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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 154 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells"

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

Journal: PLoS ONE

doi: 10.1371/journal.pone.0077443

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.
Figure Legend 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.

Techniques Used: Sequencing

2) Product Images from "Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells"

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

Journal: PLoS ONE

doi: 10.1371/journal.pone.0077443

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.
Figure Legend 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.

Techniques Used: Sequencing

3) Product Images from "Isolation and characterization of Magnetospirillum sp. strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model"

Article Title: Isolation and characterization of Magnetospirillum sp. strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model

Journal: PLoS ONE

doi: 10.1371/journal.pone.0174750

Phylogenetic tree of 16S rRNA gene sequences. The isolated strain obtained in this study is designated 15–1.
Figure Legend Snippet: Phylogenetic tree of 16S rRNA gene sequences. The isolated strain obtained in this study is designated 15–1.

Techniques Used: Isolation

4) Product Images from "Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors"

Article Title: Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors

Journal: Scientific Reports

doi: 10.1038/s41598-018-34088-1

Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3-4 16S rRNA gene amplicons obtained for individual influent, reactor, and granular samples. Each bar represents one sample. D: day; PP: pulp and paper granules; Inf HA: influent to HA reactors; Inf LA: influent to LA reactors; Cand .: Candidatus ; g.i.s .: genera_incertae_sedis . “Unclassified” indicates that OTUs could not be classified at the domain level, “Uncl” indicates that OTUs could not be classified at class level ( A ) or family level ( B ). Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” includes all reads representing the taxa with lower abundance in all samples.
Figure Legend Snippet: Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3-4 16S rRNA gene amplicons obtained for individual influent, reactor, and granular samples. Each bar represents one sample. D: day; PP: pulp and paper granules; Inf HA: influent to HA reactors; Inf LA: influent to LA reactors; Cand .: Candidatus ; g.i.s .: genera_incertae_sedis . “Unclassified” indicates that OTUs could not be classified at the domain level, “Uncl” indicates that OTUs could not be classified at class level ( A ) or family level ( B ). Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” includes all reads representing the taxa with lower abundance in all samples.

Techniques Used: Sequencing

5) Product Images from "Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems"

Article Title: Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-017-0929-3

Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown
Figure Legend Snippet: Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown

Techniques Used:

6) Product Images from "Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases"

Article Title: Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases

Journal: The ISME Journal

doi: 10.1038/s41396-017-0007-7

Number of OTU’s detected as function of the number of collected sediment samples from Vidy Bay. Plots were made with the specaccum function of the Vegan package in R. The OTU clustering was done at 97 and at 88 % similarity levels for 16S rRNA gene and hgcA gene sequences, respectively.
Figure Legend Snippet: Number of OTU’s detected as function of the number of collected sediment samples from Vidy Bay. Plots were made with the specaccum function of the Vegan package in R. The OTU clustering was done at 97 and at 88 % similarity levels for 16S rRNA gene and hgcA gene sequences, respectively.

Techniques Used:

Phylogenetic distribution of bacterial 16S rRNA gene sequences in the combined Vidy Bay sediment dataset: A . Relative abundance of major phyla and B classes within the δ- Proteobacteria . Presented data are average percentages (±SE) of reads from the 18 collected samples (6 depths in 3 cores). Categories representing > 1 % are shown.
Figure Legend Snippet: Phylogenetic distribution of bacterial 16S rRNA gene sequences in the combined Vidy Bay sediment dataset: A . Relative abundance of major phyla and B classes within the δ- Proteobacteria . Presented data are average percentages (±SE) of reads from the 18 collected samples (6 depths in 3 cores). Categories representing > 1 % are shown.

Techniques Used:

7) Product Images from "Incubation Temperature, But Not Pequi Oil Supplementation, Affects Methane Production, and the Ruminal Microbiota in a Rumen Simulation Technique (Rusitec) System"

Article Title: Incubation Temperature, But Not Pequi Oil Supplementation, Affects Methane Production, and the Ruminal Microbiota in a Rumen Simulation Technique (Rusitec) System

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2017.01076

Classification of 16S rRNA gene sequences at the genus level for each individual sampling day, incubation temperature, sample type and treatment. Only the ten most relatively abundant genera are displayed ( N = 3 for all samples). LAM = liquid-associated microbes, SAM = solid-associated microbes.
Figure Legend Snippet: Classification of 16S rRNA gene sequences at the genus level for each individual sampling day, incubation temperature, sample type and treatment. Only the ten most relatively abundant genera are displayed ( N = 3 for all samples). LAM = liquid-associated microbes, SAM = solid-associated microbes.

Techniques Used: Sampling, Incubation, Laser Capture Microdissection

8) Product Images from "Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH"

Article Title: Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2017.00308

Non-parametric Multi Dimensional Scaling (MDS) plot of microbial community diversity based upon bacterial 16S rRNA gene sequences using the Bray–Curtis similarity index. Environmental variables that correlated with community composition are represented by vectors in two-dimensional space. The dark circle represents the length of a vector with perfect correlation ( R = 1).
Figure Legend Snippet: Non-parametric Multi Dimensional Scaling (MDS) plot of microbial community diversity based upon bacterial 16S rRNA gene sequences using the Bray–Curtis similarity index. Environmental variables that correlated with community composition are represented by vectors in two-dimensional space. The dark circle represents the length of a vector with perfect correlation ( R = 1).

Techniques Used: Plasmid Preparation

9) Product Images from "Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge"

Article Title: Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.00633

Phylogenetic tree of Gammaproteobacteria related 16S rRNA gene sequences from host rock sample 30R-1A in comparison to sequences from cultivated species and other environmental studies. The sequence data of 30R-1A host rock are retrieved from Zhang et al. (2016) , and are highlighted in bold font. The numbers in parentheses indicate percent abundance of the reads clustered in genera followed by the order “Host rock” “NaHCO 3 + NH 4 Cl” “NH 4 Cl” “NaHCO 3 + NaNO 3 ” “NaNO 3, ” respectively. A representative sequence from sample 30R-1A for each genus is shown due to the high sequence number. Sequences from isolates or other environmental studies identified by Genbank accession number. Filled squares indicate known iron-oxidizing bacteria, and filled circles indicate known iron-reducing bacteria. Sequences retrieved from Atlantis Massif are in orange, East Pacific Rise in red, Loihi Seamount in purple, Juan de Fuca Ridge flank in blue, crustal fluids of Costa Rica Rift flank in brown. Potential kit contaminating sequences are in gray. The number at each branch indicates local support value, with only values > 70 shown. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.
Figure Legend Snippet: Phylogenetic tree of Gammaproteobacteria related 16S rRNA gene sequences from host rock sample 30R-1A in comparison to sequences from cultivated species and other environmental studies. The sequence data of 30R-1A host rock are retrieved from Zhang et al. (2016) , and are highlighted in bold font. The numbers in parentheses indicate percent abundance of the reads clustered in genera followed by the order “Host rock” “NaHCO 3 + NH 4 Cl” “NH 4 Cl” “NaHCO 3 + NaNO 3 ” “NaNO 3, ” respectively. A representative sequence from sample 30R-1A for each genus is shown due to the high sequence number. Sequences from isolates or other environmental studies identified by Genbank accession number. Filled squares indicate known iron-oxidizing bacteria, and filled circles indicate known iron-reducing bacteria. Sequences retrieved from Atlantis Massif are in orange, East Pacific Rise in red, Loihi Seamount in purple, Juan de Fuca Ridge flank in blue, crustal fluids of Costa Rica Rift flank in brown. Potential kit contaminating sequences are in gray. The number at each branch indicates local support value, with only values > 70 shown. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.

