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Illumina Inc 16s rrna gene
Phyla-level relative abundance of reads for each tick species analyzed. The histograms show the portion of MiSeq <t>16S</t> <t>rRNA</t> gene sequences assigned to each phylum.
16s Rrna Gene, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1085 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis"

Article Title: Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0213384

Phyla-level relative abundance of reads for each tick species analyzed. The histograms show the portion of MiSeq 16S rRNA gene sequences assigned to each phylum.
Figure Legend Snippet: Phyla-level relative abundance of reads for each tick species analyzed. The histograms show the portion of MiSeq 16S rRNA gene sequences assigned to each phylum.

Techniques Used:

Nucleotide alignment of ‘ Candidatus Midichloriaceae’ partial 16S rRNA references (according to BLAST) versus closed undefined OTUs (according to Greengenes database).
Figure Legend Snippet: Nucleotide alignment of ‘ Candidatus Midichloriaceae’ partial 16S rRNA references (according to BLAST) versus closed undefined OTUs (according to Greengenes database).

Techniques Used:

2) Product Images from "In Search of Alternative Antibiotic Drugs: Quorum-Quenching Activity in Sponges and their Bacterial Isolates"

Article Title: In Search of Alternative Antibiotic Drugs: Quorum-Quenching Activity in Sponges and their Bacterial Isolates

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.00416

Relative abundance of OTUs from the Sponge Microbiome Project with ≥98% identity to 16S rRNA sequences from strains isolated in this study. (A) Information relative to OTUs closely affiliated to isolate Cc27, (B) Information relative to OTUs closely affiliated with isolate Pv91. (C) Information relative to OTUs closely affiliated with isolates Pv86. Vertical bar represents the mean, the hinge represents SEM (Standard Error of Mean), and dots represent outlier values beyond mean.
Figure Legend Snippet: Relative abundance of OTUs from the Sponge Microbiome Project with ≥98% identity to 16S rRNA sequences from strains isolated in this study. (A) Information relative to OTUs closely affiliated to isolate Cc27, (B) Information relative to OTUs closely affiliated with isolate Pv91. (C) Information relative to OTUs closely affiliated with isolates Pv86. Vertical bar represents the mean, the hinge represents SEM (Standard Error of Mean), and dots represent outlier values beyond mean.

Techniques Used: Isolation

Relative abundance of OTUs from the Sponge Microbiome Project with ≥98% identity to 16S rRNA sequences from strains isolated in this study . (A) Information relative to OTUs closely affiliated to isolate Ss68, (B) Information relative to OTUs closely affiliated with isolate Ac17. Vertical bar represents the mean, the hinge represents SEM (Standard Error of Mean) and dots represent outlier values beyond mean.
Figure Legend Snippet: Relative abundance of OTUs from the Sponge Microbiome Project with ≥98% identity to 16S rRNA sequences from strains isolated in this study . (A) Information relative to OTUs closely affiliated to isolate Ss68, (B) Information relative to OTUs closely affiliated with isolate Ac17. Vertical bar represents the mean, the hinge represents SEM (Standard Error of Mean) and dots represent outlier values beyond mean.

Techniques Used: Isolation

3) Product Images from "Diversity of macaque microbiota compared to the human counterparts"

Article Title: Diversity of macaque microbiota compared to the human counterparts

Journal: Scientific Reports

doi: 10.1038/s41598-018-33950-6

Diversity of macaque microbiome comparing with their human counterparts. ( A ) Alpha diversity of microbiota as measured using the relative inverse Shannon index of genus level 16S rRNA gene phylotypes between macaque and human body sites. ( B ) Beta diversity of microbiota within and between body sites based on unweighted UniFrac pairwise distances. ( C ) Principal coordinate plot of unweighted UniFrac distances showing ecological clustering of microbiota by body sites and host species. Asterisks denote significance at * P
Figure Legend Snippet: Diversity of macaque microbiome comparing with their human counterparts. ( A ) Alpha diversity of microbiota as measured using the relative inverse Shannon index of genus level 16S rRNA gene phylotypes between macaque and human body sites. ( B ) Beta diversity of microbiota within and between body sites based on unweighted UniFrac pairwise distances. ( C ) Principal coordinate plot of unweighted UniFrac distances showing ecological clustering of microbiota by body sites and host species. Asterisks denote significance at * P

Techniques Used:

4) Product Images from "Interleukin-22 drives nitric oxide-dependent DNA damage and dysplasia in a murine model of colitis-associated cancer"

Article Title: Interleukin-22 drives nitric oxide-dependent DNA damage and dysplasia in a murine model of colitis-associated cancer

Journal: Mucosal immunology

doi: 10.1038/mi.2017.9

Hh infection induces IL-22 dependent dysbiosis (A) Quantification of Hh colonization density in the cecal content. n=9-11. (B) Chao and Shannon diversity indices from 16S rRNA sequencing data obtained from fecal pellets of uninfected mice and Hh infected mice treated with control or anti-IL-22 antibody as indicated. (C) Relative abundance of indicated taxa from groups described in B. (D) Relative abundance of indicated taxa as determined by taxa specific 16s rRNA qPCR from groups described in B.
Figure Legend Snippet: Hh infection induces IL-22 dependent dysbiosis (A) Quantification of Hh colonization density in the cecal content. n=9-11. (B) Chao and Shannon diversity indices from 16S rRNA sequencing data obtained from fecal pellets of uninfected mice and Hh infected mice treated with control or anti-IL-22 antibody as indicated. (C) Relative abundance of indicated taxa from groups described in B. (D) Relative abundance of indicated taxa as determined by taxa specific 16s rRNA qPCR from groups described in B.

Techniques Used: Infection, Sequencing, Mouse Assay, Real-time Polymerase Chain Reaction

5) Product Images from "A Microbiological Map of the Healthy Equine Gastrointestinal Tract"

Article Title: A Microbiological Map of the Healthy Equine Gastrointestinal Tract

Journal: PLoS ONE

doi: 10.1371/journal.pone.0166523

Richness of the luminal and mucosal equine gut microbiota. Bar charts showing the mean (± sem) number of unique 16S rRNA gene amplicon sequences ( A , B ) or operational taxonomic units (OTUs; C , D ) detected in luminal contents ( A , C ) or mucosa ( B , D ) of samples collected from dorsal stomach (DS), antral stomach (AS), jejunum (Je), ileum (Il), cecum (Ce), ventral colon (VC), or dorsal colon (DC) of nine healthy adult horses. Bars within a chart marked with like letters are significantly different ( p
Figure Legend Snippet: Richness of the luminal and mucosal equine gut microbiota. Bar charts showing the mean (± sem) number of unique 16S rRNA gene amplicon sequences ( A , B ) or operational taxonomic units (OTUs; C , D ) detected in luminal contents ( A , C ) or mucosa ( B , D ) of samples collected from dorsal stomach (DS), antral stomach (AS), jejunum (Je), ileum (Il), cecum (Ce), ventral colon (VC), or dorsal colon (DC) of nine healthy adult horses. Bars within a chart marked with like letters are significantly different ( p

Techniques Used: Amplification

6) Product Images from "High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia"

Article Title: High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.02065

Community composition of the Planctomycetes in three peatland sites (PT) and three sites of the forested tundra (FT) based on Illumina paired-end sequencing of 16S rRNA genes. The results of statistical analysis of differences between relative abundances of particular groups of planctomycetes in two study sites are given in Supplementary Table S3 .
Figure Legend Snippet: Community composition of the Planctomycetes in three peatland sites (PT) and three sites of the forested tundra (FT) based on Illumina paired-end sequencing of 16S rRNA genes. The results of statistical analysis of differences between relative abundances of particular groups of planctomycetes in two study sites are given in Supplementary Table S3 .

Techniques Used: Sequencing

16S rRNA gene-based neighbor-joining tree (Jukes–Cantor correction) showing the phylogenetic relationship of strains P12 and P515, OTUs from Table 2 and Supplementary Table S1 to representative members of the Planctomycetes . Unique OTUs identified only in the forested soil are indicated with blue color. OTUs that were found only in the peatland are indicated with green color. Black circles indicate that the corresponding nodes were also recovered in the maximum-likelihood and maximum-parsimony trees. The root (not shown) is composed of five 16S rRNA gene sequences from anammox planctomycetes (AF375994, AF375995, AY254883, AY257181, AY254882). Bar, 0.1 substitutions per nucleotide position.
Figure Legend Snippet: 16S rRNA gene-based neighbor-joining tree (Jukes–Cantor correction) showing the phylogenetic relationship of strains P12 and P515, OTUs from Table 2 and Supplementary Table S1 to representative members of the Planctomycetes . Unique OTUs identified only in the forested soil are indicated with blue color. OTUs that were found only in the peatland are indicated with green color. Black circles indicate that the corresponding nodes were also recovered in the maximum-likelihood and maximum-parsimony trees. The root (not shown) is composed of five 16S rRNA gene sequences from anammox planctomycetes (AF375994, AF375995, AY254883, AY257181, AY254882). Bar, 0.1 substitutions per nucleotide position.

Techniques Used:

7) Product Images from "Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Metritis"

Article Title: Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Metritis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0165740

Associations of Bacteroides pyogenes with a fever. (A) Relative abundance of B . pyogenes based on metagenomic sequencing. Bars represent the mean ± SEM. (B) Absolute abundance of total bacteria and B . pyogenes based on droplet digital PCR. The log 10 number of total bacteria (black circles) and B . pyogenes (blue squares) were quantified in uterine swab samples using the 16S rRNA gene and recA gene, respectively. Each symbol represents an individual cow and error bars indicate the means ± SEM. Data labeled “a” are statistically different ( P ≤ 0.05) from data labeled “b”.
Figure Legend Snippet: Associations of Bacteroides pyogenes with a fever. (A) Relative abundance of B . pyogenes based on metagenomic sequencing. Bars represent the mean ± SEM. (B) Absolute abundance of total bacteria and B . pyogenes based on droplet digital PCR. The log 10 number of total bacteria (black circles) and B . pyogenes (blue squares) were quantified in uterine swab samples using the 16S rRNA gene and recA gene, respectively. Each symbol represents an individual cow and error bars indicate the means ± SEM. Data labeled “a” are statistically different ( P ≤ 0.05) from data labeled “b”.

