGG annotated databases.
Figure Legend Snippet: Bacterial taxa associated with smoking status are related to several gene functional pathways. Bacterial gene functions were predicted from 16S rRNA gene-based microbial compositions using the PICRUSt algorithm to make inferences from KEGG annotated databases.

Techniques Used: Functional Assay

15) Product Images from "Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors"

Article Title: Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.00625

Maximum likelihood tree based on representative sequences of OTUs (98% identity) of partial 16S rRNA gene sequences (cut to 350 bp long). For clarity, the 50 most abundant OTUs for 2010 and 2011, respectively (72 OTUs in total) are shown in the tree and branches of
Figure Legend Snippet: Maximum likelihood tree based on representative sequences of OTUs (98% identity) of partial 16S rRNA gene sequences (cut to 350 bp long). For clarity, the 50 most abundant OTUs for 2010 and 2011, respectively (72 OTUs in total) are shown in the tree and branches of

Techniques Used:

16) Product Images from "Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets"

Article Title: Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2014.00415

The structure of bacterial communities at phylum level of wild beet rhizosphere (WB-CS), coastal drift line bulk soil (CS), sugar beet plants cultivated in coastal drift line soil (SB-CS), sugar beet plants cultivated in potting soil (SB-PS), and potting bulk soil (PS) . Relative composition of major phyla ( > 1% of total reads) was determined by 454 amplicon pyrosequencing of 16S rRNA extracted from all samples. Multi-colored charts at the legend are shown for each phylum and sample correspondingly. Phyla to which
Figure Legend Snippet: The structure of bacterial communities at phylum level of wild beet rhizosphere (WB-CS), coastal drift line bulk soil (CS), sugar beet plants cultivated in coastal drift line soil (SB-CS), sugar beet plants cultivated in potting soil (SB-PS), and potting bulk soil (PS) . Relative composition of major phyla ( > 1% of total reads) was determined by 454 amplicon pyrosequencing of 16S rRNA extracted from all samples. Multi-colored charts at the legend are shown for each phylum and sample correspondingly. Phyla to which

Techniques Used: Western Blot, Amplification

Dendrogram of 16S rRNA gene-based SSCP profiles of bacterial communities in association with wild beet (WB-CS) and sugar beet rhizosphere grown in coastal drift line (SB-CS) and potting soil (SB-PS) and their respective bulk soils (CS, PS) with four repetitions per sample . Following settings were used: dendrogram type: unweighted pair group method with arithmetic mean (UPGMA); similarity coefficient: curve based, Pearson correlation; optimization: 4%, position tolerance: 1%.
Figure Legend Snippet: Dendrogram of 16S rRNA gene-based SSCP profiles of bacterial communities in association with wild beet (WB-CS) and sugar beet rhizosphere grown in coastal drift line (SB-CS) and potting soil (SB-PS) and their respective bulk soils (CS, PS) with four repetitions per sample . Following settings were used: dendrogram type: unweighted pair group method with arithmetic mean (UPGMA); similarity coefficient: curve based, Pearson correlation; optimization: 4%, position tolerance: 1%.

Techniques Used: Western Blot

17) Product Images from "Microbial Dysbiosis in Colorectal Cancer (CRC) Patients"