Techniques Used: Sequencing

10) Product Images from "Microbial metal‐sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses"

Article Title: Microbial metal‐sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Journal: Environmental Microbiology

doi: 10.1111/1462-2920.14514

Microbial diversity based on relative abundances of 16S rRNA gene amplicon sequences. The upper panel shows the hierarchical clustering of the samples with average linkage method based on a Bray–Curtis dissimilarity matrix. The central panel shows the relative abundances of 16S rRNA gene sequences according to their taxonomic classification. Black lines are delineating individual OTUs generated by SWARM. The lower panel shows the radiometric ages of the chimneys.
Figure Legend Snippet: Microbial diversity based on relative abundances of 16S rRNA gene amplicon sequences. The upper panel shows the hierarchical clustering of the samples with average linkage method based on a Bray–Curtis dissimilarity matrix. The central panel shows the relative abundances of 16S rRNA gene sequences according to their taxonomic classification. Black lines are delineating individual OTUs generated by SWARM. The lower panel shows the radiometric ages of the chimneys.

Techniques Used: Amplification, Generated

11) Product Images from "Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers"

Article Title: Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers

Journal: Scientific Reports

doi: 10.1038/srep11606

Phylogenetic tree of cultivable bacteria based on the 16S rRNA gene sequence comparison. The tree was constructed from the isolated 16S rRNA bacterial sequences with their respective reference sequences from GenBank. Only bacteria isolated in this experiment are shown as tree branches (full tree is provided in additional Fig. 2 ). Numbers at the nodes indicate the percentages of occurrence in 1,000 bootstrapped trees; only values > 50% are shown. The bar indicates 0.05 substitutions per nucleotide position. The degradation capacity of the main plant polymers CMC - carboxymethylcellulose, PGA-polygalacturonic acid, proteins (casein) and starch are provided. Fixation of N 2 and sensitivity to ampicillin are also indicated. OTU-s matching to the 16S rDNA of isolated bacteria at > 99% identity have been added to the tree. M - sequences in a single sequences pool of Experiment 1 matching with > 98% identity to the corresponding cultivated 16S rDNA sequence; D - sequences in single sequences pool of Experiment 2 matching with > 98% identity to the corresponding cultivated 16S rDNA.
Figure Legend Snippet: Phylogenetic tree of cultivable bacteria based on the 16S rRNA gene sequence comparison. The tree was constructed from the isolated 16S rRNA bacterial sequences with their respective reference sequences from GenBank. Only bacteria isolated in this experiment are shown as tree branches (full tree is provided in additional Fig. 2 ). Numbers at the nodes indicate the percentages of occurrence in 1,000 bootstrapped trees; only values > 50% are shown. The bar indicates 0.05 substitutions per nucleotide position. The degradation capacity of the main plant polymers CMC - carboxymethylcellulose, PGA-polygalacturonic acid, proteins (casein) and starch are provided. Fixation of N 2 and sensitivity to ampicillin are also indicated. OTU-s matching to the 16S rDNA of isolated bacteria at > 99% identity have been added to the tree. M - sequences in a single sequences pool of Experiment 1 matching with > 98% identity to the corresponding cultivated 16S rDNA sequence; D - sequences in single sequences pool of Experiment 2 matching with > 98% identity to the corresponding cultivated 16S rDNA.

Techniques Used: Sequencing, Construct, Isolation

12) Product Images from "Macrofaunal control of microbial community structure in continental margin sediments"

Article Title: Macrofaunal control of microbial community structure in continental margin sediments

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

doi: 10.1073/pnas.1917494117

Depth profiles of microbial communities at AU1 to AU4. ( A ) 16S rRNA gene abundances of Bacteria and Archaea (red triangles, Bacteria; blue diamonds, Archaea); ( B ) Bacteria-to-Archaea ratios (BARs); ( C ) Chao1 richness of Bacteria and Archaea; ( D and E ) community compositions of Bacteria and Archaea. The VLs, RLs, and SMTs are indicated by horizontal dashed, solid, and dotted lines, respectively. The black arrows indicate local peaks in chl a or excess 210 Pb from Fig. 1 .
Figure Legend Snippet: Depth profiles of microbial communities at AU1 to AU4. ( A ) 16S rRNA gene abundances of Bacteria and Archaea (red triangles, Bacteria; blue diamonds, Archaea); ( B ) Bacteria-to-Archaea ratios (BARs); ( C ) Chao1 richness of Bacteria and Archaea; ( D and E ) community compositions of Bacteria and Archaea. The VLs, RLs, and SMTs are indicated by horizontal dashed, solid, and dotted lines, respectively. The black arrows indicate local peaks in chl a or excess 210 Pb from Fig. 1 .

Techniques Used:

13) Product Images from "Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems"

Article Title: Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-017-0929-3

Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown
Figure Legend Snippet: Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown

Techniques Used:

14) Product Images from "Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems"

Article Title: Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-017-0929-3

Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown
Figure Legend Snippet: Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown

Techniques Used:

15) Product Images from "Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir"

Article Title: Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

Journal: Environmental Microbiology

doi: 10.1111/1462-2920.13706

Taxonomic summary of the McElmo Dome microbial community constructed using RDP/Silva‐annotated 16S rRNA gene sequencing of clone and Illumina (NGS) libraries, and Illumina binned metagenome (MG) read frequencies on the (A) phylum and (B) genus level. K, P, pK, and pP refer to methods of DNA extraction and PCR template preparation, as described in experimental procedures (K = kit extracted gDNA, P = phenol extracted gDNA, p = clone library vector with 16S rRNA amplicon used as template).
Figure Legend Snippet: Taxonomic summary of the McElmo Dome microbial community constructed using RDP/Silva‐annotated 16S rRNA gene sequencing of clone and Illumina (NGS) libraries, and Illumina binned metagenome (MG) read frequencies on the (A) phylum and (B) genus level. K, P, pK, and pP refer to methods of DNA extraction and PCR template preparation, as described in experimental procedures (K = kit extracted gDNA, P = phenol extracted gDNA, p = clone library vector with 16S rRNA amplicon used as template).

Techniques Used: Construct, Sequencing, Next-Generation Sequencing, DNA Extraction, Polymerase Chain Reaction, Plasmid Preparation, Amplification

Beta diversity of 16S rRNA gene sequences from McElmo Dome well and drilling fluid pond. The first two axes of the UniFrac Principal Coordinate Analysis (PCoA) explain 97.58% cumulative percent variation. Samples cluster according to origin rather than DNA preparation method.
Figure Legend Snippet: Beta diversity of 16S rRNA gene sequences from McElmo Dome well and drilling fluid pond. The first two axes of the UniFrac Principal Coordinate Analysis (PCoA) explain 97.58% cumulative percent variation. Samples cluster according to origin rather than DNA preparation method.

Techniques Used:

16) Product Images from "Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia)"

Article Title: Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia)

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2017.01583

Maximum-likehood (ML) tree based on 16S rRNA gene sequences showing the phylogenetic position of Deltaproteobacteria enriched from marine sediment (as inoculum) using different electron donors and sulfate sources (sodium sulfate or phosphogypsum). Representative sequences in the tree were obtained from GenBank (accession number in the brackets). Bootstrap values > 75% are indicated at nodes. The bars represent the relative abundance of each OTU affiliated with Deltaproteobacteria in the enrichment cultures. The blue bars indicate the relative abundance of OTUs in sodium sulfate cultures, whereas the red bars represent the relative abundance of OTUs in PG cultures.
Figure Legend Snippet: Maximum-likehood (ML) tree based on 16S rRNA gene sequences showing the phylogenetic position of Deltaproteobacteria enriched from marine sediment (as inoculum) using different electron donors and sulfate sources (sodium sulfate or phosphogypsum). Representative sequences in the tree were obtained from GenBank (accession number in the brackets). Bootstrap values > 75% are indicated at nodes. The bars represent the relative abundance of each OTU affiliated with Deltaproteobacteria in the enrichment cultures. The blue bars indicate the relative abundance of OTUs in sodium sulfate cultures, whereas the red bars represent the relative abundance of OTUs in PG cultures.