Techniques Used: Sequencing, Digital PCR, Labeling

8) Product Images from "How, When, and Where Relic DNA Affects Microbial Diversity"

Article Title: How, When, and Where Relic DNA Affects Microbial Diversity

Journal: mBio

doi: 10.1128/mBio.00637-18

Effect of relic DNA on within-sample (alpha) bacterial diversity in different ecosystem types. We tested for the effects of bias caused by relic DNA by calculating diversity ratios for richness (a), evenness (b), and phylogenetic diversity (c). The ratios reflect the diversity of the total DNA pool (intact + relic) divided by the diversity of the intact DNA pool. Relic DNA did not bias any measures of diversity in any of the ecosystem types. Richness was calculated as the number of operational taxonomic units (97% sequence similarity of the 16S rRNA gene), evenness was calculated using Simpson’s evenness index, and phylogenetic diversity was calculated using Faith’s D index. Gray symbols are the observed data, and black symbols represent means ± 95% confidence intervals.
Figure Legend Snippet: Effect of relic DNA on within-sample (alpha) bacterial diversity in different ecosystem types. We tested for the effects of bias caused by relic DNA by calculating diversity ratios for richness (a), evenness (b), and phylogenetic diversity (c). The ratios reflect the diversity of the total DNA pool (intact + relic) divided by the diversity of the intact DNA pool. Relic DNA did not bias any measures of diversity in any of the ecosystem types. Richness was calculated as the number of operational taxonomic units (97% sequence similarity of the 16S rRNA gene), evenness was calculated using Simpson’s evenness index, and phylogenetic diversity was calculated using Faith’s D index. Gray symbols are the observed data, and black symbols represent means ± 95% confidence intervals.

Techniques Used: Sequencing

9) Product Images from "Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems"

Article Title: Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

Journal: PLoS ONE

doi: 10.1371/journal.pone.0138455

Community compositions of three treatments in T1, T2 and T3 stages. A. Phylogenetic tree of the shared 16S rRNA gene sequences constructed by the neighbor-joining method with 1,000 bootstrap replicates. The number in parentheses represented the relative abundances of each OTU, and only OTUs accounting for more than 0.05% of the shared sequences were shown. Sequences of typical indigo-producing strains reported previously were indicated with symbol (●) and the accession number. B. Relative abundance of the dominant families from the shared OTUs. C. Heat map of the 10 most abundant genera in each treatment. The color intensity in each cell showed the relative abundance of a genus in a treatment.
Figure Legend Snippet: Community compositions of three treatments in T1, T2 and T3 stages. A. Phylogenetic tree of the shared 16S rRNA gene sequences constructed by the neighbor-joining method with 1,000 bootstrap replicates. The number in parentheses represented the relative abundances of each OTU, and only OTUs accounting for more than 0.05% of the shared sequences were shown. Sequences of typical indigo-producing strains reported previously were indicated with symbol (●) and the accession number. B. Relative abundance of the dominant families from the shared OTUs. C. Heat map of the 10 most abundant genera in each treatment. The color intensity in each cell showed the relative abundance of a genus in a treatment.

Techniques Used: Construct

10) Product Images from "Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)"

Article Title: Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)

Journal: Microbiome

doi: 10.1186/s40168-015-0106-5

Impact of MBRA cultivation on microbial diversity. Microbial diversity of triplicate MBRA communities inoculated with one of three donor fecal samples (Donor A, blue circles ; Donor B, green circles ; Donor C, purple circles ) or in six replicate MBRA communities inoculated with an equal mass of all three donor fecal samples (Pool, black circles ) was determined by sequencing the V4 region of the 16S rRNA gene from samples collected daily over 21 days in culture. Microbial diversity (Inverse Simpson, a ), total number of OTUs ( b ), and evenness of OTU distribution (Simpson Evenness, c ) was calculated from OTUs (≥97 % average nucleotide identity (ANI)) that were randomly subsampled to 10,000 sequences over 100 iterations. The mean value for the replicate reactors as a function of time in culture is plotted (day 0 = fecal inoculum; error bars represent standard deviation of the mean)
Figure Legend Snippet: Impact of MBRA cultivation on microbial diversity. Microbial diversity of triplicate MBRA communities inoculated with one of three donor fecal samples (Donor A, blue circles ; Donor B, green circles ; Donor C, purple circles ) or in six replicate MBRA communities inoculated with an equal mass of all three donor fecal samples (Pool, black circles ) was determined by sequencing the V4 region of the 16S rRNA gene from samples collected daily over 21 days in culture. Microbial diversity (Inverse Simpson, a ), total number of OTUs ( b ), and evenness of OTU distribution (Simpson Evenness, c ) was calculated from OTUs (≥97 % average nucleotide identity (ANI)) that were randomly subsampled to 10,000 sequences over 100 iterations. The mean value for the replicate reactors as a function of time in culture is plotted (day 0 = fecal inoculum; error bars represent standard deviation of the mean)

Techniques Used: Sequencing, Standard Deviation

11) Product Images from "Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used"

Article Title: Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used

Journal: Heliyon

doi: 10.1016/j.heliyon.2016.e00170

Distribution size of amplicons obtained after virtual PCR of complete 16S rRNA gene (V1–V9). Amplicons with extreme sizes outside the range of mean ± 2 standard deviations were excluded.
Figure Legend Snippet: Distribution size of amplicons obtained after virtual PCR of complete 16S rRNA gene (V1–V9). Amplicons with extreme sizes outside the range of mean ± 2 standard deviations were excluded.

Techniques Used: Polymerase Chain Reaction

Classification output obtained with the internal fractions (V3–V4, V4–V5, V3–V5) respect to the complete 16S rRNA gene sequences (V1–V9). Proportion of sequences with same classification results using either the complete sequence or the internal fragment sequence are labeled as “Equal”; whereas sequences of internal fractions with similar classification but to more superficial level are represented as “Less”, and sequences with different taxonomic classification compared to the respective complete sequence (V1–V9) are named as “Low”.
Figure Legend Snippet: Classification output obtained with the internal fractions (V3–V4, V4–V5, V3–V5) respect to the complete 16S rRNA gene sequences (V1–V9). Proportion of sequences with same classification results using either the complete sequence or the internal fragment sequence are labeled as “Equal”; whereas sequences of internal fractions with similar classification but to more superficial level are represented as “Less”, and sequences with different taxonomic classification compared to the respective complete sequence (V1–V9) are named as “Low”.

Techniques Used: Sequencing, Labeling

12) Product Images from "Evaluating the Capacity of Human Gut Microorganisms to Colonize the Zebrafish Larvae (Danio rerio)"

Article Title: Evaluating the Capacity of Human Gut Microorganisms to Colonize the Zebrafish Larvae (Danio rerio)

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.01032

Composition of the bacterial microbiota of samples through 16S rRNA sequencing by MiSeq. Relative abundance of (A) phyla, (B) families (legend shows families with relative abundance greater than 1%), and (C) genera (legend shows genera with relative abundance greater than 5%). The complete description of the family and genus legends is given in the Supplementary Material (Figures S2A,B ). Samples analyzed were fecal sample, inoculum of the fecal sample, > 1,000 colonies recovered on NN and M2GSC media, inoculated larvae with fecal inoculum (in duplicate: inoculated larvae 1 and 2), and non-inoculated control larvae. (D) Principal Coordinate Analysis (PCoA) scores plot based on the relative abundance of OTUs (97% similarity level). Each colored symbol represents a sample. Blue circles grouped similar samples based on their bacterial composition. Inoculated larvae corresponded to 3 dpf larvae after 2.5 h of been inoculated with the human gut inoculum. The persistence of these transplanted human fecal microorganisms was evaluated in larvae from 4 to 7 dpf through direct sequencing of the 16S rRNA gene by MiSeq, however it was not possible to amplify bacterial DNA from these samples and persistence were checked by culture (Table 1 ). (E) Human gut microbiota transplanted to 3 dpf zebrafish larvae (the names of the transplanted species are detailed in the right side of the Venn diagram; Table S13 ). Tables S12–S17 are detailed in Supplementary Material.
Figure Legend Snippet: Composition of the bacterial microbiota of samples through 16S rRNA sequencing by MiSeq. Relative abundance of (A) phyla, (B) families (legend shows families with relative abundance greater than 1%), and (C) genera (legend shows genera with relative abundance greater than 5%). The complete description of the family and genus legends is given in the Supplementary Material (Figures S2A,B ). Samples analyzed were fecal sample, inoculum of the fecal sample, > 1,000 colonies recovered on NN and M2GSC media, inoculated larvae with fecal inoculum (in duplicate: inoculated larvae 1 and 2), and non-inoculated control larvae. (D) Principal Coordinate Analysis (PCoA) scores plot based on the relative abundance of OTUs (97% similarity level). Each colored symbol represents a sample. Blue circles grouped similar samples based on their bacterial composition. Inoculated larvae corresponded to 3 dpf larvae after 2.5 h of been inoculated with the human gut inoculum. The persistence of these transplanted human fecal microorganisms was evaluated in larvae from 4 to 7 dpf through direct sequencing of the 16S rRNA gene by MiSeq, however it was not possible to amplify bacterial DNA from these samples and persistence were checked by culture (Table 1 ). (E) Human gut microbiota transplanted to 3 dpf zebrafish larvae (the names of the transplanted species are detailed in the right side of the Venn diagram; Table S13 ). Tables S12–S17 are detailed in Supplementary Material.