Article Title: Microbial Dysbiosis in Colorectal Cancer (CRC) Patients

Journal: PLoS ONE

doi: 10.1371/journal.pone.0016393

Bacterial genera abundance differentiates cancer patients and normal colonoscopy individuals. Principal component analysis, based on the 16S rRNA gene sequence abundance of 7 discriminates genera which represented at least 1% of microbiota abundance, was carried out with 6 healthy individuals (N) and 6 cancer* patients (Ca) with two replicates (noted as mid1 and mid2). Two first components (PC1 and PC2) were plotted and represented 70.83% of whole inertia. Individuals (represented by their sample id) were clustered and centre of gravity computed for each class. * They all have been selected from stage I-II of TNM classification (see also Tables S2 and S3 and Figures S2 S3 in the supplementary File S1 ).
Figure Legend Snippet: Bacterial genera abundance differentiates cancer patients and normal colonoscopy individuals. Principal component analysis, based on the 16S rRNA gene sequence abundance of 7 discriminates genera which represented at least 1% of microbiota abundance, was carried out with 6 healthy individuals (N) and 6 cancer* patients (Ca) with two replicates (noted as mid1 and mid2). Two first components (PC1 and PC2) were plotted and represented 70.83% of whole inertia. Individuals (represented by their sample id) were clustered and centre of gravity computed for each class. * They all have been selected from stage I-II of TNM classification (see also Tables S2 and S3 and Figures S2 S3 in the supplementary File S1 ).

Techniques Used: Sequencing

18) Product Images from "Comparative evaluation of establishing a human gut microbial community within rodent models"

Article Title: Comparative evaluation of establishing a human gut microbial community within rodent models

Journal: Gut Microbes

doi: 10.4161/gmic.19934

Taxonomic distribution of the 16S rRNA gene sequence phylotypes from the human-donor bacterial community which were detected by 454-pyrosequencing analysis within the antibiotic-treated SPF C57BL/6 recipient mouse. Branching orders correspond to that
Figure Legend Snippet: Taxonomic distribution of the 16S rRNA gene sequence phylotypes from the human-donor bacterial community which were detected by 454-pyrosequencing analysis within the antibiotic-treated SPF C57BL/6 recipient mouse. Branching orders correspond to that

Techniques Used: Sequencing

Taxonomic distribution of the 16S rRNA gene sequence phylotypes from the human-donor bacterial community which were detected by 454-pyrosequencing analysis within the GF C57BL/6 recipient mouse. Branching orders correspond to that of the human-donor bacterial
Figure Legend Snippet: Taxonomic distribution of the 16S rRNA gene sequence phylotypes from the human-donor bacterial community which were detected by 454-pyrosequencing analysis within the GF C57BL/6 recipient mouse. Branching orders correspond to that of the human-donor bacterial

Techniques Used: Sequencing

Taxonomic distribution of the 16S rRNA gene sequence phylotypes from the human-donor bacterial community which were detected by 454-pyrosequencing analysis within the GF WKY recipient rat. Branching orders correspond to that of the human-donor bacterial
Figure Legend Snippet: Taxonomic distribution of the 16S rRNA gene sequence phylotypes from the human-donor bacterial community which were detected by 454-pyrosequencing analysis within the GF WKY recipient rat. Branching orders correspond to that of the human-donor bacterial

Techniques Used: Sequencing

Related Articles

Polymerase Chain Reaction:

Article Title: More Than Meets the Eye: Associations of Vaginal Bacteria with Gram Stain Morphotypes Using Molecular Phylogenetic Analysis
Article Snippet: .. Broad-range PCR and pyrosequencing of 16S rRNA gene amplicons We performed broad-range 16S-rRNA gene PCR with pyrosequencing using 454 Life Sciences FLX technology (Roche, Branford,CT) targeting the V3-V4 region of the 16S-rRNA gene [ ]. .. Sequence reads (426,602 reads) were classified using a phylogenetic placement tool pplacer [ ] and a curated reference set of key vaginal bacteria [ ].

Article Title: Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence
Article Snippet: .. Concentration of each purified PCR product was measured using a Nanodrop-1000 spectrometer (NanoDrop Technologies, Wilmington, DE, USA) and an equimolar mix of the 16S rRNA gene amplicons was used for pyrosequencing on the Genome Sequencer (GS) FLX 454 Titanium platform (Roche) at the Beckman Genomic Coulter (Danvers, MA, USA). .. A total of 415,320 16S rRNA rawdata sequences were obtained after sequencing.