Techniques Used:

Compositions of microbial communities in sulfate-reducing enrichment cultures from marine sediment using different electron donors and sulfate sources after 14 days. Relative phylogenetic abundance was based on frequencies of 16S rRNA gene sequences affiliated with Archaea and major bacterial phyla or proteobacterial classes in the microbial communities. The names of enrichment cultures (duplicates 1 and 2) have been abbreviated as follows: SF, SL, SA, and SC for Na 2 SO 4 enrichment cultures with formate, lactate, acetate and without electron donor, respectively; SPF, SPL, SPA, and SPC for PG enrichment cultures with formate, lactate, acetate, and without electron donor, respectively.
Figure Legend Snippet: Compositions of microbial communities in sulfate-reducing enrichment cultures from marine sediment using different electron donors and sulfate sources after 14 days. Relative phylogenetic abundance was based on frequencies of 16S rRNA gene sequences affiliated with Archaea and major bacterial phyla or proteobacterial classes in the microbial communities. The names of enrichment cultures (duplicates 1 and 2) have been abbreviated as follows: SF, SL, SA, and SC for Na 2 SO 4 enrichment cultures with formate, lactate, acetate and without electron donor, respectively; SPF, SPL, SPA, and SPC for PG enrichment cultures with formate, lactate, acetate, and without electron donor, respectively.

Techniques Used:

Maximum-likehood (ML) tree based on 16S rRNA gene sequences showing the phylogenetic position of Firmicutes from marine sediment (as inoculum) using different electron donors and sulfate sources (sodium sulfate or phosphogypsum). Representative sequences in the tree were obtained from GenBank (accession number in the brackets). Bootstrap values > 75% are indicated at nodes. The bars represent the relative abundance (in %) of each OTU affiliated with Firmicutes in the enrichment cultures. The blue bars indicate the relative abundance of OTUs in sodium sulfate cultures, whereas the red bars represent the relative abundance of OTUs in PG cultures.
Figure Legend Snippet: Maximum-likehood (ML) tree based on 16S rRNA gene sequences showing the phylogenetic position of Firmicutes from marine sediment (as inoculum) using different electron donors and sulfate sources (sodium sulfate or phosphogypsum). Representative sequences in the tree were obtained from GenBank (accession number in the brackets). Bootstrap values > 75% are indicated at nodes. The bars represent the relative abundance (in %) of each OTU affiliated with Firmicutes in the enrichment cultures. The blue bars indicate the relative abundance of OTUs in sodium sulfate cultures, whereas the red bars represent the relative abundance of OTUs in PG cultures.

Techniques Used:

Compositions of microbial communities in the coastal marine sediment and phosphogypsum samples of Sfax (Tunisia). Relative phylogenetic abundance was based on frequencies of 16S rRNA gene sequences affiliated with Archaea and major bacterial phyla or proteobacterial classes in the microbial communities of marine sediment (MS) and phosphogypsum (PG).
Figure Legend Snippet: Compositions of microbial communities in the coastal marine sediment and phosphogypsum samples of Sfax (Tunisia). Relative phylogenetic abundance was based on frequencies of 16S rRNA gene sequences affiliated with Archaea and major bacterial phyla or proteobacterial classes in the microbial communities of marine sediment (MS) and phosphogypsum (PG).

Techniques Used: Mass Spectrometry

17) Product Images from "From the Cover: Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestines of F344/N Male Rats"

Article Title: From the Cover: Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestines of F344/N Male Rats

Journal: Toxicological Sciences

doi: 10.1093/toxsci/kfx105

Bar chart showing the relative abundance of microbe sequences in the 16S rRNA fecal microbiota of male F-344 rats administered aloin for 13 weeks, annotated to the phylum level by treatment ( n = 5).
Figure Legend Snippet: Bar chart showing the relative abundance of microbe sequences in the 16S rRNA fecal microbiota of male F-344 rats administered aloin for 13 weeks, annotated to the phylum level by treatment ( n = 5).

Techniques Used:

18) Product Images from "Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre"

Article Title: Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2017.01122

Neighbor joining phylogenetic trees depicting the relationships between Trichodesmium OTUs (97% nucleotide similarity) from partial 16S rRNA (left) and partial nifH (right) gene sequences, together with reference sequences from cultivated representatives (accession numbers given). Major Trichodesmium clades (Lundgren et al., 2005 ) are shown in Roman numerals. Bubble plots depict the percentage of Trichodesmium DNA sequences from this study which group with each clade, according to partial 16S rRNA (left) and partial nifH (right) amplicon datasets. Bootstrap values (1,000 replicates) of > 50% are provided. Scale bars represent nucleotide substitutions per site.
Figure Legend Snippet: Neighbor joining phylogenetic trees depicting the relationships between Trichodesmium OTUs (97% nucleotide similarity) from partial 16S rRNA (left) and partial nifH (right) gene sequences, together with reference sequences from cultivated representatives (accession numbers given). Major Trichodesmium clades (Lundgren et al., 2005 ) are shown in Roman numerals. Bubble plots depict the percentage of Trichodesmium DNA sequences from this study which group with each clade, according to partial 16S rRNA (left) and partial nifH (right) amplicon datasets. Bootstrap values (1,000 replicates) of > 50% are provided. Scale bars represent nucleotide substitutions per site.

Techniques Used: Amplification

Non-metric multi-dimensional scaling (NMDS) plots derived from the Bray–Curtis dissimilarity matrix of 16S rRNA OTUs from (A) all Trichodesmium colony sample OTUs (7011 sequences per sample), (B) Trichodesmium colony and surface seawater samples excluding Trichodesmium OTUs (3128 sequences per sample), and (C) Trichodesmium colony samples excluding non- Trichodesmium OTUs (2248 sequences per sample). Each point represents an individual sample. Colors represent sample type [tuft colonies, puff colonies, mixed colonies, and bulk seawater (SW) from 25 m].
Figure Legend Snippet: Non-metric multi-dimensional scaling (NMDS) plots derived from the Bray–Curtis dissimilarity matrix of 16S rRNA OTUs from (A) all Trichodesmium colony sample OTUs (7011 sequences per sample), (B) Trichodesmium colony and surface seawater samples excluding Trichodesmium OTUs (3128 sequences per sample), and (C) Trichodesmium colony samples excluding non- Trichodesmium OTUs (2248 sequences per sample). Each point represents an individual sample. Colors represent sample type [tuft colonies, puff colonies, mixed colonies, and bulk seawater (SW) from 25 m].

Techniques Used: Derivative Assay

Percentages of partial 16S rRNA gene sequences assigned to bacterial taxa. Percentages of sequences assigned to Trichodesmium are displayed in the upper bar plot. The area plot displays the percentages of non- Trichodesmium sequences assigned to other bacterial taxa. Color indicates the sample type/morphology [green, red, blue, and gray for puff colonies, tuft colonies, mixed colonies, and bulk 25 m seawater (SW), respectively]. R denotes radial and NR denotes non-radial puff morphologies (see Figure 1 ).
Figure Legend Snippet: Percentages of partial 16S rRNA gene sequences assigned to bacterial taxa. Percentages of sequences assigned to Trichodesmium are displayed in the upper bar plot. The area plot displays the percentages of non- Trichodesmium sequences assigned to other bacterial taxa. Color indicates the sample type/morphology [green, red, blue, and gray for puff colonies, tuft colonies, mixed colonies, and bulk 25 m seawater (SW), respectively]. R denotes radial and NR denotes non-radial puff morphologies (see Figure 1 ).

Techniques Used:

19) Product Images from "Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge"

Article Title: Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.00363

The Phylogenetic tree of Gammaproteobacterial-related OTUs from seven basalt samples. Sequences recovered in this study are highlighted in bold font. The numbers in parentheses indicate percentage of the designated reads clustered in 97% cutoff OTUs in the order 72, 97, 105, 137, 145, 221, and 304 mbsf. Sequences in red are positively correlated with depth, those in blue are negatively correlated with depth, and those in gray are potential contaminants. ∗ indicates sequences from Hirayama et al. (2015) . Only those with > 70 local support values are shown as filled circles at each branch. Only those with > 0.1% OTU abundance within each sample and a representative sequence for each OTU (the most abundant one) are used due to the large number of sequences. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as the outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.
Figure Legend Snippet: The Phylogenetic tree of Gammaproteobacterial-related OTUs from seven basalt samples. Sequences recovered in this study are highlighted in bold font. The numbers in parentheses indicate percentage of the designated reads clustered in 97% cutoff OTUs in the order 72, 97, 105, 137, 145, 221, and 304 mbsf. Sequences in red are positively correlated with depth, those in blue are negatively correlated with depth, and those in gray are potential contaminants. ∗ indicates sequences from Hirayama et al. (2015) . Only those with > 70 local support values are shown as filled circles at each branch. Only those with > 0.1% OTU abundance within each sample and a representative sequence for each OTU (the most abundant one) are used due to the large number of sequences. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as the outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.