Techniques Used: Sequencing

13) Product Images from "The Host Shapes the Gut Microbiota via Fecal microRNA"

Article Title: The Host Shapes the Gut Microbiota via Fecal microRNA

Journal: Cell host & microbe

doi: 10.1016/j.chom.2015.12.005

Host miRNA Enters Bacteria and Specifically Regulates Bacterial Gene Transcripts (A-D) E. coli ). (E) Fn was cultured in the presence of 1.25 μM Cy3-labeled (red) hsa-miR-515-5p, scrambled hsa-miR-515-5p control or hsa-miR-1226-5p for 0, 5 min, 6 hrs and 12 hrs and terminated on ice, washed once with cold PBS and fixed with 2% PFA; followed by flow cytometry detection of Cy3 in the bacteria. The percentage of Cy3-miR positive Fn is shown. Representative of 2 experiments. (F) E. coli GFP was cultured in the presence of 2 μM Cy3-labeled (red) hsa-miR-1226-5p, scrambled hsa-miR-1226-5p control or hsa-miR-515-5p for 0, 5 min, 2 hrs and 4 hrs and terminated on ice, washed once with cold PBS and fixed with 2% PFA; followed by flow cytometry detection of Cy3 in the GFP+ E. coli . The percentage of Cy3-miR positive E. coli is shown. Representative of 2 experiments. (G) Fn was cultured in the presence of vehicle, 1.25 μM scrambled hsa-miR-515-5p control, hsa-miR-515-5p, mutated hsa-miR-515-5p, or hsa-miR-1226-5p for 16 hours. RNA was isolated and the ratio of Fn 16S rRNA/ 23S rRNA transcript level of was quantified by qPCR. (H) E. coli was cultured in the presence of vehicle, 1.25 μM scrambled hsa-miR-1226-5p control, hsa-miR-1226-5p, mutated hsa-miR-1226-5p, or hsa-miR-515-5p for 4 hours. RNA was isolated and transcript levels of E. coli yegH were quantified by qPCR. (G-H) Values are mean ± SEM, One-way ANOVA followed by Dunnett's multiple comparison tests. *p
Figure Legend Snippet: Host miRNA Enters Bacteria and Specifically Regulates Bacterial Gene Transcripts (A-D) E. coli ). (E) Fn was cultured in the presence of 1.25 μM Cy3-labeled (red) hsa-miR-515-5p, scrambled hsa-miR-515-5p control or hsa-miR-1226-5p for 0, 5 min, 6 hrs and 12 hrs and terminated on ice, washed once with cold PBS and fixed with 2% PFA; followed by flow cytometry detection of Cy3 in the bacteria. The percentage of Cy3-miR positive Fn is shown. Representative of 2 experiments. (F) E. coli GFP was cultured in the presence of 2 μM Cy3-labeled (red) hsa-miR-1226-5p, scrambled hsa-miR-1226-5p control or hsa-miR-515-5p for 0, 5 min, 2 hrs and 4 hrs and terminated on ice, washed once with cold PBS and fixed with 2% PFA; followed by flow cytometry detection of Cy3 in the GFP+ E. coli . The percentage of Cy3-miR positive E. coli is shown. Representative of 2 experiments. (G) Fn was cultured in the presence of vehicle, 1.25 μM scrambled hsa-miR-515-5p control, hsa-miR-515-5p, mutated hsa-miR-515-5p, or hsa-miR-1226-5p for 16 hours. RNA was isolated and the ratio of Fn 16S rRNA/ 23S rRNA transcript level of was quantified by qPCR. (H) E. coli was cultured in the presence of vehicle, 1.25 μM scrambled hsa-miR-1226-5p control, hsa-miR-1226-5p, mutated hsa-miR-1226-5p, or hsa-miR-515-5p for 4 hours. RNA was isolated and transcript levels of E. coli yegH were quantified by qPCR. (G-H) Values are mean ± SEM, One-way ANOVA followed by Dunnett's multiple comparison tests. *p

Techniques Used: Cell Culture, Labeling, Flow Cytometry, Cytometry, Isolation, Real-time Polymerase Chain Reaction

Host miRNA Directly Affects the Growth of Gut Bacteria ), (A) Fn was grown in media with 1.25 μM miRNA mimics hsa-miR-515-5p, mutated hsa-miR-515-5p, scrambled control and hsa-miR-1226-5p. Growth was monitored as absorbance at 600 nm (OD 600 for additional growth curves. (B) E. coli was grown in media with 2 μM miRNA mimics hsa-miR-1226-5p, mutated hsa-miR-1226-5p, scrambled control and hsa-miR-515-5p. Growth was monitored as absorbance at 600 nm (OD 600 for additional growth curves. Upper panels show target site sequence alignment of hsa-miR-515-5p and mutant (mutant site highlighted) vs Fn 16S rRNA (A) and hsa-miR-1226-5p and mutant vs E. coli .
Figure Legend Snippet: Host miRNA Directly Affects the Growth of Gut Bacteria ), (A) Fn was grown in media with 1.25 μM miRNA mimics hsa-miR-515-5p, mutated hsa-miR-515-5p, scrambled control and hsa-miR-1226-5p. Growth was monitored as absorbance at 600 nm (OD 600 for additional growth curves. (B) E. coli was grown in media with 2 μM miRNA mimics hsa-miR-1226-5p, mutated hsa-miR-1226-5p, scrambled control and hsa-miR-515-5p. Growth was monitored as absorbance at 600 nm (OD 600 for additional growth curves. Upper panels show target site sequence alignment of hsa-miR-515-5p and mutant (mutant site highlighted) vs Fn 16S rRNA (A) and hsa-miR-1226-5p and mutant vs E. coli .

Techniques Used: Sequencing, Mutagenesis

14) Product Images from "Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake"

Article Title: Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.00478-16

Principle-coordinate analysis (PCoA) of weighted UniFrac distances of 16S rRNA genes associated with eukaryote SAGs of Isochrysis sp. MDV (+), Chlamydomonas sp. ICE-MDV (♢), Pteridomonas (□), and Pirsonia (○). Each data point represents
Figure Legend Snippet: Principle-coordinate analysis (PCoA) of weighted UniFrac distances of 16S rRNA genes associated with eukaryote SAGs of Isochrysis sp. MDV (+), Chlamydomonas sp. ICE-MDV (♢), Pteridomonas (□), and Pirsonia (○). Each data point represents

Techniques Used:

Evidence of parasite-host interactions among Lake Bonney microbial eukaryotes. (a) Chart showing the diversity of 16S rRNA gene OTUs recovered from Pirsonia eukaryote SAGs ( n = 22). (b and c) SEM images showing the sizes of Pirsonia and Chlamydomonas
Figure Legend Snippet: Evidence of parasite-host interactions among Lake Bonney microbial eukaryotes. (a) Chart showing the diversity of 16S rRNA gene OTUs recovered from Pirsonia eukaryote SAGs ( n = 22). (b and c) SEM images showing the sizes of Pirsonia and Chlamydomonas

Techniques Used:

SEM images and the diversity of microbial partners associated with the heterotrophic nanoflagellate Pteridomonas ( n = 22). (a) Chart showing the diversity of 16S rRNA gene OTUs recovered from Pteridomonas eukaryote SAGs. (b to d) SEM images of Pteridomonas
Figure Legend Snippet: SEM images and the diversity of microbial partners associated with the heterotrophic nanoflagellate Pteridomonas ( n = 22). (a) Chart showing the diversity of 16S rRNA gene OTUs recovered from Pteridomonas eukaryote SAGs. (b to d) SEM images of Pteridomonas

Techniques Used:

15) Product Images from "Detection of Orientia sp. DNA in rodents from Asia, West Africa and Europe"

Article Title: Detection of Orientia sp. DNA in rodents from Asia, West Africa and Europe

Journal: Parasites & Vectors

doi: 10.1186/s13071-015-0784-7

Phylogenetic tree based on the V4 region of the 16S rRNA gene. GenBank accession numbers are indicated. Only different haplotypes were shown. A complete list of sequences uploaded to GenBank can be provided upon request. Numbers beside branches indicate bootstrap values ( > 80). O: Orientia ; R: Rickettsia ; N: Neorickettsia ; A: Anaplasma . The tree was rooted with the phylogenetically closest genus Anaplasma and Neorickettsia . Scale bar indicates evolutionary distances. Samples sequenced in the present study are marked with _*.
Figure Legend Snippet: Phylogenetic tree based on the V4 region of the 16S rRNA gene. GenBank accession numbers are indicated. Only different haplotypes were shown. A complete list of sequences uploaded to GenBank can be provided upon request. Numbers beside branches indicate bootstrap values ( > 80). O: Orientia ; R: Rickettsia ; N: Neorickettsia ; A: Anaplasma . The tree was rooted with the phylogenetically closest genus Anaplasma and Neorickettsia . Scale bar indicates evolutionary distances. Samples sequenced in the present study are marked with _*.

Techniques Used:

16) Product Images from "Ureolytic Prokaryotes in Soil: Community Abundance and Diversity"

Article Title: Ureolytic Prokaryotes in Soil: Community Abundance and Diversity

Journal: Microbes and Environments

doi: 10.1264/jsme2.ME17188

Urea degradation rates (circles) and abundance of the ur e C gene (white bars) and 16S rRNA gene (grey bars). The abundance of the genes was shown as mean values of triplicate qPCR assays.
Figure Legend Snippet: Urea degradation rates (circles) and abundance of the ur e C gene (white bars) and 16S rRNA gene (grey bars). The abundance of the genes was shown as mean values of triplicate qPCR assays.

Techniques Used: Real-time Polymerase Chain Reaction

17) Product Images from "Estrogen Degraders and Estrogen Degradation Pathway Identified in an Activated Sludge"

Article Title: Estrogen Degraders and Estrogen Degradation Pathway Identified in an Activated Sludge

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.00001-18

Real-time quantitative PCR indicated temporal changes in the 16S rRNA gene copies of the Novosphingobium sp. strain SLCC in E1-amended sludge treatments. Relative abundance of the strain SLCC 16S rRNA gene was calculated as a proportion of the total number of bacterial 16S rRNA gene copies. SLCC and Eub primer pairs were used to amplify the 16S rRNA gene of strain SLCC and total eubacterial population, respectively. Data are shown as the mean ± standard deviation (SD) of three experimental measurements. Standard curves of real-time quantitative PCR are shown in Fig. S4.
Figure Legend Snippet: Real-time quantitative PCR indicated temporal changes in the 16S rRNA gene copies of the Novosphingobium sp. strain SLCC in E1-amended sludge treatments. Relative abundance of the strain SLCC 16S rRNA gene was calculated as a proportion of the total number of bacterial 16S rRNA gene copies. SLCC and Eub primer pairs were used to amplify the 16S rRNA gene of strain SLCC and total eubacterial population, respectively. Data are shown as the mean ± standard deviation (SD) of three experimental measurements. Standard curves of real-time quantitative PCR are shown in Fig. S4.

Techniques Used: Real-time Polymerase Chain Reaction, Standard Deviation

18) Product Images from "Structure of the gut microbiome following colonization with human feces determines colonic tumor burden"

Article Title: Structure of the gut microbiome following colonization with human feces determines colonic tumor burden

Journal: Microbiome

doi: 10.1186/2049-2618-2-20

Experimental design. Germ-free mice were inoculated by oral gavage with one of six human inocula. Twenty-one days later (day 0), they received a single intraperitoneal injection of AOM (10 mg/kg). Mice were subsequently administered three five-day rounds of 2% DSS in the drinking water, with 16 days of rest in between. Mice were euthanized 73 days after the AOM injection for enumeration of colonic tumors. The inocula and samples collected on day 0 and day 73 were used for 16S rRNA gene sequencing. AOM, azoxymethane; DSS, dextran sulfate sodium.
Figure Legend Snippet: Experimental design. Germ-free mice were inoculated by oral gavage with one of six human inocula. Twenty-one days later (day 0), they received a single intraperitoneal injection of AOM (10 mg/kg). Mice were subsequently administered three five-day rounds of 2% DSS in the drinking water, with 16 days of rest in between. Mice were euthanized 73 days after the AOM injection for enumeration of colonic tumors. The inocula and samples collected on day 0 and day 73 were used for 16S rRNA gene sequencing. AOM, azoxymethane; DSS, dextran sulfate sodium.