Article Title: Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance
Article Snippet: .. 2.3 Pyrosequencing of 16S rRNA gene amplicons and their taxonomic analysis The detailed analysis of the soil microbial communities on the basis of 16S rRNA gene sequences was performed by the Roche 454 pyrosequencing of PCR amplicons of 16S rRNA genes using 11 metagenomic DNA samples that were prepared from the control and polluted soils as well as the soil just before the pollution. .. Parts of the 16S rRNA genes [the V3–V4 region (positions from 342 to 806 in the Escherichia coli numbering)] were PCR-amplified using our non-degenerate universal primer set of 342F and 806R ( Supplementary Table S2 ) and EX Taq HS polymerase (TAKARA BIO, Ohtsu, Japan).

Next-Generation Sequencing:

Article Title: Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon
Article Snippet: .. Equal amounts of the 16S rRNA gene amplicons from individual samples were bar-coded, pooled, and sequenced on a Roche GS FLX 454 sequencer (High Throughput Sequencing Facility, Chapel Hill NC) using the Titanium sequencing reagents and protocols. .. Sequence analysis was performed using Quantitative Insights Into Microbial Ecology (QIIME) [ ] with default parameters, including removing sequence artifacts using Denoiser [ ] and chimera removal with ChimeraSlayer; clustering via uclust [ ] at 97% similarity; then classified taxonomically using the RDP classifier [ ] retrained with Greengenes [ ].

Purification:

Article Title: Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence
Article Snippet: .. Concentration of each purified PCR product was measured using a Nanodrop-1000 spectrometer (NanoDrop Technologies, Wilmington, DE, USA) and an equimolar mix of the 16S rRNA gene amplicons was used for pyrosequencing on the Genome Sequencer (GS) FLX 454 Titanium platform (Roche) at the Beckman Genomic Coulter (Danvers, MA, USA). .. A total of 415,320 16S rRNA rawdata sequences were obtained after sequencing.

SYBR Green Assay:

Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization
Article Snippet: .. 16S rRNA gene amplicons were generated using universal primers (Supplementary Table ) , and the SYBR-green based Essential DNA Green Start Master Mix (Roche, Indianapolis, IN, USA). .. Samples were amplified on the Roche Light Cycler™ 96 system.

Concentration Assay:

Article Title: Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence
Article Snippet: .. Concentration of each purified PCR product was measured using a Nanodrop-1000 spectrometer (NanoDrop Technologies, Wilmington, DE, USA) and an equimolar mix of the 16S rRNA gene amplicons was used for pyrosequencing on the Genome Sequencer (GS) FLX 454 Titanium platform (Roche) at the Beckman Genomic Coulter (Danvers, MA, USA). .. A total of 415,320 16S rRNA rawdata sequences were obtained after sequencing.

Generated:

Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization
Article Snippet: .. 16S rRNA gene amplicons were generated using universal primers (Supplementary Table ) , and the SYBR-green based Essential DNA Green Start Master Mix (Roche, Indianapolis, IN, USA). .. Samples were amplified on the Roche Light Cycler™ 96 system.

Article Title: Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia
Article Snippet: .. Pyrosequencing analyses of bacterial 16S rRNA gene fragments The mixtures of 16S rRNA gene amplicons were generated from a 341F/815R bacterial primer set, as previously described by Dowd et al. , and were sequenced on a 454 GS-FLX Titanium sequencer (Roche Life Sciences, USA) by the Molecular Research Laboratory (Texas, USA). .. Raw sequence data generated by pyrosequencing were uploaded into QIIME 1.8.0 and processed as described by Caporaso et al. ( ).

Sequencing:

Article Title: Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes
Article Snippet: .. Because of its advantages over the traditional Sanger sequencing, the massively parallel sequencing has been applied to large-scale sequencing projects, including the analysis of 16S rRNA gene amplicons from diverse microbial communities., The Roche 454 Genome Sequencer FLX system is commonly used for the massively parallel sequencing of the 16S rRNA gene amplicons. ..