Techniques Used: Sequencing

The phylogenetic tree of Beta-, Alpha-, and Delta-proteobacterial-related OTUs from seven basalt samples. Sequences recovered in this study are highlighted in bold font. The numbers in parentheses indicate the percentage of the designated reads clustered in 97% cutoff OTUs in the order 72, 97, 105, 137, 145, 221, and 304 mbsf. Sequences in red are positively correlated with depth, those in blue are negatively correlated with depth, and those in gray are potential contaminants. ∗ indicates sequences from Hirayama et al. (2015) . Only those with > 70 local support values are shown as filled circles at each branch. Only those with > 0.1% OTU abundance within each sample and a representative sequence for each OTU (the most abundant one) are used due to the large number of sequences. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as the outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.
Figure Legend Snippet: The phylogenetic tree of Beta-, Alpha-, and Delta-proteobacterial-related OTUs from seven basalt samples. Sequences recovered in this study are highlighted in bold font. The numbers in parentheses indicate the percentage of the designated reads clustered in 97% cutoff OTUs in the order 72, 97, 105, 137, 145, 221, and 304 mbsf. Sequences in red are positively correlated with depth, those in blue are negatively correlated with depth, and those in gray are potential contaminants. ∗ indicates sequences from Hirayama et al. (2015) . Only those with > 70 local support values are shown as filled circles at each branch. Only those with > 0.1% OTU abundance within each sample and a representative sequence for each OTU (the most abundant one) are used due to the large number of sequences. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as the outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.

Techniques Used: Sequencing

The phylogenetic tree of Bacteroidetes-related OTUs from seven basalt samples. Sequences recovered in this study are highlighted in bold font. The numbers in parentheses indicate the percentage of the designated reads clustered in 97% cutoff OTUs in the order 72, 97, 105, 137, 145, 221, and 304 mbsf. Sequences in red are positively correlated with depth, those in blue are negatively correlated with depth. Only those with > 70 local support values are shown as filled circles at each branch. Only those with > 0.1% OTU abundance within each sample, and a representative sequence for each OTU (the most abundant one) is used due to the large number of sequences. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as the outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.
Figure Legend Snippet: The phylogenetic tree of Bacteroidetes-related OTUs from seven basalt samples. Sequences recovered in this study are highlighted in bold font. The numbers in parentheses indicate the percentage of the designated reads clustered in 97% cutoff OTUs in the order 72, 97, 105, 137, 145, 221, and 304 mbsf. Sequences in red are positively correlated with depth, those in blue are negatively correlated with depth. Only those with > 70 local support values are shown as filled circles at each branch. Only those with > 0.1% OTU abundance within each sample, and a representative sequence for each OTU (the most abundant one) is used due to the large number of sequences. The 16S rRNA gene of Aquifex aeolicus (AE000657) is used as the outgroup. The scale bar indicates 0.1 nucleotide substitutions per site.

Techniques Used: Sequencing

20) Product Images from "Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions"

Article Title: Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

Journal: Scientific Reports

doi: 10.1038/srep25719

The effect of ( A ) decrease in dissolved oxygen concentration in the aerobic zone on the ( B ) phosphate and nitrogen removal efficiency at Ulu Pandan South Works and the specific phosphate and acetate uptake activity of Ulu Pandan biomass determined in lab–scale batch experiments conducted with freshly collected full–scale plant biomass; ( C ) community composition (operational taxonomic units (OTU) defined by 16S rRNA gene amplicon sequencing data); and ( D ) poly–β–hydroxyalkanoate (PHA) content and ratio and glycogen content in the biomass throughout the two month sampling period between the 29th May–14th August 2013. Relative abundances of OTUs in ( C ) are plotted on a square root scale; OTUs annotated to Accumulibacter PAO and Competibacter GAO are highlighted. Dashed line indicates the sampling point when dissolved oxygen was decreased in the aerobic zone of Ulu Pandan South Works.
Figure Legend Snippet: The effect of ( A ) decrease in dissolved oxygen concentration in the aerobic zone on the ( B ) phosphate and nitrogen removal efficiency at Ulu Pandan South Works and the specific phosphate and acetate uptake activity of Ulu Pandan biomass determined in lab–scale batch experiments conducted with freshly collected full–scale plant biomass; ( C ) community composition (operational taxonomic units (OTU) defined by 16S rRNA gene amplicon sequencing data); and ( D ) poly–β–hydroxyalkanoate (PHA) content and ratio and glycogen content in the biomass throughout the two month sampling period between the 29th May–14th August 2013. Relative abundances of OTUs in ( C ) are plotted on a square root scale; OTUs annotated to Accumulibacter PAO and Competibacter GAO are highlighted. Dashed line indicates the sampling point when dissolved oxygen was decreased in the aerobic zone of Ulu Pandan South Works.

Techniques Used: Concentration Assay, Activity Assay, Amplification, Sequencing, Sampling

21) Product Images from "Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area"

Article Title: Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area

Journal: PLoS ONE

doi: 10.1371/journal.pone.0234128

High-throughput sequencing of 16S rRNA gene revealing the relative abundance of phylum (A) and class (B) in the sediment (S1S and S2S) and seawater (S1 and S2) samples. The top 15 phyla or classes with the largest relative abundance were presented and the rest phyla or classes were set as others or unclassified.
Figure Legend Snippet: High-throughput sequencing of 16S rRNA gene revealing the relative abundance of phylum (A) and class (B) in the sediment (S1S and S2S) and seawater (S1 and S2) samples. The top 15 phyla or classes with the largest relative abundance were presented and the rest phyla or classes were set as others or unclassified.

Techniques Used: Next-Generation Sequencing

PCA analysis results based on (A) genus abundance from 16S rRNA gene amplicon sequencing and (B) functional abundance of level 3 KEGG pathways. The red and black dots are sediment and seawater samples, respectively. The abscissa and the ordinate represent the first principal component (PC1) and the second principal component (PC2) respectively. The percentage represents the contribution of the principal components to the samples difference.
Figure Legend Snippet: PCA analysis results based on (A) genus abundance from 16S rRNA gene amplicon sequencing and (B) functional abundance of level 3 KEGG pathways. The red and black dots are sediment and seawater samples, respectively. The abscissa and the ordinate represent the first principal component (PC1) and the second principal component (PC2) respectively. The percentage represents the contribution of the principal components to the samples difference.

Techniques Used: Amplification, Sequencing, Functional Assay

22) Product Images from "Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors"

Article Title: Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors

Journal: Scientific Reports

doi: 10.1038/s41598-018-34088-1

Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3-4 16S rRNA gene amplicons obtained for individual influent, reactor, and granular samples. Each bar represents one sample. D: day; PP: pulp and paper granules; Inf HA: influent to HA reactors; Inf LA: influent to LA reactors; Cand .: Candidatus ; g.i.s .: genera_incertae_sedis . “Unclassified” indicates that OTUs could not be classified at the domain level, “Uncl” indicates that OTUs could not be classified at class level ( A ) or family level ( B ). Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” includes all reads representing the taxa with lower abundance in all samples.
Figure Legend Snippet: Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3-4 16S rRNA gene amplicons obtained for individual influent, reactor, and granular samples. Each bar represents one sample. D: day; PP: pulp and paper granules; Inf HA: influent to HA reactors; Inf LA: influent to LA reactors; Cand .: Candidatus ; g.i.s .: genera_incertae_sedis . “Unclassified” indicates that OTUs could not be classified at the domain level, “Uncl” indicates that OTUs could not be classified at class level ( A ) or family level ( B ). Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” includes all reads representing the taxa with lower abundance in all samples.

Techniques Used: Sequencing

23) Product Images from "Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems"

Article Title: Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-017-0929-3

Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown
Figure Legend Snippet: Taxonomic classification of bacterial 16S rRNA sequences from bacterial communities of PEMF-MMFCs and PEMF-OFF-MMFCs at the phylum level ( a ) and class level ( b ). The relative abundances of the top 10 phyla and classes are shown

Techniques Used:

24) Product Images from "Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake"

Article Title: Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake

Journal: mBio

doi: 10.1128/mBio.00916-18

Microbial community composition in the lake Alinen Mustajärvi based on 16S rRNA genes in 2008 (a clone library) (A), 16S rRNA genes in 2013 (Illumina MiSeq) (B), and metagenome-assembled genomes from 2013 (Illumina HiSeq) (C). In panels B and C, different operational taxonomic units (OTUs) of the same phylum are separated by black lines. The black bars on the y axes show the location of the oxygen depletion zone.
Figure Legend Snippet: Microbial community composition in the lake Alinen Mustajärvi based on 16S rRNA genes in 2008 (a clone library) (A), 16S rRNA genes in 2013 (Illumina MiSeq) (B), and metagenome-assembled genomes from 2013 (Illumina HiSeq) (C). In panels B and C, different operational taxonomic units (OTUs) of the same phylum are separated by black lines. The black bars on the y axes show the location of the oxygen depletion zone.

Techniques Used:

25) Product Images from "Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge"

Article Title: Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge

Journal: Microbes and Environments

doi: 10.1264/jsme2.ME16067

Taxonomic classification of bacterial communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each bacterial phylum and class. Sequence reads that are not classified into any known bacterial group were labeled as “other”. Approximately 4% of all reads were archeal 16S rRNA gene sequences, which are not shown in this figure (but are shown in Fig. 6a ). (b) Abundance of 16S rRNA gene sequences from each bacterial genus in major bacterial groups (the class Deltaproteobacteria and phyla Bacteroidetes , Firmicutes , and Chloroflexi ). Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively.
Figure Legend Snippet: Taxonomic classification of bacterial communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each bacterial phylum and class. Sequence reads that are not classified into any known bacterial group were labeled as “other”. Approximately 4% of all reads were archeal 16S rRNA gene sequences, which are not shown in this figure (but are shown in Fig. 6a ). (b) Abundance of 16S rRNA gene sequences from each bacterial genus in major bacterial groups (the class Deltaproteobacteria and phyla Bacteroidetes , Firmicutes , and Chloroflexi ). Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively.

Techniques Used: Flow Cytometry, Sequencing, Labeling

Taxonomic classification of archaeal communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each archaeal class. Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively. (b) A 16S rRNA-based neighbor-joining (NJ) tree showing the phylogenetic affiliations of archaeal operational taxonomic units (OTUs) in the UASB reactors. Boldface indicates OTUs found in the present study. The scale bar represents the substitution of 5% of bases. Branching points that support probability > 75% in the bootstrap analyses (based on 1,000 replicates, estimated using the NJ method, maximum likelihood method [ML], maximum parsimony method [MP], and unweighted pair group method with an arithmetic mean [UPGMA]) are shown as black squares. The abundance of sequence reads that are affiliated with each OTU is shown in the graph on the right.
Figure Legend Snippet: Taxonomic classification of archaeal communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each archaeal class. Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively. (b) A 16S rRNA-based neighbor-joining (NJ) tree showing the phylogenetic affiliations of archaeal operational taxonomic units (OTUs) in the UASB reactors. Boldface indicates OTUs found in the present study. The scale bar represents the substitution of 5% of bases. Branching points that support probability > 75% in the bootstrap analyses (based on 1,000 replicates, estimated using the NJ method, maximum likelihood method [ML], maximum parsimony method [MP], and unweighted pair group method with an arithmetic mean [UPGMA]) are shown as black squares. The abundance of sequence reads that are affiliated with each OTU is shown in the graph on the right.

Techniques Used: Flow Cytometry, Sequencing

26) Product Images from "Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge"

Article Title: Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge

Journal: Microbes and Environments

doi: 10.1264/jsme2.ME16067

Taxonomic classification of bacterial communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each bacterial phylum and class. Sequence reads that are not classified into any known bacterial group were labeled as “other”. Approximately 4% of all reads were archeal 16S rRNA gene sequences, which are not shown in this figure (but are shown in Fig. 6a ). (b) Abundance of 16S rRNA gene sequences from each bacterial genus in major bacterial groups (the class Deltaproteobacteria and phyla Bacteroidetes , Firmicutes , and Chloroflexi ). Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively.
Figure Legend Snippet: Taxonomic classification of bacterial communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each bacterial phylum and class. Sequence reads that are not classified into any known bacterial group were labeled as “other”. Approximately 4% of all reads were archeal 16S rRNA gene sequences, which are not shown in this figure (but are shown in Fig. 6a ). (b) Abundance of 16S rRNA gene sequences from each bacterial genus in major bacterial groups (the class Deltaproteobacteria and phyla Bacteroidetes , Firmicutes , and Chloroflexi ). Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively.

Techniques Used: Flow Cytometry, Sequencing, Labeling

Taxonomic classification of archaeal communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each archaeal class. Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively. (b) A 16S rRNA-based neighbor-joining (NJ) tree showing the phylogenetic affiliations of archaeal operational taxonomic units (OTUs) in the UASB reactors. Boldface indicates OTUs found in the present study. The scale bar represents the substitution of 5% of bases. Branching points that support probability > 75% in the bootstrap analyses (based on 1,000 replicates, estimated using the NJ method, maximum likelihood method [ML], maximum parsimony method [MP], and unweighted pair group method with an arithmetic mean [UPGMA]) are shown as black squares. The abundance of sequence reads that are affiliated with each OTU is shown in the graph on the right.
Figure Legend Snippet: Taxonomic classification of archaeal communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each archaeal class. Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively. (b) A 16S rRNA-based neighbor-joining (NJ) tree showing the phylogenetic affiliations of archaeal operational taxonomic units (OTUs) in the UASB reactors. Boldface indicates OTUs found in the present study. The scale bar represents the substitution of 5% of bases. Branching points that support probability > 75% in the bootstrap analyses (based on 1,000 replicates, estimated using the NJ method, maximum likelihood method [ML], maximum parsimony method [MP], and unweighted pair group method with an arithmetic mean [UPGMA]) are shown as black squares. The abundance of sequence reads that are affiliated with each OTU is shown in the graph on the right.

Techniques Used: Flow Cytometry, Sequencing

27) Product Images from "Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester"

Article Title: Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.01955-16

Phylogenetic distribution of the most dominant 16S rRNA gene sequences in FrBGR. Details for the Euryarchaeota (not visible in the major plot because of low abundance) are provided in a separate plot to the lower left. Scattered areas contain two or more
Figure Legend Snippet: Phylogenetic distribution of the most dominant 16S rRNA gene sequences in FrBGR. Details for the Euryarchaeota (not visible in the major plot because of low abundance) are provided in a separate plot to the lower left. Scattered areas contain two or more

Techniques Used:

28) Product Images from "The Microbiome of Ehrlichia-Infected and Uninfected Lone Star Ticks (Amblyomma americanum)"

Article Title: The Microbiome of Ehrlichia-Infected and Uninfected Lone Star Ticks (Amblyomma americanum)

Journal: PLoS ONE

doi: 10.1371/journal.pone.0146651

Female ticks had significantly higher relative abundance of Ehrlichia compared to males. The relative abundance of Ehrlichia (OTU052) in the 16S rRNA gene libraries was significantly higher in females compared to males (ANOVA F = 3.587, P = 0.064).
Figure Legend Snippet: Female ticks had significantly higher relative abundance of Ehrlichia compared to males. The relative abundance of Ehrlichia (OTU052) in the 16S rRNA gene libraries was significantly higher in females compared to males (ANOVA F = 3.587, P = 0.064).

Techniques Used:

29) Product Images from "A Methanogenic Consortium Was Active and Exhibited Long-Term Survival in an Extremely Acidified Thermophilic Bioreactor"

Article Title: A Methanogenic Consortium Was Active and Exhibited Long-Term Survival in an Extremely Acidified Thermophilic Bioreactor

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2019.02757

Heatmap of (A) archaeal and (B) bacterial composition of the microbial communities at the genus level in different reactors based on the 16S rRNA data. Only genera with relative percentage higher than 1% are shown. The genera with relative percentage lower than 1% were aggregated as Other archaeal genera and Other bacterial genera. (C) Principal component analysis (PCA) based on the relative abundance of microbial species. (▼) Reactor RS_7.0, (▲) Reactor RA_7.0-8.0, (●) Reactor RB_6.0-5.5-5.0, (◆) Reactor RC_6.0-5.0, (■) Reactor RD_5.5.
Figure Legend Snippet: Heatmap of (A) archaeal and (B) bacterial composition of the microbial communities at the genus level in different reactors based on the 16S rRNA data. Only genera with relative percentage higher than 1% are shown. The genera with relative percentage lower than 1% were aggregated as Other archaeal genera and Other bacterial genera. (C) Principal component analysis (PCA) based on the relative abundance of microbial species. (▼) Reactor RS_7.0, (▲) Reactor RA_7.0-8.0, (●) Reactor RB_6.0-5.5-5.0, (◆) Reactor RC_6.0-5.0, (■) Reactor RD_5.5.

Techniques Used:

30) Product Images from "Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells"

Article Title: Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0098425

Relative abundances of genus-level phylogenetic groups based on pyrosequenced 16S rRNA-gene amplicons showing structures of bacterial communities in the original sludge, anode biofilm, cathode biofilm, and electrolyte.
Figure Legend Snippet: Relative abundances of genus-level phylogenetic groups based on pyrosequenced 16S rRNA-gene amplicons showing structures of bacterial communities in the original sludge, anode biofilm, cathode biofilm, and electrolyte.

Techniques Used:

31) Product Images from "Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells"

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

Journal: PLoS ONE

doi: 10.1371/journal.pone.0077443

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.
Figure Legend 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.

Techniques Used: Sequencing

32) Product Images from "Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge"

Article Title: Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge

Journal: Microbes and Environments

doi: 10.1264/jsme2.ME16067

Taxonomic classification of bacterial communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each bacterial phylum and class. Sequence reads that are not classified into any known bacterial group were labeled as “other”. Approximately 4% of all reads were archeal 16S rRNA gene sequences, which are not shown in this figure (but are shown in Fig. 6a ). (b) Abundance of 16S rRNA gene sequences from each bacterial genus in major bacterial groups (the class Deltaproteobacteria and phyla Bacteroidetes , Firmicutes , and Chloroflexi ). Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively.
Figure Legend Snippet: Taxonomic classification of bacterial communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each bacterial phylum and class. Sequence reads that are not classified into any known bacterial group were labeled as “other”. Approximately 4% of all reads were archeal 16S rRNA gene sequences, which are not shown in this figure (but are shown in Fig. 6a ). (b) Abundance of 16S rRNA gene sequences from each bacterial genus in major bacterial groups (the class Deltaproteobacteria and phyla Bacteroidetes , Firmicutes , and Chloroflexi ). Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively.

Techniques Used: Flow Cytometry, Sequencing, Labeling

Taxonomic classification of archaeal communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each archaeal class. Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively. (b) A 16S rRNA-based neighbor-joining (NJ) tree showing the phylogenetic affiliations of archaeal operational taxonomic units (OTUs) in the UASB reactors. Boldface indicates OTUs found in the present study. The scale bar represents the substitution of 5% of bases. Branching points that support probability > 75% in the bootstrap analyses (based on 1,000 replicates, estimated using the NJ method, maximum likelihood method [ML], maximum parsimony method [MP], and unweighted pair group method with an arithmetic mean [UPGMA]) are shown as black squares. The abundance of sequence reads that are affiliated with each OTU is shown in the graph on the right.
Figure Legend Snippet: Taxonomic classification of archaeal communities in anaerobic granular sludge collected after 171 d of operation of an up-flow anaerobic sludge blanket (UASB) reactor. (a) Abundance of 16S rRNA gene sequences from each archaeal class. Coculture and control: UASB reactors with and without Metopus and Caenomorpha ciliates, respectively. (b) A 16S rRNA-based neighbor-joining (NJ) tree showing the phylogenetic affiliations of archaeal operational taxonomic units (OTUs) in the UASB reactors. Boldface indicates OTUs found in the present study. The scale bar represents the substitution of 5% of bases. Branching points that support probability > 75% in the bootstrap analyses (based on 1,000 replicates, estimated using the NJ method, maximum likelihood method [ML], maximum parsimony method [MP], and unweighted pair group method with an arithmetic mean [UPGMA]) are shown as black squares. The abundance of sequence reads that are affiliated with each OTU is shown in the graph on the right.

Techniques Used: Flow Cytometry, Sequencing

33) Product Images from "Analysis of the Bacterial Communities in Two Liquors of Soy Sauce Aroma as Revealed by High-Throughput Sequencing of the 16S rRNA V4 Hypervariable Region"

Article Title: Analysis of the Bacterial Communities in Two Liquors of Soy Sauce Aroma as Revealed by High-Throughput Sequencing of the 16S rRNA V4 Hypervariable Region

Journal: BioMed Research International

doi: 10.1155/2017/6271358

Abundance of the dominant taxonomy (relative abundance of phylum > 0.1% and of family > 1.0%) determined by 16S rRNA gene sequencing. Numbers in cells are percentages of relative abundance, highest abundances are red, middle values are in white, and lowest values are in blue. An asterisk indicates a significant different between the Guotai-liquor Daqu and the Maotai-liquor Daqu. ( t -test, ∗ p
Figure Legend Snippet: Abundance of the dominant taxonomy (relative abundance of phylum > 0.1% and of family > 1.0%) determined by 16S rRNA gene sequencing. Numbers in cells are percentages of relative abundance, highest abundances are red, middle values are in white, and lowest values are in blue. An asterisk indicates a significant different between the Guotai-liquor Daqu and the Maotai-liquor Daqu. ( t -test, ∗ p

Techniques Used: Sequencing

34) Product Images from "Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ"

Article Title: Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ

Journal: ERJ Open Research

doi: 10.1183/23120541.00008-2017

Microbiomic changes during inhaled interferon (IFN)-γ. a) Comparison of α diversity (based on the Shannon Index where sequences were rarified at 1000 reads per sample) before and after treatment. b) Changes in β diversity (based on UniFrac distances) before and after IFN-γ (p-value based on PERMANOVA (permutational multivariate ANOVA)). PC: principal coordinate; ns : nonsignificant. c) β diversity distance (based on UniFrac distances) between pairs of samples comparing within subject (before–after IFN-γ) versus between subjects (p-value based on Mann–Whitney test). d) Linear discriminant analysis (LDA) effect size was calculated comparing 16S rRNA data at baseline and after IFN-γ.
Figure Legend Snippet: Microbiomic changes during inhaled interferon (IFN)-γ. a) Comparison of α diversity (based on the Shannon Index where sequences were rarified at 1000 reads per sample) before and after treatment. b) Changes in β diversity (based on UniFrac distances) before and after IFN-γ (p-value based on PERMANOVA (permutational multivariate ANOVA)). PC: principal coordinate; ns : nonsignificant. c) β diversity distance (based on UniFrac distances) between pairs of samples comparing within subject (before–after IFN-γ) versus between subjects (p-value based on Mann–Whitney test). d) Linear discriminant analysis (LDA) effect size was calculated comparing 16S rRNA data at baseline and after IFN-γ.

Techniques Used: Significance Assay, MANN-WHITNEY

35) Product Images from "Reagent and laboratory contamination can critically impact sequence-based microbiome analyses"

Article Title: Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Journal: BMC Biology

doi: 10.1186/s12915-014-0087-z

Summary of 16S rRNA gene sequencing taxonomic assignment from ten-fold diluted pure cultures and controls. Undiluted DNA extractions contained approximately 10 8 cells, and controls (annotated in the Figure with 'con') were template-free PCRs. DNA was extracted at ICL, UB and WTSI laboratories and amplified with 40 PCR cycles. Each column represents a single sample; sections (a) and (b) describe the same samples at different taxonomic levels. a) Proportion of S. bongori sequence reads in black. The proportional abundance of non- Salmonella reads at the Class level is indicated by other colours. As the sample becomes more dilute, the proportion of the sequenced bacterial amplicons from the cultured microorganism decreases and contaminants become more dominant. b) Abundance of genera which make up > 0.5% of the results from at least one laboratory, excluding S. bongori . The profiles of the non- Salmonella reads within each laboratory/kit batch are consistent but differ between sites.
Figure Legend Snippet: Summary of 16S rRNA gene sequencing taxonomic assignment from ten-fold diluted pure cultures and controls. Undiluted DNA extractions contained approximately 10 8 cells, and controls (annotated in the Figure with 'con') were template-free PCRs. DNA was extracted at ICL, UB and WTSI laboratories and amplified with 40 PCR cycles. Each column represents a single sample; sections (a) and (b) describe the same samples at different taxonomic levels. a) Proportion of S. bongori sequence reads in black. The proportional abundance of non- Salmonella reads at the Class level is indicated by other colours. As the sample becomes more dilute, the proportion of the sequenced bacterial amplicons from the cultured microorganism decreases and contaminants become more dominant. b) Abundance of genera which make up > 0.5% of the results from at least one laboratory, excluding S. bongori . The profiles of the non- Salmonella reads within each laboratory/kit batch are consistent but differ between sites.

Techniques Used: Sequencing, Amplification, Polymerase Chain Reaction, Cell Culture

Copy number of total 16S rRNA genes present in a dilution series of S. bongori culture. Total bacterial DNA present in serial ten-fold dilutions of a pure S. bongori culture was quantified using qPCR. While the copy number initially reduces in tandem with increased dilution, plateauing after four dilutions indicates consistent background levels of contaminating DNA. Error bars indicate standard deviation of triplicate reactions. The broken red line indicates the detection limit of 45 copies of 16S rRNA genes. The no template internal control for the qPCR reactions (shown in blue) was below the cycle threshold selected for interpreting the fluorescence values (that is, less than 0), indicating the contamination did not come from the qPCR reagents themselves.
Figure Legend Snippet: Copy number of total 16S rRNA genes present in a dilution series of S. bongori culture. Total bacterial DNA present in serial ten-fold dilutions of a pure S. bongori culture was quantified using qPCR. While the copy number initially reduces in tandem with increased dilution, plateauing after four dilutions indicates consistent background levels of contaminating DNA. Error bars indicate standard deviation of triplicate reactions. The broken red line indicates the detection limit of 45 copies of 16S rRNA genes. The no template internal control for the qPCR reactions (shown in blue) was below the cycle threshold selected for interpreting the fluorescence values (that is, less than 0), indicating the contamination did not come from the qPCR reagents themselves.

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

36) Product Images from "Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells"

Article Title: Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0098425

Relative abundances of genus-level phylogenetic groups based on pyrosequenced 16S rRNA-gene amplicons showing structures of bacterial communities in the original sludge, anode biofilm, cathode biofilm, and electrolyte.
Figure Legend Snippet: Relative abundances of genus-level phylogenetic groups based on pyrosequenced 16S rRNA-gene amplicons showing structures of bacterial communities in the original sludge, anode biofilm, cathode biofilm, and electrolyte.

Techniques Used:

37) Product Images from "Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells"

Article Title: Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0098425

Relative abundances of genus-level phylogenetic groups based on pyrosequenced 16S rRNA-gene amplicons showing structures of bacterial communities in the original sludge, anode biofilm, cathode biofilm, and electrolyte.
Figure Legend Snippet: Relative abundances of genus-level phylogenetic groups based on pyrosequenced 16S rRNA-gene amplicons showing structures of bacterial communities in the original sludge, anode biofilm, cathode biofilm, and electrolyte.

Techniques Used:

38) Product Images from "Characterization of sediment bacterial communities in plain lakes with different trophic statuses. Characterization of sediment bacterial communities in plain lakes with different trophic statuses"

Article Title: Characterization of sediment bacterial communities in plain lakes with different trophic statuses. Characterization of sediment bacterial communities in plain lakes with different trophic statuses

Journal: MicrobiologyOpen

doi: 10.1002/mbo3.503

Diversity indices of 16S rRNA gene libraries with significant differences ( p
Figure Legend Snippet: Diversity indices of 16S rRNA gene libraries with significant differences ( p

Techniques Used:

39) Product Images from "Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar"

Article Title: Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar

Journal: Scientific Reports

doi: 10.1038/srep44382

Effect of greenhouse waste (GHW-350) biochar on relative abundances of rhizosphere bacterial composition at Phylum level (inner circle) and Order level (outer circle) as identified by using the Illumina sequencing of 16S rRNA gene amplicons.
Figure Legend Snippet: Effect of greenhouse waste (GHW-350) biochar on relative abundances of rhizosphere bacterial composition at Phylum level (inner circle) and Order level (outer circle) as identified by using the Illumina sequencing of 16S rRNA gene amplicons.

Techniques Used: Sequencing

Effect of greenhouse waste (GHW-350) biochar amendments on alpha diversity of rhizosphere microbial community composition and microbial metabolic potential. Taxon based Shannon’s diversity index ( A ), Taxon based phylotype richness, using OTUs (97% identity) as identified by the Illumina sequencing of 16S rRNA gene amplicons using QIIME ( B ), Functional Shannon’s diversity index ( C ), Functional richness, based on 95 carbon substrate utilization patterns obtained with Biolog Microplates ( D ). Columns labeled by a different capital letter are significantly different at P ≤ 0.05 according to Student’s t-test. Bars represent the standard error.
Figure Legend Snippet: Effect of greenhouse waste (GHW-350) biochar amendments on alpha diversity of rhizosphere microbial community composition and microbial metabolic potential. Taxon based Shannon’s diversity index ( A ), Taxon based phylotype richness, using OTUs (97% identity) as identified by the Illumina sequencing of 16S rRNA gene amplicons using QIIME ( B ), Functional Shannon’s diversity index ( C ), Functional richness, based on 95 carbon substrate utilization patterns obtained with Biolog Microplates ( D ). Columns labeled by a different capital letter are significantly different at P ≤ 0.05 according to Student’s t-test. Bars represent the standard error.

Techniques Used: Sequencing, Functional Assay, Labeling

40) Product Images from "Desulfitobacterium contributes to the microbial transformation of 2,4,5‐T by methanogenic enrichment cultures from a Vietnamese active landfill"

Article Title: Desulfitobacterium contributes to the microbial transformation of 2,4,5‐T by methanogenic enrichment cultures from a Vietnamese active landfill

Journal: Microbial Biotechnology

doi: 10.1111/1751-7915.13301

Increase in the copy number of Desulfitobacterium sp. 16S rRNA genes during 2,4,5‐T conversion to 3,4‐ DCP in culture BH 1.1. The concentration of 2,4,5‐ TCP did not exceed 2 μM over the course of the experiment (not shown). After 8 days, pyruvate and citrate were completely converted to acetate (data not shown). Mean values and SD from duplicate cultures and triplicate qPCR analyses are given.
Figure Legend Snippet: Increase in the copy number of Desulfitobacterium sp. 16S rRNA genes during 2,4,5‐T conversion to 3,4‐ DCP in culture BH 1.1. The concentration of 2,4,5‐ TCP did not exceed 2 μM over the course of the experiment (not shown). After 8 days, pyruvate and citrate were completely converted to acetate (data not shown). Mean values and SD from duplicate cultures and triplicate qPCR analyses are given.

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

Related Articles

Sequencing:

Article Title: Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors
Article Snippet: .. Illumina sequencing of 16S rRNA gene amplicons was applied for detailed characterization of bacterial and archaeal communities associated both with liquid fraction and the aggregates in the solid fraction of both the influents and reactors. ..

Article Title: Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells
Article Snippet: .. The microbiomes established in each system were compared by pyrotag sequencing of 16S rRNA gene amplicons and shotgun metagenomics. ..

Article Title: Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells
Article Snippet: .. Phylogenetic analyses of 16S rRNA pyrotag sequences To compare the phylogenetic compositions of bacteria associated with anodes of the sMFC and acetate- and glucose-fed MFCs, pyrotag sequencing of 16S rRNA-gene amplicons [ ] was conducted using DNA samples obtained from anode-associated soil of rhizosphere sMFCs (anode-associated soil), and the anode biofilms of acetate-fed MFCs (AM-anode biofilm) and glucose-fed MFC (GM-anode biofilm). ..

Article Title: Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems
Article Snippet: .. High-throughput sequencing of 16S rRNA gene amplicons was carried out on the Illumina HiSeq 2500 platform. .. Effective reads were obtained after the raw reads were trimmed, filtered, and removed chimeric sequences using QIIME software ( http://qiime.org ).

High Throughput Screening Assay:

Article Title: Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems
Article Snippet: .. High-throughput sequencing of 16S rRNA gene amplicons was carried out on the Illumina HiSeq 2500 platform. .. Effective reads were obtained after the raw reads were trimmed, filtered, and removed chimeric sequences using QIIME software ( http://qiime.org ).

Amplification:

Article Title: Isolation and characterization of Magnetospirillum sp. strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model
Article Snippet: .. Those Illumina 16S rRNA gene amplicons obtained previously from the PFRs that affiliated with Magnetospirillum (OTU 10-PFR-2; 6% relative abundance of all OTUs) had 100% identity with the respective 16S rRNA amplified region of strain 15–1 ( ). .. Growth with toluene under nitrate-reducing conditions Cells of strain 15–1 were cultured anaerobically in mineral medium using toluene at different concentrations (0.3 to 1 mM) as sole energy and carbon source and 5 mM of KNO3 as terminal electron acceptor.

other:

Article Title: Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases
Article Snippet: Sinclair L, Osman OA, Bertilsson S, Eiler A. Microbial community composition and diversity via 16S rRNA gene amplicons: Evaluating the Illumina platform.

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  • 93
    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 154 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/16s rrna gene amplicons/product/Illumina Inc
    Average 93 stars, based on 154 article reviews
    Price from $9.99 to $1999.99
    16s rrna gene amplicons - by Bioz Stars, 2020-08
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    90
    Illumina Inc bacterial 16s rrna gene amplicons
    Sequence abundances of the top most abundant unique OTUs for each sample size and their corresponding classification for the bacterial <t>16S</t> <t>rRNA</t> gene sequences . OTUs that were shared among all sample sizes are shown in the “All Shared” inset with those shared between the SARDI 10 g and MoBIO 10 g in an additional inset. Within the Venn diagram, top numbers indicate the percent of total OTUs while the bottom represents the percent of total sequences.
    Bacterial 16s Rrna Gene Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bacterial 16s rrna gene amplicons/product/Illumina Inc
    Average 90 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    bacterial 16s rrna gene amplicons - by Bioz Stars, 2020-08
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    94
    Illumina Inc 16s rrna gene amplicon illumina miseq sequencing
    <t>16S</t> <t>rRNA</t> gene <t>amplicon</t> sequencing of 15 samples including 8 whole community samples and 7 sorted subcommunities. Data are shown for Setup 1. The 8 whole community samples included inoculum, silver ion negative control (Neg, 7 and 24 d) and 0.1 mg/L AgNP-10 (LAg10, 7 and 24 d), silver ion positive control (Pos, 24 d), 2.25 mg/L AgNP-10 (EC 50 Ag10, 24 d), 7.13 mg/L AgNP-30 (EC 50 .
    16s Rrna Gene Amplicon Illumina Miseq Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/16s rrna gene amplicon illumina miseq sequencing/product/Illumina Inc
    Average 94 stars, based on 6 article reviews
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    16s rrna gene amplicon illumina miseq sequencing - by Bioz Stars, 2020-08
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    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

    Sequence abundances of the top most abundant unique OTUs for each sample size and their corresponding classification for the bacterial 16S rRNA gene sequences . OTUs that were shared among all sample sizes are shown in the “All Shared” inset with those shared between the SARDI 10 g and MoBIO 10 g in an additional inset. Within the Venn diagram, top numbers indicate the percent of total OTUs while the bottom represents the percent of total sequences.

    Journal: Frontiers in Microbiology

    Article Title: Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

    doi: 10.3389/fmicb.2016.00824

    Figure Lengend Snippet: Sequence abundances of the top most abundant unique OTUs for each sample size and their corresponding classification for the bacterial 16S rRNA gene sequences . OTUs that were shared among all sample sizes are shown in the “All Shared” inset with those shared between the SARDI 10 g and MoBIO 10 g in an additional inset. Within the Venn diagram, top numbers indicate the percent of total OTUs while the bottom represents the percent of total sequences.

    Article Snippet: Bacterial 16S rRNA gene amplicons were sequenced on the Illumina MiSeq platform (2 bp × 250 bp paired end reads).

    Techniques: Sequencing

    Non-metric dimensional scaling (NMDS) of 28S rRNA gene data (A) and of 16S rRNA gene data (B) . Groupings are based on SIMPROF with complete linkage clustering at 95% confidence at 30% (28S) and 60% (16S) similarities. 2D stress was 0.21 (A) and 0.14 (B) .

    Journal: Frontiers in Microbiology

    Article Title: Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

    doi: 10.3389/fmicb.2016.00824

    Figure Lengend Snippet: Non-metric dimensional scaling (NMDS) of 28S rRNA gene data (A) and of 16S rRNA gene data (B) . Groupings are based on SIMPROF with complete linkage clustering at 95% confidence at 30% (28S) and 60% (16S) similarities. 2D stress was 0.21 (A) and 0.14 (B) .

    Article Snippet: Bacterial 16S rRNA gene amplicons were sequenced on the Illumina MiSeq platform (2 bp × 250 bp paired end reads).

    Techniques:

    16S rRNA gene amplicon sequencing of 15 samples including 8 whole community samples and 7 sorted subcommunities. Data are shown for Setup 1. The 8 whole community samples included inoculum, silver ion negative control (Neg, 7 and 24 d) and 0.1 mg/L AgNP-10 (LAg10, 7 and 24 d), silver ion positive control (Pos, 24 d), 2.25 mg/L AgNP-10 (EC 50 Ag10, 24 d), 7.13 mg/L AgNP-30 (EC 50 .

    Journal: Frontiers in Microbiology

    Article Title: AgNPs Change Microbial Community Structures of Wastewater

    doi: 10.3389/fmicb.2018.03211

    Figure Lengend Snippet: 16S rRNA gene amplicon sequencing of 15 samples including 8 whole community samples and 7 sorted subcommunities. Data are shown for Setup 1. The 8 whole community samples included inoculum, silver ion negative control (Neg, 7 and 24 d) and 0.1 mg/L AgNP-10 (LAg10, 7 and 24 d), silver ion positive control (Pos, 24 d), 2.25 mg/L AgNP-10 (EC 50 Ag10, 24 d), 7.13 mg/L AgNP-30 (EC 50 .

    Article Snippet: In this lab-scale study, flow cytometry as a high-throughput method and 16S rRNA gene amplicon Illumina MiSeq sequencing were used to track microbial community structure changes when being exposed to AgNPs.

    Techniques: Amplification, Sequencing, Negative Control, Positive Control