Techniques Used: Mouse Assay, Injection, Sequencing

19) Product Images from "Effect of Oral Administration of Metronidazole or Prednisolone on Fecal Microbiota in Dogs"

Article Title: Effect of Oral Administration of Metronidazole or Prednisolone on Fecal Microbiota in Dogs

Journal: PLoS ONE

doi: 10.1371/journal.pone.0107909

Rarefraction analysis of V4 16S rRNA gene sequences obtained from fecal samples. Results from dogs administered metronidazole (A) and prednisolone (B). Lines represent the average of each time point and the error bars represent standard deviations. This analysis was performed using a randomly selected subset of 9,915 (A) or 8,153 (B) sequences per sample. Operational Taxonomical Units (OTUs) in this analysis were defined by 97–100% similarity.
Figure Legend Snippet: Rarefraction analysis of V4 16S rRNA gene sequences obtained from fecal samples. Results from dogs administered metronidazole (A) and prednisolone (B). Lines represent the average of each time point and the error bars represent standard deviations. This analysis was performed using a randomly selected subset of 9,915 (A) or 8,153 (B) sequences per sample. Operational Taxonomical Units (OTUs) in this analysis were defined by 97–100% similarity.

Techniques Used:

Principal coordinates analysis (PCoA) of V4 16S rRNA genes from canine fecal samples. Figures were calculated using unweighted UniFrac distances. (A) Result of dogs administered metronidazole. Metronidazole-affected samples (blue, day 14) were separated from the other samples, primarily along PCoA axis 1 (accounting for 33.94% of all variability among samples). (B) Result of dogs administered prednisolone. Prednisolone administration did not induce alteration of bacterial composition.
Figure Legend Snippet: Principal coordinates analysis (PCoA) of V4 16S rRNA genes from canine fecal samples. Figures were calculated using unweighted UniFrac distances. (A) Result of dogs administered metronidazole. Metronidazole-affected samples (blue, day 14) were separated from the other samples, primarily along PCoA axis 1 (accounting for 33.94% of all variability among samples). (B) Result of dogs administered prednisolone. Prednisolone administration did not induce alteration of bacterial composition.

Techniques Used:

20) Product Images from "Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages"

Article Title: Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages

Journal: PLoS ONE

doi: 10.1371/journal.pone.0187461

Summary graph of bacterial OTUs found in Colobopsis riehlii , Camponotus floridanus and Camponotus planatus colonies with 16S rRNA amplicon sequencing. A. Different colonies and species used in this study and their bacterial communities. B. Summary of all OTUs found in Colobopsis riehlii . The main bacterium is Enterobacteriaceae in pink, followed by Wolbachia in brown C. Summary of all OTUs found in Ca . floridanus and Ca . planatus . The main bacterium is Candidatus Blochmannia in green. The yellow stars highlight samples that were excluded after the read depth standardization of 400 reads was implemented.
Figure Legend Snippet: Summary graph of bacterial OTUs found in Colobopsis riehlii , Camponotus floridanus and Camponotus planatus colonies with 16S rRNA amplicon sequencing. A. Different colonies and species used in this study and their bacterial communities. B. Summary of all OTUs found in Colobopsis riehlii . The main bacterium is Enterobacteriaceae in pink, followed by Wolbachia in brown C. Summary of all OTUs found in Ca . floridanus and Ca . planatus . The main bacterium is Candidatus Blochmannia in green. The yellow stars highlight samples that were excluded after the read depth standardization of 400 reads was implemented.

Techniques Used: Amplification, Sequencing

Phylogenetic tree of the main OTUs, their closest relatives, and Blochmannia from Camponotini genera sequences available in GenBank. The maximum likelihood phylogeny of the 16S rRNA region of the main bacterial symbionts of this study along with the closests matches on GenBank. Bootstrap support is shown on branches. The labels are given with GenBank accession number (GenBank sequences) or collection code (sequences generated in the present study—colored in red). The branch color refers to bacteria with Wolbachia in brown and Blochmannia in green.
Figure Legend Snippet: Phylogenetic tree of the main OTUs, their closest relatives, and Blochmannia from Camponotini genera sequences available in GenBank. The maximum likelihood phylogeny of the 16S rRNA region of the main bacterial symbionts of this study along with the closests matches on GenBank. Bootstrap support is shown on branches. The labels are given with GenBank accession number (GenBank sequences) or collection code (sequences generated in the present study—colored in red). The branch color refers to bacteria with Wolbachia in brown and Blochmannia in green.

Techniques Used: Generated

21) Product Images from "Bacteria Associated With a Commercial Mycorrhizal Inoculum: Community Composition and Multifunctional Activity as Assessed by Illumina Sequencing and Culture-Dependent Tools"

Article Title: Bacteria Associated With a Commercial Mycorrhizal Inoculum: Community Composition and Multifunctional Activity as Assessed by Illumina Sequencing and Culture-Dependent Tools

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2018.01956

Affiliation of the sequences of the 14 bacterial strains showing the best PGP traits with the existing 16S rRNA gene sequences. Phylogenetic analysis was inferred by using the Neighbor-Joining method. The evolutionary distances were computed using the Tamura 3-parameter method. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1). Bootstrap (1,000 replicates) values below 70 are not shown. Evolutionary analyses were conducted in MEGA10.
Figure Legend Snippet: Affiliation of the sequences of the 14 bacterial strains showing the best PGP traits with the existing 16S rRNA gene sequences. Phylogenetic analysis was inferred by using the Neighbor-Joining method. The evolutionary distances were computed using the Tamura 3-parameter method. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1). Bootstrap (1,000 replicates) values below 70 are not shown. Evolutionary analyses were conducted in MEGA10.

Techniques Used:

22) Product Images from "Faecal and mucosal microbiota in patients with functional gastrointestinal disorders: Correlation with toll-like receptor 2/toll-like receptor 4 expression"

Article Title: Faecal and mucosal microbiota in patients with functional gastrointestinal disorders: Correlation with toll-like receptor 2/toll-like receptor 4 expression

Journal: World Journal of Gastroenterology

doi: 10.3748/wjg.v23.i36.6665

16S rRNA gene surveys reveal a clear separation between luminal microbiota and mucosa-associated microbiota. A: Dendrogram obtained from the complete linkage hierarchical clustering of the stool and mucosa samples based on the total operational taxonomic units; B: Principal coordinate analysis plot based on the weighted UniFrac metric.
Figure Legend Snippet: 16S rRNA gene surveys reveal a clear separation between luminal microbiota and mucosa-associated microbiota. A: Dendrogram obtained from the complete linkage hierarchical clustering of the stool and mucosa samples based on the total operational taxonomic units; B: Principal coordinate analysis plot based on the weighted UniFrac metric.

Techniques Used:

23) Product Images from "The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms"

Article Title: The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.01692-15

Ordination plots of bacterial community structures as determined by nonmetric multidimensional scaling (nMDS) of PCR-Illumina profiles of 16S rRNA gene fragments in the BAC filters at SPRWS. (A) Bacterial community dynamics in filter 3. (B) Bacterial community dynamics in filter 6. (C) Bacterial community dynamics in filter 13. (D) Comparison of bacterial community structures in different filters on 1 July 2011; different filters are represented by a number. ●, 15 March 2011; ■, 31 May 2011; ▲, 1 July 2011; ◆, 11 August 2011; ○, 22 November 2011; □, 15 December 2011; △, 14 February 2012. The data are shown as the arithmetic means of triplicate profiles (±1 standard deviation).
Figure Legend Snippet: Ordination plots of bacterial community structures as determined by nonmetric multidimensional scaling (nMDS) of PCR-Illumina profiles of 16S rRNA gene fragments in the BAC filters at SPRWS. (A) Bacterial community dynamics in filter 3. (B) Bacterial community dynamics in filter 6. (C) Bacterial community dynamics in filter 13. (D) Comparison of bacterial community structures in different filters on 1 July 2011; different filters are represented by a number. ●, 15 March 2011; ■, 31 May 2011; ▲, 1 July 2011; ◆, 11 August 2011; ○, 22 November 2011; □, 15 December 2011; △, 14 February 2012. The data are shown as the arithmetic means of triplicate profiles (±1 standard deviation).

Techniques Used: Polymerase Chain Reaction, BAC Assay, Standard Deviation

Comparison of the relative quantities of ammonia-oxidizing and nitrite-oxidizing bacteria in three SPRWS BAC filters. The values for AOB (Illumina) and NOB (Illumina) represent the fractions of known AOB and Nitrospira sequences, respectively, found in an Illumina profile divided by the total number of sequences in that profile. The amoA /16S rRNA represents the ratio of amoA to 16S rRNA genes as measured by quantitative real-time PCR (see Data Sets S2 to S4 in the supplemental material).
Figure Legend Snippet: Comparison of the relative quantities of ammonia-oxidizing and nitrite-oxidizing bacteria in three SPRWS BAC filters. The values for AOB (Illumina) and NOB (Illumina) represent the fractions of known AOB and Nitrospira sequences, respectively, found in an Illumina profile divided by the total number of sequences in that profile. The amoA /16S rRNA represents the ratio of amoA to 16S rRNA genes as measured by quantitative real-time PCR (see Data Sets S2 to S4 in the supplemental material).

Techniques Used: BAC Assay, Real-time Polymerase Chain Reaction

24) Product Images from "How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis"

Article Title: How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms19103256

Comparison of median levels of ( a ) DNA extraction yield, ( b ) coefficient of variation between replicates, ( c ) 16s rRNA gene real-time PCR results, and ( d ) coefficient of variation between replicates across dithiothreitol (DTT)-untreated sputum vs. DTT-treated (Experiment 1).
Figure Legend Snippet: Comparison of median levels of ( a ) DNA extraction yield, ( b ) coefficient of variation between replicates, ( c ) 16s rRNA gene real-time PCR results, and ( d ) coefficient of variation between replicates across dithiothreitol (DTT)-untreated sputum vs. DTT-treated (Experiment 1).