Article Title: Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon
Article Snippet: .. Equal amounts of the 16S rRNA gene amplicons from individual samples were bar-coded, pooled, and sequenced on a Roche GS FLX 454 sequencer (High Throughput Sequencing Facility, Chapel Hill NC) using the Titanium sequencing reagents and protocols. .. Sequence analysis was performed using Quantitative Insights Into Microbial Ecology (QIIME) [ ] with default parameters, including removing sequence artifacts using Denoiser [ ] and chimera removal with ChimeraSlayer; clustering via uclust [ ] at 97% similarity; then classified taxonomically using the RDP classifier [ ] retrained with Greengenes [ ].

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    Roche 16s rrna gene amplicons
    Characterization of sulfate-reducing and methanogenic populations using dsrB and <t>16S</t> <t>rRNA</t> gene analyses. (a) Number of bacterial 16S rRNA copies detected in groundwater using quantitative PCR on RNA extracts. (b) Number of dsrB mRNA transcript copies
    16s Rrna Gene Amplicons, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 33 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 16s rrna gene amplicon sequencing
    Relative abundances of the bacterial <t>16S</t> <t>rRNA</t> gene sequence (V3-V4 regions) in the 13 coastal sediments. Left panels: relative sequence abundance of most frequent bacterial phyla and classes. Right panels: relative sequence abundance of most frequent taxonomic groups (family to order level) within the class of Gammaproteobacteria according to the taxonomy of SILVA release 117 ( Pruesse et al. , 2007 ). The five candidate chemolithoautotrophic clades are given in bold. Upper panels: relative sequence abundance in 13 coastal surface sediments from 0 to 23 cm below surface (cmbsf) max. A=uppermost sediment layer (0.5 or 1 cmbsf), B=sulfide transition zone, C=sulfidic layer. For the detailed depths ranges see Supplementary Table 1 . Lower panels: relative sequence abundance in subsurface sediments at site Janssand (JS) from 50 to 490 cmbsf. For comparison, samples from 10 cmbsf are included. Sediment samples from 10 cmbsf and 490 cmbsf were run in duplicate (10ab, 490ab). All but one amplicons were pyrosequenced, samples from DB were sequenced via the Illumina MiSeq platform.
    16s Rrna Gene Amplicon Sequencing, supplied by Roche, 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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    Roche archaeal 16s rrna gene tag encoded flx titanium amplicon pyrosequencing bacterial
    Taxonomic classification of <t>archaeal</t> reads retrieved from different wells at genus levels from <t>16S</t> <t>rRNA</t> gene <t>pyrosequencing.</t>
    Archaeal 16s Rrna Gene Tag Encoded Flx Titanium Amplicon Pyrosequencing Bacterial, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Characterization of sulfate-reducing and methanogenic populations using dsrB and 16S rRNA gene analyses. (a) Number of bacterial 16S rRNA copies detected in groundwater using quantitative PCR on RNA extracts. (b) Number of dsrB mRNA transcript copies

    Journal: Applied and Environmental Microbiology

    Article Title: A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿ †

    doi: 10.1128/AEM.00220-11

    Figure Lengend Snippet: Characterization of sulfate-reducing and methanogenic populations using dsrB and 16S rRNA gene analyses. (a) Number of bacterial 16S rRNA copies detected in groundwater using quantitative PCR on RNA extracts. (b) Number of dsrB mRNA transcript copies

    Article Snippet: The 16S rRNA gene amplicons were sequenced using a 454 Life Sciences genome sequencer FLX system following 454 protocols (454 Life Sciences-Roche, Branford, CT).

    Techniques: Real-time Polymerase Chain Reaction

    Comparisons of groundwater archaeal community structures and composition during the EVO experiment. (A) Samples clustered according to abundance-based Sorenson's indices of 16S rRNA gene libraries normalized to 650 reads each. Sample names are the monitoring

    Journal: Applied and Environmental Microbiology

    Article Title: A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer ▿ †

    doi: 10.1128/AEM.00220-11

    Figure Lengend Snippet: Comparisons of groundwater archaeal community structures and composition during the EVO experiment. (A) Samples clustered according to abundance-based Sorenson's indices of 16S rRNA gene libraries normalized to 650 reads each. Sample names are the monitoring

    Article Snippet: The 16S rRNA gene amplicons were sequenced using a 454 Life Sciences genome sequencer FLX system following 454 protocols (454 Life Sciences-Roche, Branford, CT).

    Techniques:

    Comparison of Hypervariable Regions for the Analysis of the Alpha Diversity of Saliva Samples. ( A ) Rarefaction curves of sequencing data obtained using saliva samples for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 27,000 sequences per sample. ( B ) Average Shannon diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection. ( C ) Average Simpson diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection.

    Journal: Scientific Reports

    Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

    doi: 10.1038/s41598-017-11427-2

    Figure Lengend Snippet: Comparison of Hypervariable Regions for the Analysis of the Alpha Diversity of Saliva Samples. ( A ) Rarefaction curves of sequencing data obtained using saliva samples for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 27,000 sequences per sample. ( B ) Average Shannon diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection. ( C ) Average Simpson diversity calculated for saliva samples using V1V2 and V4V5 hypervariable regions on both days of collection.

    Article Snippet: 16S rRNA gene amplicons were generated using universal primers (Supplementary Table ) , and the SYBR-green based Essential DNA Green Start Master Mix (Roche, Indianapolis, IN, USA).

    Techniques: Sequencing

    Analysis of Microbial Mock Community HM-783D. ( A ) Rarefaction curves of sequencing data obtained using mock microbial community HM-783D for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 14,000 sequences per sample. ( B ) Shannon and ( C ) Simpson diversity calculated for the mock community using the V1V2 and V4V5 hypervariable regions. ( D ) Theoretical and observed relative abundances of genera detected in HM-783D using the V1V2 and V4V5 hypervariable regions.

    Journal: Scientific Reports

    Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

    doi: 10.1038/s41598-017-11427-2

    Figure Lengend Snippet: Analysis of Microbial Mock Community HM-783D. ( A ) Rarefaction curves of sequencing data obtained using mock microbial community HM-783D for both V1V2 and V4V5 regions of the 16S rRNA gene. Sequences were subsampled in increments of 500 to an even depth of 14,000 sequences per sample. ( B ) Shannon and ( C ) Simpson diversity calculated for the mock community using the V1V2 and V4V5 hypervariable regions. ( D ) Theoretical and observed relative abundances of genera detected in HM-783D using the V1V2 and V4V5 hypervariable regions.

    Article Snippet: 16S rRNA gene amplicons were generated using universal primers (Supplementary Table ) , and the SYBR-green based Essential DNA Green Start Master Mix (Roche, Indianapolis, IN, USA).

    Techniques: Sequencing

    Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.

    Journal: Scientific Reports

    Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

    doi: 10.1038/s41598-017-11427-2

    Figure Lengend Snippet: Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.

    Article Snippet: 16S rRNA gene amplicons were generated using universal primers (Supplementary Table ) , and the SYBR-green based Essential DNA Green Start Master Mix (Roche, Indianapolis, IN, USA).

    Techniques: Generated

    Relative abundances of the bacterial 16S rRNA gene sequence (V3-V4 regions) in the 13 coastal sediments. Left panels: relative sequence abundance of most frequent bacterial phyla and classes. Right panels: relative sequence abundance of most frequent taxonomic groups (family to order level) within the class of Gammaproteobacteria according to the taxonomy of SILVA release 117 ( Pruesse et al. , 2007 ). The five candidate chemolithoautotrophic clades are given in bold. Upper panels: relative sequence abundance in 13 coastal surface sediments from 0 to 23 cm below surface (cmbsf) max. A=uppermost sediment layer (0.5 or 1 cmbsf), B=sulfide transition zone, C=sulfidic layer. For the detailed depths ranges see Supplementary Table 1 . Lower panels: relative sequence abundance in subsurface sediments at site Janssand (JS) from 50 to 490 cmbsf. For comparison, samples from 10 cmbsf are included. Sediment samples from 10 cmbsf and 490 cmbsf were run in duplicate (10ab, 490ab). All but one amplicons were pyrosequenced, samples from DB were sequenced via the Illumina MiSeq platform.