Techniques Used: DNA Extraction, Real-time Polymerase Chain Reaction

25) Product Images from "Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation"

Article Title: Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation

Journal: Scientific Reports

doi: 10.1038/s41598-017-08732-1

Stability of the microbial functional potential prior to the development of colitis. Microbial genes were inferred by PICRUSt from 16S rRNA gene sequences and assigned to functional pathways as organized in KEGG database. Principal Coordinate Analysis (PCoA) plot of Bray-Curtis distance comparing microbial functional profiles between mdr1a −/− and WT littermates at 6 and 18 weeks showed clustering of samples according to sampling location (i.e. mucus and stools). Bray-Curtis distances were calculated based on KEGG pathway abundance values. WT mice are shown in circles and knockout (KO) mice in triangles; open symbols correspond to 6 weeks whereas filled ones to 18 weeks. Mucus is depicted in blue and stools in red.
Figure Legend Snippet: Stability of the microbial functional potential prior to the development of colitis. Microbial genes were inferred by PICRUSt from 16S rRNA gene sequences and assigned to functional pathways as organized in KEGG database. Principal Coordinate Analysis (PCoA) plot of Bray-Curtis distance comparing microbial functional profiles between mdr1a −/− and WT littermates at 6 and 18 weeks showed clustering of samples according to sampling location (i.e. mucus and stools). Bray-Curtis distances were calculated based on KEGG pathway abundance values. WT mice are shown in circles and knockout (KO) mice in triangles; open symbols correspond to 6 weeks whereas filled ones to 18 weeks. Mucus is depicted in blue and stools in red.

Techniques Used: Functional Assay, Sampling, Mouse Assay, Knock-Out

26) Product Images from "A non-endoscopic device to sample the oesophageal microbiota: a case-control study"

Article Title: A non-endoscopic device to sample the oesophageal microbiota: a case-control study

Journal: The Lancet. Gastroenterology & Hepatology

doi: 10.1016/S2468-1253(16)30086-3

Microbial alpha diversity in oesophageal adenocarcinoma (A) Observed richness of bacterial operational taxonomic units (OTUs). (B) The Chao estimate of total OTU richness and (C) the Shannon diversity index are shown for tissue samples from healthy control patients (n=16), patients with Barrett's oesophagus (n=17), and patients with oesophageal adenocarcinoma (n=15). Statistical significance was calculated with the Kruskal-Wallis test and Dunns multiple comparisons post test. Data were subsampled at 631 reads per sample. (D) Observed richness of bacterial OTUs for paired normal squamous and tumour tissue samples from 13 patients (26 samples), Wilcoxon signed rank test. Data were subsampled at 656 reads per sample. (E) Overall bacterial abundance using 16S rRNA gene qPCR in matched tumour and normal squamous tissue from 16 patients (32 samples), Wilcoxon signed rank test. Error bars represent standard deviation. *p
Figure Legend Snippet: Microbial alpha diversity in oesophageal adenocarcinoma (A) Observed richness of bacterial operational taxonomic units (OTUs). (B) The Chao estimate of total OTU richness and (C) the Shannon diversity index are shown for tissue samples from healthy control patients (n=16), patients with Barrett's oesophagus (n=17), and patients with oesophageal adenocarcinoma (n=15). Statistical significance was calculated with the Kruskal-Wallis test and Dunns multiple comparisons post test. Data were subsampled at 631 reads per sample. (D) Observed richness of bacterial OTUs for paired normal squamous and tumour tissue samples from 13 patients (26 samples), Wilcoxon signed rank test. Data were subsampled at 656 reads per sample. (E) Overall bacterial abundance using 16S rRNA gene qPCR in matched tumour and normal squamous tissue from 16 patients (32 samples), Wilcoxon signed rank test. Error bars represent standard deviation. *p

Techniques Used: Real-time Polymerase Chain Reaction, Standard Deviation

Comparison of different methods to sample the oesophageal microbiota (A) Principal coordinate analysis with the Bray-Curtis algorithm for matched endoscopic biopsies, brushes, and Cytosponge samples (31 patients) and 13 throat swabs from a subset of these patients. The first axis (PC1) accounts for 19·6% of the sample variance and the second axis (PC2) accounts for 6·3% of the variance. Data were subsampled at 631 reads per sample. (B) Overall bacterial abundance using 16S rRNA gene-based quantitative PCR in matched endoscopic biopsies, brushes, and Cytosponge samples (20 patients), Friedman test and Dunns multiple comparisons post test. (C) The observed diversity of bacterial operational taxonomic units (OTUs), (D) the Chao estimate of total OTU richness, and (E) the Shannon diversity index for matched endoscopic biopsies, brushes, and Cytosponge samples (31 patients), Friedman test and Dunns multiple comparisons post test. Data were subsampled at 631 reads per sample. *p
Figure Legend Snippet: Comparison of different methods to sample the oesophageal microbiota (A) Principal coordinate analysis with the Bray-Curtis algorithm for matched endoscopic biopsies, brushes, and Cytosponge samples (31 patients) and 13 throat swabs from a subset of these patients. The first axis (PC1) accounts for 19·6% of the sample variance and the second axis (PC2) accounts for 6·3% of the variance. Data were subsampled at 631 reads per sample. (B) Overall bacterial abundance using 16S rRNA gene-based quantitative PCR in matched endoscopic biopsies, brushes, and Cytosponge samples (20 patients), Friedman test and Dunns multiple comparisons post test. (C) The observed diversity of bacterial operational taxonomic units (OTUs), (D) the Chao estimate of total OTU richness, and (E) the Shannon diversity index for matched endoscopic biopsies, brushes, and Cytosponge samples (31 patients), Friedman test and Dunns multiple comparisons post test. Data were subsampled at 631 reads per sample. *p

Techniques Used: Real-time Polymerase Chain Reaction

27) Product Images from "A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship"

Article Title: A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02246

16S rRNA Fluorescence in situ hybridization of Oncholaimus dyvae . (A) Whole male O. dyvae . (B–E) Long thin Epsilonproteobacteria throughout the intestine of the host. The position of each image on the whole specimen is shown by a numbered star. In blue, DAPI-stained host nuclei; in orange, Epsilonproteobacteria hybridized with a Cy3-labeled probe. b = bacteria, c = cuticle, e = esophagus, h = head, i = intestine, s = spicules.
Figure Legend Snippet: 16S rRNA Fluorescence in situ hybridization of Oncholaimus dyvae . (A) Whole male O. dyvae . (B–E) Long thin Epsilonproteobacteria throughout the intestine of the host. The position of each image on the whole specimen is shown by a numbered star. In blue, DAPI-stained host nuclei; in orange, Epsilonproteobacteria hybridized with a Cy3-labeled probe. b = bacteria, c = cuticle, e = esophagus, h = head, i = intestine, s = spicules.

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

28) Product Images from "Microbiota alteration is associated with the development of stress-induced despair behavior"

Article Title: Microbiota alteration is associated with the development of stress-induced despair behavior

Journal: Scientific Reports

doi: 10.1038/srep43859

Lactobacillus levels correlate with depressive behavior. ( a ) Lactobacillus quantification in fecal samples by qRT-PCR, relative to 16S rRNA (n = 10 naïve and 11 stressed; representative of 3 independent experiments; two-tailed t-test with Welch’s correction, ***p
Figure Legend Snippet: Lactobacillus levels correlate with depressive behavior. ( a ) Lactobacillus quantification in fecal samples by qRT-PCR, relative to 16S rRNA (n = 10 naïve and 11 stressed; representative of 3 independent experiments; two-tailed t-test with Welch’s correction, ***p

Techniques Used: Quantitative RT-PCR, Two Tailed Test

Treatment with probiotic L. reuteri ameliorates the escape behavior induced by chronic stress. ( a ) Experimental design of L. reuteri supplementation regimen. ( b ) qRT-PCR quantification of Lactobacillus levels in fecal samples of L. reuteri or broth-control treated mice, relative to 16S rRNA (n = 5; representative of 2 independent experiments; two-tailed t-test, *p
Figure Legend Snippet: Treatment with probiotic L. reuteri ameliorates the escape behavior induced by chronic stress. ( a ) Experimental design of L. reuteri supplementation regimen. ( b ) qRT-PCR quantification of Lactobacillus levels in fecal samples of L. reuteri or broth-control treated mice, relative to 16S rRNA (n = 5; representative of 2 independent experiments; two-tailed t-test, *p

Techniques Used: Quantitative RT-PCR, Mouse Assay, Two Tailed Test

29) Product Images from "Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life"

Article Title: Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life

Journal: BMC Veterinary Research

doi: 10.1186/s12917-017-1064-x

Rarefication analysis (number of observed species) of the 16S rRNA gene sequences obtained from foal fecal samples, T1: 1–14 days of age, T2: 15–28 days of age. Each line represents the average of a group: healthy foals ( n = 11) and foals with diarrhea ( n = 4 at T1 and n = 3 each at T2). The analysis was performed on a selected subset of 17,800 sequences (lowest sequence number of all samples)
Figure Legend Snippet: Rarefication analysis (number of observed species) of the 16S rRNA gene sequences obtained from foal fecal samples, T1: 1–14 days of age, T2: 15–28 days of age. Each line represents the average of a group: healthy foals ( n = 11) and foals with diarrhea ( n = 4 at T1 and n = 3 each at T2). The analysis was performed on a selected subset of 17,800 sequences (lowest sequence number of all samples)

Techniques Used: Sequencing

30) Product Images from "Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples"

Article Title: Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples

Journal: Scientific Reports

doi: 10.1038/s41598-018-22408-4

For each taxa at the family level present in at least 25% of samples, p-values for a null hypothesis of no difference by stool vs. swab vs. by participant. Red symbols are taxa that have a p-value that is significant at a 10% false discovery rate. Taxa higher in swab than stool have a negative x coordinate and taxa higher in stool than swab have a positive x-coordinate. Data was generated using closed-reference OTUs classified at the family level using 16S rRNA gene sequence reads.
Figure Legend Snippet: For each taxa at the family level present in at least 25% of samples, p-values for a null hypothesis of no difference by stool vs. swab vs. by participant. Red symbols are taxa that have a p-value that is significant at a 10% false discovery rate. Taxa higher in swab than stool have a negative x coordinate and taxa higher in stool than swab have a positive x-coordinate. Data was generated using closed-reference OTUs classified at the family level using 16S rRNA gene sequence reads.

Techniques Used: Generated, Sequencing

Multidimensional scaling (MDS) of closed-reference OTUs classified at the family level using 16S rRNA gene sequence reads. There are four samples (two each of stool and swab) from each of the 60 participants in our study colored by sample origin (red is stool and blue is swab). Repeated samples collected from individuals were collected with an average separation of 3 months. The distinct separation of colors shows that there is separation by sample type in MDS axis 1 and MDS axis 2 ( a , c ) but not in MDS axes 3 and 4 ( b ). However, MDS axis 4 shows strong clustering by participant ( d ).
Figure Legend Snippet: Multidimensional scaling (MDS) of closed-reference OTUs classified at the family level using 16S rRNA gene sequence reads. There are four samples (two each of stool and swab) from each of the 60 participants in our study colored by sample origin (red is stool and blue is swab). Repeated samples collected from individuals were collected with an average separation of 3 months. The distinct separation of colors shows that there is separation by sample type in MDS axis 1 and MDS axis 2 ( a , c ) but not in MDS axes 3 and 4 ( b ). However, MDS axis 4 shows strong clustering by participant ( d ).

Techniques Used: Sequencing

31) Product Images from "DADA2: High resolution sample inference from Illumina amplicon data"

Article Title: DADA2: High resolution sample inference from Illumina amplicon data

Journal: Nature methods

doi: 10.1038/nmeth.3869

Lactobacillus crispatus sequence variants in the human vaginal community during pregnancy DADA2 identified six Lactobacillus crispatus 16S rRNA sequence variants present in multiple samples and a significant fraction of all reads (L1: 19.7%, L2: 11.1%, L3: 6.5%, L4: 3.1%, L5: 1.3%, L6: 0.4%). (a) The frequency of L1–L6 in each sample. Black bars at the bottom link samples from the same subject. The frequency of (b) L1 vs. L2, and (c) L1 vs. L3, by sample. The dashed line indicates a total frequency of 1.
Figure Legend Snippet: Lactobacillus crispatus sequence variants in the human vaginal community during pregnancy DADA2 identified six Lactobacillus crispatus 16S rRNA sequence variants present in multiple samples and a significant fraction of all reads (L1: 19.7%, L2: 11.1%, L3: 6.5%, L4: 3.1%, L5: 1.3%, L6: 0.4%). (a) The frequency of L1–L6 in each sample. Black bars at the bottom link samples from the same subject. The frequency of (b) L1 vs. L2, and (c) L1 vs. L3, by sample. The dashed line indicates a total frequency of 1.

Techniques Used: Sequencing

32) Product Images from "Influence of CO2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift)"

Article Title: Influence of CO2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift)

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02787

Lithological profile of the reference and mofette core (A) . The water content (B) , pH (C) , TOC (D) , conductivity (E) , sulfate concentration (F) , bacterial 16s rRNA gene copy number (G) , dsrB gene copy number (H) , mcrA gene copy number (I) , Shannon H index (J) and Shannon EH index (K) of reference (blue dots) and mofette (red squares) core.
Figure Legend Snippet: Lithological profile of the reference and mofette core (A) . The water content (B) , pH (C) , TOC (D) , conductivity (E) , sulfate concentration (F) , bacterial 16s rRNA gene copy number (G) , dsrB gene copy number (H) , mcrA gene copy number (I) , Shannon H index (J) and Shannon EH index (K) of reference (blue dots) and mofette (red squares) core.

Techniques Used: Concentration Assay

33) Product Images from "Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland"

Article Title: Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.00645-17

AOM with AQDS as electron acceptor by an enrichment derived from wetland sediment. (a) Kinetics of methane consumption linked to AQDS reduction (to AH 2 QDS) observed during the last 11 days of the entire enrichment process lasting 151 days: filled squares (■) represent microcosms with CH 4 as an electron donor and AQDS as an electron acceptor (complete experiments, n = 3), open squares (□) represent controls without an electron acceptor provided (without AQDS control, n = 3), filled circles (●) represent CH 4 -free microcosms (endogenous controls, n = 3), and crosses (×) represent heat-killed controls (sterile controls, n = 2). Error bars represent the standard error among replicates. (b and c) Microbial community changes at the end of the enrichment (151 days of incubation) at the phylum level based on Illumina sequencing of 16S rRNA V3 to V4 region. Fresh sediment composition was used as a reference.
Figure Legend Snippet: AOM with AQDS as electron acceptor by an enrichment derived from wetland sediment. (a) Kinetics of methane consumption linked to AQDS reduction (to AH 2 QDS) observed during the last 11 days of the entire enrichment process lasting 151 days: filled squares (■) represent microcosms with CH 4 as an electron donor and AQDS as an electron acceptor (complete experiments, n = 3), open squares (□) represent controls without an electron acceptor provided (without AQDS control, n = 3), filled circles (●) represent CH 4 -free microcosms (endogenous controls, n = 3), and crosses (×) represent heat-killed controls (sterile controls, n = 2). Error bars represent the standard error among replicates. (b and c) Microbial community changes at the end of the enrichment (151 days of incubation) at the phylum level based on Illumina sequencing of 16S rRNA V3 to V4 region. Fresh sediment composition was used as a reference.

Techniques Used: Derivative Assay, Incubation, Sequencing

34) Product Images from "An Expanded Genomic Representation of the Phylum Cyanobacteria"

Article Title: An Expanded Genomic Representation of the Phylum Cyanobacteria

Journal: Genome Biology and Evolution

doi: 10.1093/gbe/evu073

Phylogenetic trees of the phylum Cyanobacteria. ( a ) A maximum likelihood tree of the phylum Cyanobacteria based on the concatenated alignment of 83 phylogenetically conserved proteins ( supplementary table S2 , Supplementary Material online). Chloroflexi genomes were used as the outgroup ( supplementary table S3 , Supplementary Material online). Groups A–G for the Oxyphotobacteria were based on the names given by Shih et al . (2013) . Candidatus has been abbreviated to Ca. Bootstrap resampling analyses (100 times) with maximum likelihood (ML; using RAxML and FastTree), and maximum parsimony (MP; using PAUP*) methods were performed for different taxon configurations with 38 or 83 conserved proteins ( supplementary figs. S1–3 , Supplementary Material online), and the phylogenetic robustness (monophyly score) of taxa is indicated at the node: Black circles in the tree represent nodes with > 90% bootstrap supports by all calculations, white circles represent nodes with > 80% bootstrap supports by all calculations. Putative acquisitions of photosystem and flagella genes are indicated by colored arrows. Genomes in green are representatives from Di Rienzi et al. (2013) , and genomes in red are Melainabacteria from this study. ( b ) A maximum likelihood tree based on 16S rRNA genes from the class Melainabacteria obtained by Di Rienzi et al . (2013) and this study, together with public representatives from the Greengenes database version 13_05 and Silva 115 database. 16S sequences in green are Melainabacteria representatives from Di Rienzi et al. (2013) , the Melainabacteria in red are representatives from this study and the 16S from the cultured representative, V. chlorellavorus, is highlighted in blue. Node support values are as described for panel (a). Proposed order level designations within the class Melainabacteria are shown to the right of the figure. A third potential class-level lineage in the Cyanobacteria, ML635J-21 ( supplementary fig. S5 , Supplementary Material online) is not shown.
Figure Legend Snippet: Phylogenetic trees of the phylum Cyanobacteria. ( a ) A maximum likelihood tree of the phylum Cyanobacteria based on the concatenated alignment of 83 phylogenetically conserved proteins ( supplementary table S2 , Supplementary Material online). Chloroflexi genomes were used as the outgroup ( supplementary table S3 , Supplementary Material online). Groups A–G for the Oxyphotobacteria were based on the names given by Shih et al . (2013) . Candidatus has been abbreviated to Ca. Bootstrap resampling analyses (100 times) with maximum likelihood (ML; using RAxML and FastTree), and maximum parsimony (MP; using PAUP*) methods were performed for different taxon configurations with 38 or 83 conserved proteins ( supplementary figs. S1–3 , Supplementary Material online), and the phylogenetic robustness (monophyly score) of taxa is indicated at the node: Black circles in the tree represent nodes with > 90% bootstrap supports by all calculations, white circles represent nodes with > 80% bootstrap supports by all calculations. Putative acquisitions of photosystem and flagella genes are indicated by colored arrows. Genomes in green are representatives from Di Rienzi et al. (2013) , and genomes in red are Melainabacteria from this study. ( b ) A maximum likelihood tree based on 16S rRNA genes from the class Melainabacteria obtained by Di Rienzi et al . (2013) and this study, together with public representatives from the Greengenes database version 13_05 and Silva 115 database. 16S sequences in green are Melainabacteria representatives from Di Rienzi et al. (2013) , the Melainabacteria in red are representatives from this study and the 16S from the cultured representative, V. chlorellavorus, is highlighted in blue. Node support values are as described for panel (a). Proposed order level designations within the class Melainabacteria are shown to the right of the figure. A third potential class-level lineage in the Cyanobacteria, ML635J-21 ( supplementary fig. S5 , Supplementary Material online) is not shown.

Techniques Used: Cell Culture

35) Product Images from "Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing"

Article Title: Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

Journal: PLoS ONE

doi: 10.1371/journal.pone.0227434

Hamming distance from each ASV/OTU sequence to the closest other ASV/OTU sequence. Dashed line marks the Hamming distance = 7 threshold, corresponding to the 97% identity threshold for OTUs in V4 16S rRNA gene amplicons. Blue ellipses highlight ASVs that are only 1 Hamming distance away from each other.
Figure Legend Snippet: Hamming distance from each ASV/OTU sequence to the closest other ASV/OTU sequence. Dashed line marks the Hamming distance = 7 threshold, corresponding to the 97% identity threshold for OTUs in V4 16S rRNA gene amplicons. Blue ellipses highlight ASVs that are only 1 Hamming distance away from each other.

Techniques Used: Sequencing

36) Product Images from "The composition of the perinatal intestinal microbiota in horse"

Article Title: The composition of the perinatal intestinal microbiota in horse

Journal: Scientific Reports

doi: 10.1038/s41598-019-57003-8

Accepted and rejected 16S rRNA gene sequence reads per sample. Accepted reads are indicated as blue. Deleted reads are indicated as yellow-orange, with reads classified as Ralstonia in orange. Seven 0 h samples and two 24 h samples were excluded from further analysis due to low quality (red bars). Negative control data processed with the 0 h foal data is shown.
Figure Legend Snippet: Accepted and rejected 16S rRNA gene sequence reads per sample. Accepted reads are indicated as blue. Deleted reads are indicated as yellow-orange, with reads classified as Ralstonia in orange. Seven 0 h samples and two 24 h samples were excluded from further analysis due to low quality (red bars). Negative control data processed with the 0 h foal data is shown.

Techniques Used: Sequencing, Negative Control

16S rRNA gene copy numbers per sample. Blue colour indicates the negative controls and green the foal rectal samples. The boxes represent the interquartile ranges (IQR) containing 50% of samples. The horizontal line in a box indicates the median. Whiskers show maxima and minima within 1.5 × IQR. The circle indicates an outlier.
Figure Legend Snippet: 16S rRNA gene copy numbers per sample. Blue colour indicates the negative controls and green the foal rectal samples. The boxes represent the interquartile ranges (IQR) containing 50% of samples. The horizontal line in a box indicates the median. Whiskers show maxima and minima within 1.5 × IQR. The circle indicates an outlier.

Techniques Used:

37) Product Images from "Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk"

Article Title: Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk

Journal: Applied Microbiology and Biotechnology

doi: 10.1007/s00253-020-10493-3

In vitro colon model fermentations with L. gasseri LM19 and C. perfringens. a C. perfringens NCTC 3110 population measured by qPCR when inoculated alone (Cp) or co-inoculated with L. gasseri LM19 (Cp + Lg) in three different fermentations with faeces from donors 1, 2 and 3. b Expression of bacteriocin genes in vessels from all 4 treatments (control, L. gasseri LM19 alone, C. perfringens alone, L. gassieri LM19 with C. perfringens ) at 24 h in fermentations with faeces from donor 1: lane 1, negative control; lanes 2 and 10, bact_1 ; lanes 3 and 11, bact_2 ; lanes 4 and 12, gamA ; lanes 5 and 13, gamX ; lanes 6 and 14, helveticin J-like ; lanes 7 and 15, gyrA ; lanes 8 and 17, C. perfringens ; lanes 9 and 20, molecular marker; lanes 18 and 21, gamM ; lanes 19 and 22, gamY . c Microbial profiles obtained by 16S rRNA analysis showing relative abundance at the order level in the faecal batch model fermentation for the three donors (C, control, Lg, L. gasseri LM19 alone, Cp, C. perfringens alone, Lg + Cp, co-inoculation of L. gasseri LM19 and C. perfringens ). d Production of SCFA in batch model faecal fermentations from control vessels (C) and vessels inoculated with L. gasseri LM19 alone (Lg) using faecal inoculum from three different donors: blue, formate; orange, acetate; red, propionate; purple, butyrate; green, lactate
Figure Legend Snippet: In vitro colon model fermentations with L. gasseri LM19 and C. perfringens. a C. perfringens NCTC 3110 population measured by qPCR when inoculated alone (Cp) or co-inoculated with L. gasseri LM19 (Cp + Lg) in three different fermentations with faeces from donors 1, 2 and 3. b Expression of bacteriocin genes in vessels from all 4 treatments (control, L. gasseri LM19 alone, C. perfringens alone, L. gassieri LM19 with C. perfringens ) at 24 h in fermentations with faeces from donor 1: lane 1, negative control; lanes 2 and 10, bact_1 ; lanes 3 and 11, bact_2 ; lanes 4 and 12, gamA ; lanes 5 and 13, gamX ; lanes 6 and 14, helveticin J-like ; lanes 7 and 15, gyrA ; lanes 8 and 17, C. perfringens ; lanes 9 and 20, molecular marker; lanes 18 and 21, gamM ; lanes 19 and 22, gamY . c Microbial profiles obtained by 16S rRNA analysis showing relative abundance at the order level in the faecal batch model fermentation for the three donors (C, control, Lg, L. gasseri LM19 alone, Cp, C. perfringens alone, Lg + Cp, co-inoculation of L. gasseri LM19 and C. perfringens ). d Production of SCFA in batch model faecal fermentations from control vessels (C) and vessels inoculated with L. gasseri LM19 alone (Lg) using faecal inoculum from three different donors: blue, formate; orange, acetate; red, propionate; purple, butyrate; green, lactate

Techniques Used: In Vitro, Real-time Polymerase Chain Reaction, Expressing, Negative Control, Marker

38) Product Images from "Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage"

Article Title: Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage

Journal: Science Advances

doi: 10.1126/sciadv.aay8562

Relative abundance of bacterial phylotypes, based on 16 S rRNA. Bacterial community structure for crown radioles of ( A ) the serpulid Laminatubus n. sp. and ( B ) sabellid Bispira n. sp. from Jaco Scar seep, Costa Rica. Tissues were sampled directly upon worm collection from the active seep (native), after transplant for 16 months to areas of very little/no methane venting (“600 m” and “1400 m” away) or after shipboard incubation in either 12 CH 4 or 13 CH 4 (example “ 13 CH 4 -incubated”). Bispira were not transplanted and thus do not have specimens for those categories (“N/A”). Each color on the graph represents a distinct genus-level phylotype or lowest level available. Phylotypes were grouped to 99% 16 S rRNA sequence similarity. Dominant phylotypes within the Methylococcales Marine Group 2 are indicated by either purple or orange bars. Genera that were not putative aerobic methanotrophs are shown in light blue ( Arenicella ), black ( Moritella ) or gray (all others). The raw Illumina 16S rRNA barcode sequences and metadata collected in this study are available from the Dryad Digital Repository ( https://doi.org/10.5061/dryad.wdbrv15jq ) and the NCBI Small Read Archive (BioProject # PRJNA599018).
Figure Legend Snippet: Relative abundance of bacterial phylotypes, based on 16 S rRNA. Bacterial community structure for crown radioles of ( A ) the serpulid Laminatubus n. sp. and ( B ) sabellid Bispira n. sp. from Jaco Scar seep, Costa Rica. Tissues were sampled directly upon worm collection from the active seep (native), after transplant for 16 months to areas of very little/no methane venting (“600 m” and “1400 m” away) or after shipboard incubation in either 12 CH 4 or 13 CH 4 (example “ 13 CH 4 -incubated”). Bispira were not transplanted and thus do not have specimens for those categories (“N/A”). Each color on the graph represents a distinct genus-level phylotype or lowest level available. Phylotypes were grouped to 99% 16 S rRNA sequence similarity. Dominant phylotypes within the Methylococcales Marine Group 2 are indicated by either purple or orange bars. Genera that were not putative aerobic methanotrophs are shown in light blue ( Arenicella ), black ( Moritella ) or gray (all others). The raw Illumina 16S rRNA barcode sequences and metadata collected in this study are available from the Dryad Digital Repository ( https://doi.org/10.5061/dryad.wdbrv15jq ) and the NCBI Small Read Archive (BioProject # PRJNA599018).

Techniques Used: Incubation, Sequencing

39) Product Images from "Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome"

Article Title: Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome

Journal: mSystems

doi: 10.1128/mSystems.00777-19

Relative abundance estimates can misrepresent actual concentrations due to shifts in total bacterial load. Examples of species-specific profiles in two participants for two different species L. crispatus , participant 06 (a), and Megasphaera , participant 17 (b). Vertical bars show the relative abundance (%, left y axis), solid lines indicate the absolute concentrations measured by qPCR, the gray line indicates the total bacterial load, and the dashed lines indicate inferred concentrations (all right y axis). The dashed black line indicates detection threshold for qPCR data (93.8 16S rRNA gene copies per swab). Arrows indicate time points when the relative abundance changes are discordant from the absolute concentration changes, which often occur when bacterial loads shift dramatically or when the relative abundance is low. Examples for the remaining species can be found in Fig. S2 .
Figure Legend Snippet: Relative abundance estimates can misrepresent actual concentrations due to shifts in total bacterial load. Examples of species-specific profiles in two participants for two different species L. crispatus , participant 06 (a), and Megasphaera , participant 17 (b). Vertical bars show the relative abundance (%, left y axis), solid lines indicate the absolute concentrations measured by qPCR, the gray line indicates the total bacterial load, and the dashed lines indicate inferred concentrations (all right y axis). The dashed black line indicates detection threshold for qPCR data (93.8 16S rRNA gene copies per swab). Arrows indicate time points when the relative abundance changes are discordant from the absolute concentration changes, which often occur when bacterial loads shift dramatically or when the relative abundance is low. Examples for the remaining species can be found in Fig. S2 .

Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

Complex bacterial kinetics in the vaginal niche in a representative study participant. Daily samples from a woman, participant 18, who performed self-swabbing of the vagina were analyzed by targeted qPCR of seven specific species (a), high-throughput sequencing using 16S rRNA (b), and inferred concentration for species with a relative abundance above 1% (c). Boxes around taxa indicate they were measured using qPCR. qPCR allows measures of the absolute concentration, whereas broad-range PCR with sequencing provides a measure of the bacterial diversity in a given sample. Targeted qPCR often detects shifts in single species prior to NGS. Inferred concentration follows qPCR more closely than does the relative abundance and may project the concentration of species for which targeted qPCR assays are not available. Traces for the remaining participants can be found in Fig. S1 .
Figure Legend Snippet: Complex bacterial kinetics in the vaginal niche in a representative study participant. Daily samples from a woman, participant 18, who performed self-swabbing of the vagina were analyzed by targeted qPCR of seven specific species (a), high-throughput sequencing using 16S rRNA (b), and inferred concentration for species with a relative abundance above 1% (c). Boxes around taxa indicate they were measured using qPCR. qPCR allows measures of the absolute concentration, whereas broad-range PCR with sequencing provides a measure of the bacterial diversity in a given sample. Targeted qPCR often detects shifts in single species prior to NGS. Inferred concentration follows qPCR more closely than does the relative abundance and may project the concentration of species for which targeted qPCR assays are not available. Traces for the remaining participants can be found in Fig. S1 .

Techniques Used: Real-time Polymerase Chain Reaction, Next-Generation Sequencing, Concentration Assay, Polymerase Chain Reaction, Sequencing

40) Product Images from "An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform"

Article Title: An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

Journal: Microbiome

doi: 10.1186/2049-2618-2-6

Dual-indexed 16S rRNA gene PCR amplification strategy with heterogeneity spacer primers for sequencing on the MiSeq platform. (A) Dual-indexed PCR amplification primers targeting the V3-V4 hypervariable regions of the 16S rRNA gene contain a heterogeneity spacer region and linker sequence optimized for sequencing on the Illumina MiSeq platform. Using this approach enables sequencing using the standard Illumina HP10 and HP11 sequencing primers allowing for additional sequencing flexibility. (B) Schematic showing the first thirty sequencing cycles of eight mock amplicons prepared using the dual-indexed approach. This diagram illustrates how the index sequence and heterogeneity spacer (colored letters, white background) helps to alleviate the “low sequence diversity” issue associated with the MiSeq platform by creating a more even base composition at each cycle of the run.
Figure Legend Snippet: Dual-indexed 16S rRNA gene PCR amplification strategy with heterogeneity spacer primers for sequencing on the MiSeq platform. (A) Dual-indexed PCR amplification primers targeting the V3-V4 hypervariable regions of the 16S rRNA gene contain a heterogeneity spacer region and linker sequence optimized for sequencing on the Illumina MiSeq platform. Using this approach enables sequencing using the standard Illumina HP10 and HP11 sequencing primers allowing for additional sequencing flexibility. (B) Schematic showing the first thirty sequencing cycles of eight mock amplicons prepared using the dual-indexed approach. This diagram illustrates how the index sequence and heterogeneity spacer (colored letters, white background) helps to alleviate the “low sequence diversity” issue associated with the MiSeq platform by creating a more even base composition at each cycle of the run.

Techniques Used: Polymerase Chain Reaction, Amplification, Sequencing

Related Articles

Amplification:

Article Title: Diversity of macaque microbiota compared to the human counterparts
Article Snippet: .. We performed amplicon sequencing on the V4 region of the 16S rRNA gene, producing 13,583,251 high-quality sequences from a total of 318 samples using an Illumina MiSeq sequencing (mean 42,715 ± 15,848 reads per sample). ..

Article Title: In Search of Alternative Antibiotic Drugs: Quorum-Quenching Activity in Sponges and their Bacterial Isolates
Article Snippet: .. The V4 region of the 16S rRNA gene was amplified using the primers 515F and 806R and sequenced using the HiSeq2500 platform (Illumina) (Caporaso et al., ). ..

Article Title: A Microbiological Map of the Healthy Equine Gastrointestinal Tract
Article Snippet: .. Bacterial/archaeal 16S rRNA gene 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) . .. Amplicons were then pooled for sequencing using the Illumina MiSeq platform and V2 chemistry with 2×250 bp paired-end reads, as previously described [ ].

Terminal Restriction Fragment Length Polymorphism:

Article Title: Detection of novel syntrophic acetate‐oxidizing bacteria from biogas processes by continuous acetate enrichment approaches
Article Snippet: .. A combination of molecular methods, including Illumina sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T‐RFLP) analysis, was used to identify microbial structure patterns over time and to quantify abundant species. ..

Real-time Polymerase Chain Reaction:

Article Title: Detection of novel syntrophic acetate‐oxidizing bacteria from biogas processes by continuous acetate enrichment approaches
Article Snippet: .. A combination of molecular methods, including Illumina sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T‐RFLP) analysis, was used to identify microbial structure patterns over time and to quantify abundant species. ..

Generated:

Article Title: Interleukin-22 drives nitric oxide-dependent DNA damage and dysplasia in a murine model of colitis-associated cancer
Article Snippet: .. Amplicons were generated using oligonucleotide primers that target approximately 300 bp of the V4 variable region of the 16S rRNA gene (primers 515F and 806R) and also were barcoded and pooled to construct the sequencing library, followed by sequencing with an Illumina MiSeq instrument to generate paired-end 150×150 reads. .. The software package QIIME 1.7.0 was used to analyze, display, and generate figures of microbiome data using a previously defined method .

Article Title: A Microbiological Map of the Healthy Equine Gastrointestinal Tract
Article Snippet: .. Bacterial/archaeal 16S rRNA gene 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) . .. Amplicons were then pooled for sequencing using the Illumina MiSeq platform and V2 chemistry with 2×250 bp paired-end reads, as previously described [ ].

other:

Article Title: Dynamic transition of chemolithotrophic sulfur-oxidizing bacteria in response to amendment with nitrate in deposited marine sediments
Article Snippet: In addition, the libraries of 16S rRNA genes were located far from those of the transcripts, implying that only selected members of the microbial communities expressed 16S rRNA.

Article Title: Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis
Article Snippet: Variations in techniques, target regions of the 16S rRNA gene, reference taxonomic databases or source of tick samples may hinder comparisons.

Construct:

Article Title: Interleukin-22 drives nitric oxide-dependent DNA damage and dysplasia in a murine model of colitis-associated cancer
Article Snippet: .. Amplicons were generated using oligonucleotide primers that target approximately 300 bp of the V4 variable region of the 16S rRNA gene (primers 515F and 806R) and also were barcoded and pooled to construct the sequencing library, followed by sequencing with an Illumina MiSeq instrument to generate paired-end 150×150 reads. .. The software package QIIME 1.7.0 was used to analyze, display, and generate figures of microbiome data using a previously defined method .

Sequencing:

Article Title: Diversity of macaque microbiota compared to the human counterparts
Article Snippet: .. We performed amplicon sequencing on the V4 region of the 16S rRNA gene, producing 13,583,251 high-quality sequences from a total of 318 samples using an Illumina MiSeq sequencing (mean 42,715 ± 15,848 reads per sample). ..

Article Title: Interleukin-22 drives nitric oxide-dependent DNA damage and dysplasia in a murine model of colitis-associated cancer
Article Snippet: .. Amplicons were generated using oligonucleotide primers that target approximately 300 bp of the V4 variable region of the 16S rRNA gene (primers 515F and 806R) and also were barcoded and pooled to construct the sequencing library, followed by sequencing with an Illumina MiSeq instrument to generate paired-end 150×150 reads. .. The software package QIIME 1.7.0 was used to analyze, display, and generate figures of microbiome data using a previously defined method .

Article Title: Detection of novel syntrophic acetate‐oxidizing bacteria from biogas processes by continuous acetate enrichment approaches
Article Snippet: .. A combination of molecular methods, including Illumina sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T‐RFLP) analysis, was used to identify microbial structure patterns over time and to quantify abundant species. ..

Article Title: High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia
Article Snippet: .. 16S rRNA gene fragments from the Planctomycetes comprised 8–13% of total 16S rRNA gene reads retrieved using Illumina pair-end sequencing from the soil and peat samples. .. Lichen-associated assemblages of planctomycetes displayed unexpectedly high diversity, with a total of 89,662 reads representing 1723 operational taxonomic units determined at 97% sequence identity.

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    Illumina Inc 16s rrna genes
    Percentage contribution of <t>16S</t> <t>rRNA</t> gene sequences (grouped by class) during acetate enrichment under mesophilic (M) or thermophilic (T) temperature conditions, as determined using Illumina MiSeq sequencing. Chemostats designated M H /T H and M L /T L received medium containing 7.5 and 0.4 g acetate l −1 respectively. The corresponding hydraulic retention time ( HRT ) at the point of sampling is given on the x ‐axis. Yellow, green, blue and red bars represent classes within the phyla Bacteriodetes, Firmicutes, Proteobacteria and Thermotogae respectively. Purple indicates methanogenic archaea. Classes representing
    16s Rrna Genes, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1277 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc 16s rrna gene amplicons
    Neighbor-joining tree based on <t>16S</t> <t>rRNA</t> gene sequences showing phylogenetic relationships in the genus Geobacter . Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.
    16s Rrna Gene Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Percentage contribution of 16S rRNA gene sequences (grouped by class) during acetate enrichment under mesophilic (M) or thermophilic (T) temperature conditions, as determined using Illumina MiSeq sequencing. Chemostats designated M H /T H and M L /T L received medium containing 7.5 and 0.4 g acetate l −1 respectively. The corresponding hydraulic retention time ( HRT ) at the point of sampling is given on the x ‐axis. Yellow, green, blue and red bars represent classes within the phyla Bacteriodetes, Firmicutes, Proteobacteria and Thermotogae respectively. Purple indicates methanogenic archaea. Classes representing

    Journal: Microbial Biotechnology

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

    doi: 10.1111/1751-7915.13035

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

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

    Techniques: Sequencing, Sampling

    Phyla-level relative abundance of reads for each tick species analyzed. The histograms show the portion of MiSeq 16S rRNA gene sequences assigned to each phylum.

    Journal: PLoS ONE

    Article Title: Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis

    doi: 10.1371/journal.pone.0213384

    Figure Lengend Snippet: Phyla-level relative abundance of reads for each tick species analyzed. The histograms show the portion of MiSeq 16S rRNA gene sequences assigned to each phylum.

    Article Snippet: Variations in techniques, target regions of the 16S rRNA gene, reference taxonomic databases or source of tick samples may hinder comparisons.

    Techniques:

    Nucleotide alignment of ‘ Candidatus Midichloriaceae’ partial 16S rRNA references (according to BLAST) versus closed undefined OTUs (according to Greengenes database).

    Journal: PLoS ONE

    Article Title: Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis

    doi: 10.1371/journal.pone.0213384

    Figure Lengend Snippet: Nucleotide alignment of ‘ Candidatus Midichloriaceae’ partial 16S rRNA references (according to BLAST) versus closed undefined OTUs (according to Greengenes database).

    Article Snippet: Variations in techniques, target regions of the 16S rRNA gene, reference taxonomic databases or source of tick samples may hinder comparisons.

    Techniques:

    Matching assembled cyanophage with Synechococcus host using expression patterns. Presence and activity of the assembled cyanophage and its potential hosts in October 2012: a Mean coverage (after removing the top 25% most abundant contig positions) of the assembled cyanophage, b Amplicon single variants (ASVs) relative gene and transcript abundance of 16S-rRNA of the two most abundant cyanobacterial ASVs: Prochlorococcus ASV4 and Synechococcus ASV10. Note the near-absence of Prochlorococcus in POLA, in contrast to Synechococcus and the phage RNA, leading us to infer that the phage infected Synechococcus . Each group of bar plots, denoted by site name, represents data from a single sample

    Journal: Nature Communications

    Article Title: Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

    doi: 10.1038/s41467-019-09106-z

    Figure Lengend Snippet: Matching assembled cyanophage with Synechococcus host using expression patterns. Presence and activity of the assembled cyanophage and its potential hosts in October 2012: a Mean coverage (after removing the top 25% most abundant contig positions) of the assembled cyanophage, b Amplicon single variants (ASVs) relative gene and transcript abundance of 16S-rRNA of the two most abundant cyanobacterial ASVs: Prochlorococcus ASV4 and Synechococcus ASV10. Note the near-absence of Prochlorococcus in POLA, in contrast to Synechococcus and the phage RNA, leading us to infer that the phage infected Synechococcus . Each group of bar plots, denoted by site name, represents data from a single sample

    Article Snippet: Microbial community composition analysis The V4-V5 regions of the 16S-rRNA coding gene were amplified from DNA and cDNA from all samples using the 515(N)-F and 926-R primers, and sequenced on an Illumina MiSeq 2 × 300 bp (UC Davis genome center) along with a negative controls and even and staggered mock communities.

    Techniques: Expressing, Activity Assay, Amplification, Infection

    Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter . Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.

    Journal: PLoS ONE

    Article Title: Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells

    doi: 10.1371/journal.pone.0077443

    Figure Lengend Snippet: Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter . Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.

    Article Snippet: The microbiomes established in each system were compared by pyrotag sequencing of 16S rRNA gene amplicons and shotgun metagenomics.

    Techniques: Sequencing