    Journal: The ISME journal

    Article Title: Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

    doi: 10.1038/ismej.2015.257

    Figure Lengend Snippet: Relative abundances of the bacterial 16S rRNA gene sequence (V3-V4 regions) in the 13 coastal sediments. Left panels: relative sequence abundance of most frequent bacterial phyla and classes. Right panels: relative sequence abundance of most frequent taxonomic groups (family to order level) within the class of Gammaproteobacteria according to the taxonomy of SILVA release 117 ( Pruesse et al. , 2007 ). The five candidate chemolithoautotrophic clades are given in bold. Upper panels: relative sequence abundance in 13 coastal surface sediments from 0 to 23 cm below surface (cmbsf) max. A=uppermost sediment layer (0.5 or 1 cmbsf), B=sulfide transition zone, C=sulfidic layer. For the detailed depths ranges see Supplementary Table 1 . Lower panels: relative sequence abundance in subsurface sediments at site Janssand (JS) from 50 to 490 cmbsf. For comparison, samples from 10 cmbsf are included. Sediment samples from 10 cmbsf and 490 cmbsf were run in duplicate (10ab, 490ab). All but one amplicons were pyrosequenced, samples from DB were sequenced via the Illumina MiSeq platform.

    Article Snippet: Barcoded 16S rRNA gene amplicon sequencing The bacterial diversity in all sediment samples was determined by analyzing the hypervariable V3-V4 region of the 16S rRNA gene using Roche 454 pyro- or Illumina MiSeq-sequencing of barcoded amplicons.

    Techniques: Sequencing

    Sampling sites of the 16S rRNA gene survey (a). Example for a typical stratification of a sediment core from coastal sandy sediments (b). A=uppermost sediment layer, B=sulfide transition zone and C=sulfidic layer refer to the different sampling depths in this study. During sampling the sediment colors were used as indicator for the presence of iron sulfide (dark grey to black). Asterisk indicates samples from sublittoral sediments.

    Journal: The ISME journal

    Article Title: Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

    doi: 10.1038/ismej.2015.257

    Figure Lengend Snippet: Sampling sites of the 16S rRNA gene survey (a). Example for a typical stratification of a sediment core from coastal sandy sediments (b). A=uppermost sediment layer, B=sulfide transition zone and C=sulfidic layer refer to the different sampling depths in this study. During sampling the sediment colors were used as indicator for the presence of iron sulfide (dark grey to black). Asterisk indicates samples from sublittoral sediments.

    Article Snippet: Barcoded 16S rRNA gene amplicon sequencing The bacterial diversity in all sediment samples was determined by analyzing the hypervariable V3-V4 region of the 16S rRNA gene using Roche 454 pyro- or Illumina MiSeq-sequencing of barcoded amplicons.

    Techniques: Sampling

    Taxonomic classification of archaeal reads retrieved from different wells at genus levels from 16S rRNA gene pyrosequencing.

    Journal: PLoS ONE

    Article Title: Diversity of Microbial Communities in Production and Injection Waters of Algerian Oilfields Revealed by 16S rRNA Gene Amplicon 454 Pyrosequencing

    doi: 10.1371/journal.pone.0066588

    Figure Lengend Snippet: Taxonomic classification of archaeal reads retrieved from different wells at genus levels from 16S rRNA gene pyrosequencing.

    Article Snippet: Bacterial and Archaeal 16S rRNA Gene Tag-encoded FLX-titanium Amplicon Pyrosequencing Bacterial and archaeal tag-encoded FLX gene amplicon pyrosequencing (bTEFAP and aTEFAP, respectively) analysis were carried out by means of a Roche 454 FLX instrument with titanium reagents.

    Techniques: