Structured Review

Illumina Inc 16s rrna amplicons
LEfSe analysis identified the most differentially abundant taxa between CA and PA. The taxonomic cladogram was obtained from LEfSe analysis of <t>16S</t> <t>rRNA</t> sequences; only taxa meeting an LDA significance threshold of 4.0 are shown. Small circles and shading with different colors in the diagram represent the abundance of those taxa in the respective group. Yellow circles represent nonsignificant differences in abundance between CA and PA for that particular taxonomic group. The brightness of each dot is proportional to its effect size. Taxa enriched in PA are shown with a positive LDA score (green) and taxa enriched in CA have a negative score (red). CA means sparging air; PA means culturing C. pyrenoidosa with sparging air
16s Rrna Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 88 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Comprehensive evaluation of a cost-effective method of culturing Chlorella pyrenoidosa with unsterilized piggery wastewater for biofuel production"

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

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-019-1407-x

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

Techniques Used: Sparging

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

Techniques Used: Sparging

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

Techniques Used: Sparging, Standard Deviation

2) Product Images from "Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products"

Article Title: Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products

Journal: mSphere

doi: 10.1128/mSphere.00410-18

Relative abundance of taxa in the 16S rRNA PCR amplicon and gDNA mock communities. Relative abundances of expected taxa are labeled with the corresponding taxonomic level from sequencing results. “Amplicon” represents the 16S rRNA PCR amplicon mock community, and “gDNA” represents the gDNA mock community. The results shown were analyzed following the DADA2 pipeline with the Greengenes database. Each bar represents the mean ± SD from three replicates. Proportions for each community were compared to expected proportions using ANOVA with Bonferroni’s multiple-comparison test. P values of
Figure Legend Snippet: Relative abundance of taxa in the 16S rRNA PCR amplicon and gDNA mock communities. Relative abundances of expected taxa are labeled with the corresponding taxonomic level from sequencing results. “Amplicon” represents the 16S rRNA PCR amplicon mock community, and “gDNA” represents the gDNA mock community. The results shown were analyzed following the DADA2 pipeline with the Greengenes database. Each bar represents the mean ± SD from three replicates. Proportions for each community were compared to expected proportions using ANOVA with Bonferroni’s multiple-comparison test. P values of

Techniques Used: Polymerase Chain Reaction, Amplification, Labeling, Sequencing

3) Product Images from "The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights"

Article Title: The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2017.01387

Taxonomic abundance of microbial reads in sponges and seawater at the phylum level. Microbial reads of 16S rRNA gene amplicons were assigned taxonomically using the RDP classifier against the SILVA 111 database with a confidence threshold of 50%. Sample IDs are referred to Table 1 .
Figure Legend Snippet: Taxonomic abundance of microbial reads in sponges and seawater at the phylum level. Microbial reads of 16S rRNA gene amplicons were assigned taxonomically using the RDP classifier against the SILVA 111 database with a confidence threshold of 50%. Sample IDs are referred to Table 1 .

Techniques Used:

Phylogenetic tree of representative highly abundant OTUs and their relatives. The tree was constructed based on partial 16S rRNA gene sequences by the neighbor-joining method. Bootstrap values are expressed based on 1,000 replications, and only values more than 50% are shown. Bar, 5% estimated sequences divergence. The abundance of OTUs included on the tree are shown in Figure 3 . The brackets including “G” indicates strains with reported genomes.
Figure Legend Snippet: Phylogenetic tree of representative highly abundant OTUs and their relatives. The tree was constructed based on partial 16S rRNA gene sequences by the neighbor-joining method. Bootstrap values are expressed based on 1,000 replications, and only values more than 50% are shown. Bar, 5% estimated sequences divergence. The abundance of OTUs included on the tree are shown in Figure 3 . The brackets including “G” indicates strains with reported genomes.

Techniques Used: Construct

4) Product Images from "Comparison of Nitrate and Perchlorate in Controlling Sulfidogenesis in Heavy Oil-Containing Bioreactors"

Article Title: Comparison of Nitrate and Perchlorate in Controlling Sulfidogenesis in Heavy Oil-Containing Bioreactors

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02423

Relational tree for 16S rRNA gene libraries from incubations of CSBK medium, inoculated with 18PW and amended with 1 mL MHGC oil and sulfate (SO); sulfate and nitrate (SNO); sulfate and perchlorate (PSO); sulfate, nitrate, and perchlorate (PSNO); or perchlorate only (PO). Community DNA was obtained from cells harvested at day 9, 65, 85, or 123 as indicated. The fractions of reads in classes of Proteobacteria (A) and in other phyla (B) are shown.
Figure Legend Snippet: Relational tree for 16S rRNA gene libraries from incubations of CSBK medium, inoculated with 18PW and amended with 1 mL MHGC oil and sulfate (SO); sulfate and nitrate (SNO); sulfate and perchlorate (PSO); sulfate, nitrate, and perchlorate (PSNO); or perchlorate only (PO). Community DNA was obtained from cells harvested at day 9, 65, 85, or 123 as indicated. The fractions of reads in classes of Proteobacteria (A) and in other phyla (B) are shown.

Techniques Used:

Neighbor-joining phylogenetic tree indicating the affiliation of isolates PRB2 and PRB4 with members of the genus Magnetospirillum based on the 16S rRNA gene sequences. Branching points are determined as percentage of bootstrap values based on 1000 replications with those having a cut-off at 50% shown. The scale bar of 0.05 represents the fractional change per nucleotide. The sequence of Magnetococcus marinus MC-1 (NR_074371) was used as an outgroup.
Figure Legend Snippet: Neighbor-joining phylogenetic tree indicating the affiliation of isolates PRB2 and PRB4 with members of the genus Magnetospirillum based on the 16S rRNA gene sequences. Branching points are determined as percentage of bootstrap values based on 1000 replications with those having a cut-off at 50% shown. The scale bar of 0.05 represents the fractional change per nucleotide. The sequence of Magnetococcus marinus MC-1 (NR_074371) was used as an outgroup.

Techniques Used: Sequencing

5) Product Images from "Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing"

Article Title: Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing

Journal: MicrobiologyOpen

doi: 10.1002/mbo3.367

Denaturing gradient gel electrophoresis band profiles of the V3 region of 16S rRNA produced from the cecal bacterial communities of seven types of chicken. LM , Lohmann laying hens; DH , Daheng broiler chickens; LS , Lhasa Tibetan Chicken; GZ , Ganzi Tibetan Chicken; AB , Aba Tibetan Chicken; QH , Qinghai Tibetan Chicken; and DQ , Diqing Tibetan Chicken.
Figure Legend Snippet: Denaturing gradient gel electrophoresis band profiles of the V3 region of 16S rRNA produced from the cecal bacterial communities of seven types of chicken. LM , Lohmann laying hens; DH , Daheng broiler chickens; LS , Lhasa Tibetan Chicken; GZ , Ganzi Tibetan Chicken; AB , Aba Tibetan Chicken; QH , Qinghai Tibetan Chicken; and DQ , Diqing Tibetan Chicken.

Techniques Used: Denaturing Gradient Gel Electrophoresis, Produced

6) 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

7) Product Images from "The Fecal Microbiome in Cats with Diarrhea"

Article Title: The Fecal Microbiome in Cats with Diarrhea

Journal: PLoS ONE

doi: 10.1371/journal.pone.0127378

Predicted functional composition of metagenomes based on 16S rRNA gene sequencing data. LEfSe based on the PICRUSt data set revealed differentially enriched bacterial functions associated either with healthy (green) or diseased cats (red).
Figure Legend Snippet: Predicted functional composition of metagenomes based on 16S rRNA gene sequencing data. LEfSe based on the PICRUSt data set revealed differentially enriched bacterial functions associated either with healthy (green) or diseased cats (red).

Techniques Used: Functional Assay, Sequencing

Rarefaction analysis of 16S rRNA gene sequences obtained from feline fecal samples. Lines represent the mean and error bars represent standard deviations. The analysis was performed on a randomly selected subset of 12,000 sequences per sample. (A) Analysis based on duration of diarrhea. (B) Analysis based on the number of stools per day.
Figure Legend Snippet: Rarefaction analysis of 16S rRNA gene sequences obtained from feline fecal samples. Lines represent the mean and error bars represent standard deviations. The analysis was performed on a randomly selected subset of 12,000 sequences per sample. (A) Analysis based on duration of diarrhea. (B) Analysis based on the number of stools per day.

Techniques Used:

Principal Coordinate Analysis (PCoA) of unweighted UniFrac distances of 16S rRNA genes.
Figure Legend Snippet: Principal Coordinate Analysis (PCoA) of unweighted UniFrac distances of 16S rRNA genes.

Techniques Used:

8) Product Images from "Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge"

Article Title: Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge

Journal: mSystems

doi: 10.1128/mSystems.00113-18

(A) Maximum likelihood tree of 16S rRNA gene of steroid-degrading anaerobes and Sterolibacterium -like OTUs. Only enriched OTUs are highlighted. (B) AtcA and its homologues and other molybdopterin-containing xanthine oxidase family members. (C) Alpha subunit of C25DH and its homologues. Subunits (A1 to A4) displaying specificity for side chain substrates are highlighted in blue. Branch support of higher than 50% of bootstrapping time is shown. Details for all reference sequences are provided in Table S3 .
Figure Legend Snippet: (A) Maximum likelihood tree of 16S rRNA gene of steroid-degrading anaerobes and Sterolibacterium -like OTUs. Only enriched OTUs are highlighted. (B) AtcA and its homologues and other molybdopterin-containing xanthine oxidase family members. (C) Alpha subunit of C25DH and its homologues. Subunits (A1 to A4) displaying specificity for side chain substrates are highlighted in blue. Branch support of higher than 50% of bootstrapping time is shown. Details for all reference sequences are provided in Table S3 .

Techniques Used:

9) Product Images from "The metagenomic approach to characterization of the microbial community shift during the long-term cultivation of anammox-enriched granular sludge"

Article Title: The metagenomic approach to characterization of the microbial community shift during the long-term cultivation of anammox-enriched granular sludge

Journal: Journal of Applied Genetics

doi: 10.1007/s13353-017-0418-1

Family level affiliations assigned to contigs with 16S rRNA genes in analyzed samples. Only orders with abundance higher than 1.0% are given
Figure Legend Snippet: Family level affiliations assigned to contigs with 16S rRNA genes in analyzed samples. Only orders with abundance higher than 1.0% are given

Techniques Used:

10) Product Images from "Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture"

Article Title: Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture

Journal: Microorganisms

doi: 10.3390/microorganisms6030065

Distribution of bacterial and archaeal 16S rRNA gene pyrotag sequences in an active naphthalene-degrading replicate of NDC. Values are shown as the percentage of sequences per taxon based on 2034 bacterial sequences and 1881 archaeal sequences. OTUs included in ‘Other’ make up less than 0.4% of prokaryotic sequences each and include Spirochaeta (0.26%), Proteiniphilum (0.13%), and Candidatus Methanoregula (0.36%).
Figure Legend Snippet: Distribution of bacterial and archaeal 16S rRNA gene pyrotag sequences in an active naphthalene-degrading replicate of NDC. Values are shown as the percentage of sequences per taxon based on 2034 bacterial sequences and 1881 archaeal sequences. OTUs included in ‘Other’ make up less than 0.4% of prokaryotic sequences each and include Spirochaeta (0.26%), Proteiniphilum (0.13%), and Candidatus Methanoregula (0.36%).

Techniques Used:

11) Product Images from "High-Throughput 16S rRNA Sequencing to Assess Potentially Active Bacteria and Foodborne Pathogens: A Case Example in Ready-to-Eat Food"

Article Title: High-Throughput 16S rRNA Sequencing to Assess Potentially Active Bacteria and Foodborne Pathogens: A Case Example in Ready-to-Eat Food

Journal: Foods

doi: 10.3390/foods8100480

Principal component analysis (PcoA) of bacterial community structure at the genus level from the analysed RTE salads. The PcoA was performed with “qiime tool collapse” at the desired taxa level using the Euclidean metric to calculate the matrix distance. Samples from total bacterial cells (dormant, dead, and active cells containing 16S rDNA genes) and metabolically active bacteria (cells containing ribosomal RNA, 16S rRNA) are depicted in red and blue colors, respectively. Two close samples in the PcoA indicated that they had similar bacterial species composition and relative abundances of taxa. Although no major differences were observed regarding the abundant bacterial species composition, significant differences in relative abundances were observed (see Figure 2 ), especially for those low abundant species.
Figure Legend Snippet: Principal component analysis (PcoA) of bacterial community structure at the genus level from the analysed RTE salads. The PcoA was performed with “qiime tool collapse” at the desired taxa level using the Euclidean metric to calculate the matrix distance. Samples from total bacterial cells (dormant, dead, and active cells containing 16S rDNA genes) and metabolically active bacteria (cells containing ribosomal RNA, 16S rRNA) are depicted in red and blue colors, respectively. Two close samples in the PcoA indicated that they had similar bacterial species composition and relative abundances of taxa. Although no major differences were observed regarding the abundant bacterial species composition, significant differences in relative abundances were observed (see Figure 2 ), especially for those low abundant species.

Techniques Used: Metabolic Labelling

Workflow of the molecular approach (DNA- and RNA-based) used to characterize the bacterial community and the active bacterial fraction in the studied RTE salads. Electrophoresis shows the PCR and RT-PCR results of the 16S rDNA/rRNA. PCR control of undigested 16S rDNA genes is shown. C+: positive control of PCR and RT-PCR; C-: negative control of PCR and RT-PCR; L: ladder indicating the size (bp). Lanes marked as S1, S2, and S3 correspond to the analyzed RTE samples.
Figure Legend Snippet: Workflow of the molecular approach (DNA- and RNA-based) used to characterize the bacterial community and the active bacterial fraction in the studied RTE salads. Electrophoresis shows the PCR and RT-PCR results of the 16S rDNA/rRNA. PCR control of undigested 16S rDNA genes is shown. C+: positive control of PCR and RT-PCR; C-: negative control of PCR and RT-PCR; L: ladder indicating the size (bp). Lanes marked as S1, S2, and S3 correspond to the analyzed RTE samples.

Techniques Used: Electrophoresis, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Positive Control, Negative Control

High-throughput sequencing data of 16S rDNA and rRNA from RTE salads. Taxonomic assignment of reads at the phylum and genus level is shown. From each RTE salad brand, taxonomic assignment data from total bacterial cells (dormant, dead, and active cells containing 16S rDNA genes) and metabolically active bacteria (cells containing ribosomal RNA, 16S rRNA) is indicated as “DNA” and “RNA”, respectively. Those low abundant genera that showed
Figure Legend Snippet: High-throughput sequencing data of 16S rDNA and rRNA from RTE salads. Taxonomic assignment of reads at the phylum and genus level is shown. From each RTE salad brand, taxonomic assignment data from total bacterial cells (dormant, dead, and active cells containing 16S rDNA genes) and metabolically active bacteria (cells containing ribosomal RNA, 16S rRNA) is indicated as “DNA” and “RNA”, respectively. Those low abundant genera that showed

Techniques Used: Next-Generation Sequencing, Metabolic Labelling

12) Product Images from "Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea"

Article Title: Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea

Journal: Scientific Reports

doi: 10.1038/s41598-017-14527-1

Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3–4 16S rDNA amplicons obtained for individual reactor samples. Each bar represents one sample, and is labelled as follows: D indicates the experimental day; HA1 and HA2 refer to the two reactors operated at 3.7 ± 0.2 g NH 4 -N L −1 , and LA1, and LA2 refers to the reactors operated at 1.9 ± 0.2 g NH 4 -N L −1 . OTUs that could not be classified at the domain level are labeled “Unclassified”, while OTUs that could not be classified at class or genus level for bacteria and archaea, respectively, are labeled *. Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” include all reads representing the taxa with
Figure Legend Snippet: Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3–4 16S rDNA amplicons obtained for individual reactor samples. Each bar represents one sample, and is labelled as follows: D indicates the experimental day; HA1 and HA2 refer to the two reactors operated at 3.7 ± 0.2 g NH 4 -N L −1 , and LA1, and LA2 refers to the reactors operated at 1.9 ± 0.2 g NH 4 -N L −1 . OTUs that could not be classified at the domain level are labeled “Unclassified”, while OTUs that could not be classified at class or genus level for bacteria and archaea, respectively, are labeled *. Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” include all reads representing the taxa with

Techniques Used: Labeling, Sequencing

13) Product Images from "K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture"

Article Title: K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02730

Effects of r- and K-selection on microbial community composition in four different experiments with different seawater inoculum. Each experimental group was sampled twice during the periods of r- and K-selection. r-selection was obtained by pulsing with resources for growth (organic and mineral nutrients), whereas K-selection was obtained by resource depletion and competition for more than 2 weeks. r-selected communities were sampled at days 1 and 2 after addition of resources, whereas K-selected communities were sampled on days 17 and 24. Microbial community composition was analysed by Illumina sequencing of 16S-rDNA amplicons. Unpublished results.
Figure Legend Snippet: Effects of r- and K-selection on microbial community composition in four different experiments with different seawater inoculum. Each experimental group was sampled twice during the periods of r- and K-selection. r-selection was obtained by pulsing with resources for growth (organic and mineral nutrients), whereas K-selection was obtained by resource depletion and competition for more than 2 weeks. r-selected communities were sampled at days 1 and 2 after addition of resources, whereas K-selected communities were sampled on days 17 and 24. Microbial community composition was analysed by Illumina sequencing of 16S-rDNA amplicons. Unpublished results.

Techniques Used: Selection, Sequencing

14) Product Images from "Changes in rhizosphere bacterial communities during remediation of heavy metal-accumulating plants around the Xikuangshan mine in southern China"

Article Title: Changes in rhizosphere bacterial communities during remediation of heavy metal-accumulating plants around the Xikuangshan mine in southern China

Journal: Scientific Reports

doi: 10.1038/s41598-018-38360-2

Number of sequences analyzed and diversity/richness indices of the 16S rRNA bacterial libraries obtained from clustering at 97% identity.
Figure Legend Snippet: Number of sequences analyzed and diversity/richness indices of the 16S rRNA bacterial libraries obtained from clustering at 97% identity.

Techniques Used:

15) Product Images from "Sialylated milk oligosaccharides promote microbiota-dependent growth in models of infant undernutrition"

Article Title: Sialylated milk oligosaccharides promote microbiota-dependent growth in models of infant undernutrition

Journal: Cell

doi: 10.1016/j.cell.2016.01.024

Cultured bacterial strain collection generated from the fecal microbiota of a 6-month old stunted Malawian infant ( A ) Taxonomic representation of 97% ID OTUs in the intact, uncultured infant fecal sample from which the culture collection was generated. ( B ) Comparison of culture collection strains and representative type strains. Black dots indicate percent identity between full-length 16S rRNA gene sequences from each strain and its most similar reference type strain’s 16S rRNA sequence. Bars indicate percent nucleotide sequence similarity between the strain’s de novo assembled genome and its most similar type strain’s genome. Strains are clustered by Euclidean distance between full-length 16S rRNA gene sequences. ( C .
Figure Legend Snippet: Cultured bacterial strain collection generated from the fecal microbiota of a 6-month old stunted Malawian infant ( A ) Taxonomic representation of 97% ID OTUs in the intact, uncultured infant fecal sample from which the culture collection was generated. ( B ) Comparison of culture collection strains and representative type strains. Black dots indicate percent identity between full-length 16S rRNA gene sequences from each strain and its most similar reference type strain’s 16S rRNA sequence. Bars indicate percent nucleotide sequence similarity between the strain’s de novo assembled genome and its most similar type strain’s genome. Strains are clustered by Euclidean distance between full-length 16S rRNA gene sequences. ( C .

Techniques Used: Cell Culture, Generated, Sequencing

16) Product Images from "JTD special edition ‘Hot Topics in COPD’—The microbiome in COPD"

Article Title: JTD special edition ‘Hot Topics in COPD’—The microbiome in COPD

Journal: Journal of Thoracic Disease

doi: 10.3978/j.issn.2072-1439.2014.11.08

Bacterial community profiling using high throughput DNA sequencing of a highly conserved bacteria-specific gene ( 16S rRNA gene). In this example the microbial community composition in bronchoalveolar lavage samples obtained from lung transplant patients
Figure Legend Snippet: Bacterial community profiling using high throughput DNA sequencing of a highly conserved bacteria-specific gene ( 16S rRNA gene). In this example the microbial community composition in bronchoalveolar lavage samples obtained from lung transplant patients

Techniques Used: High Throughput Screening Assay, DNA Sequencing

17) Product Images from "Synergism of gut microbiota to double-stranded RNAs in RNA interference of a leaf beetle"

Article Title: Synergism of gut microbiota to double-stranded RNAs in RNA interference of a leaf beetle

Journal: bioRxiv

doi: 10.1101/824581

Ingestion of dsRNA alters gut microbiota composition of P. versicolora . ( a ) Principal co-ordinates analysis (PCoA) of Bray-Curtis distances at the genus level for 16S rRNA gene sequences. ( b ) Typing analysis of Jensen-Shannon divergence distance at the OTU level for 16S rRNA gene sequence data. ( c ) Kruskal-Wallis H test bar plot analysis of the relative proportions of major genera of gut bacteria. The relative abundances of the identified microbial taxa were determined in gut samples collected from larvae fed with ds GFP, ds Srp54k , ds Actin , or H 2 O. P -values were calculated using the Kruskal-Wallis H test. ** P
Figure Legend Snippet: Ingestion of dsRNA alters gut microbiota composition of P. versicolora . ( a ) Principal co-ordinates analysis (PCoA) of Bray-Curtis distances at the genus level for 16S rRNA gene sequences. ( b ) Typing analysis of Jensen-Shannon divergence distance at the OTU level for 16S rRNA gene sequence data. ( c ) Kruskal-Wallis H test bar plot analysis of the relative proportions of major genera of gut bacteria. The relative abundances of the identified microbial taxa were determined in gut samples collected from larvae fed with ds GFP, ds Srp54k , ds Actin , or H 2 O. P -values were calculated using the Kruskal-Wallis H test. ** P

Techniques Used: Sequencing

Ingestion of dsRNA promotes the growth of gut bacteria in P. versicolora larvae. qRT-PCR analyses were performed to determine the relative abundance of gut bacteria in P. versicolora larvae fed with ds GFP ( a ), ds Srp54k ( b ) and ds Actin ( c ) (n = 5), and the abundances of three major bacterial genera in non-axenic P. versicolora larvae fed with ds GFP ( d ), ds Srp54k ( e ) and ds Actin ( f ). The measurements were performed at different time points (after 2-5 days of feeding). The qRT-PCR value obtained for gut bacterial 16S rRNA in P. versicolora control larvae (fed with water-treated leaves) was set as 1.0. P -values were calculated using the independent-samples t -test. Data are presented as means ± SE, *** P
Figure Legend Snippet: Ingestion of dsRNA promotes the growth of gut bacteria in P. versicolora larvae. qRT-PCR analyses were performed to determine the relative abundance of gut bacteria in P. versicolora larvae fed with ds GFP ( a ), ds Srp54k ( b ) and ds Actin ( c ) (n = 5), and the abundances of three major bacterial genera in non-axenic P. versicolora larvae fed with ds GFP ( d ), ds Srp54k ( e ) and ds Actin ( f ). The measurements were performed at different time points (after 2-5 days of feeding). The qRT-PCR value obtained for gut bacterial 16S rRNA in P. versicolora control larvae (fed with water-treated leaves) was set as 1.0. P -values were calculated using the independent-samples t -test. Data are presented as means ± SE, *** P

Techniques Used: Quantitative RT-PCR

18) Product Images from "Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea"

Article Title: Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea

Journal: Scientific Reports

doi: 10.1038/s41598-017-14527-1

Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3–4 16S rDNA amplicons obtained for individual reactor samples. Each bar represents one sample, and is labelled as follows: D indicates the experimental day; HA1 and HA2 refer to the two reactors operated at 3.7 ± 0.2 g NH 4 -N L −1 , and LA1, and LA2 refers to the reactors operated at 1.9 ± 0.2 g NH 4 -N L −1 . OTUs that could not be classified at the domain level are labeled “Unclassified”, while OTUs that could not be classified at class or genus level for bacteria and archaea, respectively, are labeled *. Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” include all reads representing the taxa with
Figure Legend Snippet: Relative abundances of bacterial classes ( A ) and archaeal genera ( B ) represented in the v3–4 16S rDNA amplicons obtained for individual reactor samples. Each bar represents one sample, and is labelled as follows: D indicates the experimental day; HA1 and HA2 refer to the two reactors operated at 3.7 ± 0.2 g NH 4 -N L −1 , and LA1, and LA2 refers to the reactors operated at 1.9 ± 0.2 g NH 4 -N L −1 . OTUs that could not be classified at the domain level are labeled “Unclassified”, while OTUs that could not be classified at class or genus level for bacteria and archaea, respectively, are labeled *. Only taxa represented by a portion of ≥1% of the sequence reads in at least one of the samples are shown. “Others” include all reads representing the taxa with

Techniques Used: Labeling, Sequencing

19) Product Images from "Cutaneous leishmaniasis induces a transmissible dysbiotic skin microbiota that promotes skin inflammation"

Article Title: Cutaneous leishmaniasis induces a transmissible dysbiotic skin microbiota that promotes skin inflammation

Journal: Cell host & microbe

doi: 10.1016/j.chom.2017.06.006

Skin microbiota alterations in L. major infection are dependent on disease severity C57BL/6 and BALB/c mice were intradermally infected with L. major parasites. Lesional severity was assessed by (A) ear thickness and (B) a pathology score over the course of infection. Swabs for sequencing of 16S rRNA genes were collected from the lesions at 0 and 6 weeks post-infection. (C) Alpha diversity was assessed by Shannon Index. (D) Stacked bar charts represent the proportion of the top 10 taxa present in each sample. Data are representative of two independent experiments (n = 1 skin swab each from 10 mice in each group). C57BL/6 mice were treated with an isotype or anti-IL-12 mAb and intradermally infected in the ear with L. major parasites. Lesional severity was assessed by (E) ear thickness and (F) a pathology score over the course of infection. Anti-IL-12 mAb treated mice were euthanized at 6 weeks post-infection due to severe disease. (G) Swabs were collected from the lesions at 2, 4 and 6 weeks post-infection and proportions of Staphylococcus and Streptococcus .
Figure Legend Snippet: Skin microbiota alterations in L. major infection are dependent on disease severity C57BL/6 and BALB/c mice were intradermally infected with L. major parasites. Lesional severity was assessed by (A) ear thickness and (B) a pathology score over the course of infection. Swabs for sequencing of 16S rRNA genes were collected from the lesions at 0 and 6 weeks post-infection. (C) Alpha diversity was assessed by Shannon Index. (D) Stacked bar charts represent the proportion of the top 10 taxa present in each sample. Data are representative of two independent experiments (n = 1 skin swab each from 10 mice in each group). C57BL/6 mice were treated with an isotype or anti-IL-12 mAb and intradermally infected in the ear with L. major parasites. Lesional severity was assessed by (E) ear thickness and (F) a pathology score over the course of infection. Anti-IL-12 mAb treated mice were euthanized at 6 weeks post-infection due to severe disease. (G) Swabs were collected from the lesions at 2, 4 and 6 weeks post-infection and proportions of Staphylococcus and Streptococcus .

Techniques Used: Infection, Mouse Assay, Sequencing

L. major induced dysbiosis is transmissible to uninfected skin (A) C57BL/6 mice were intradermally infected with L. major and swabs were collected from the infected and contralateral ears at 6 weeks post-infected for 16S rRNA gene analysis. Stacked bar charts represent the proportion of the top 10 taxa present in each sample. Data are representative of three independent experiments (n = 1 swab of each ear from 15 mice). (B) Swabs from naïve or L. major infected C57BL/6 mice were cultured on mannitol salt agar plates and CFUs were counted to determine bacteria burden. Data are representative of 1 experiment (For naïve group, n = 1 swab from the ear of 10 mice; for infected and contralateral ears, n = 1 swab of each ear from 12 mice). (C) Naïve C57BL/6 mice were co-housed with L. major .
Figure Legend Snippet: L. major induced dysbiosis is transmissible to uninfected skin (A) C57BL/6 mice were intradermally infected with L. major and swabs were collected from the infected and contralateral ears at 6 weeks post-infected for 16S rRNA gene analysis. Stacked bar charts represent the proportion of the top 10 taxa present in each sample. Data are representative of three independent experiments (n = 1 swab of each ear from 15 mice). (B) Swabs from naïve or L. major infected C57BL/6 mice were cultured on mannitol salt agar plates and CFUs were counted to determine bacteria burden. Data are representative of 1 experiment (For naïve group, n = 1 swab from the ear of 10 mice; for infected and contralateral ears, n = 1 swab of each ear from 12 mice). (C) Naïve C57BL/6 mice were co-housed with L. major .

Techniques Used: Mouse Assay, Infection, Cell Culture

20) Product Images from "Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis"

Article Title: Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0152044

PICRUSt prediction of functional profiling of the microbial communities based on the 16S rRNA gene sequences. Extended error bar plot indicating differences in functional profiles of the Rag+AT and DKO+AT microbiota (at taxonomic Level 3). All unclassified reads were removed and categories with minimum of 20 reads, and P value greater than 0.01 is displayed. Categories are sorted by P value calculated using two-sided Welch’s t-test.
Figure Legend Snippet: PICRUSt prediction of functional profiling of the microbial communities based on the 16S rRNA gene sequences. Extended error bar plot indicating differences in functional profiles of the Rag+AT and DKO+AT microbiota (at taxonomic Level 3). All unclassified reads were removed and categories with minimum of 20 reads, and P value greater than 0.01 is displayed. Categories are sorted by P value calculated using two-sided Welch’s t-test.

Techniques Used: Functional Assay

21) Product Images from "Comparison of Nitrate and Perchlorate in Controlling Sulfidogenesis in Heavy Oil-Containing Bioreactors"

Article Title: Comparison of Nitrate and Perchlorate in Controlling Sulfidogenesis in Heavy Oil-Containing Bioreactors

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02423

Relational tree for 16S rRNA gene libraries from incubations of CSBK medium, inoculated with 18PW and amended with 1 mL MHGC oil and sulfate (SO); sulfate and nitrate (SNO); sulfate and perchlorate (PSO); sulfate, nitrate, and perchlorate (PSNO); or perchlorate only (PO). Community DNA was obtained from cells harvested at day 9, 65, 85, or 123 as indicated. The fractions of reads in classes of Proteobacteria (A) and in other phyla (B) are shown.
Figure Legend Snippet: Relational tree for 16S rRNA gene libraries from incubations of CSBK medium, inoculated with 18PW and amended with 1 mL MHGC oil and sulfate (SO); sulfate and nitrate (SNO); sulfate and perchlorate (PSO); sulfate, nitrate, and perchlorate (PSNO); or perchlorate only (PO). Community DNA was obtained from cells harvested at day 9, 65, 85, or 123 as indicated. The fractions of reads in classes of Proteobacteria (A) and in other phyla (B) are shown.

Techniques Used:

Related Articles

Amplification:

Article Title: Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing
Article Snippet: .. The amplified, individually barcoded, 16S rRNA amplicons from each sample were sequenced on the Illumina Miseq PE300 platform, which provided millions of reads up to 300 × 2 bp in length. ..

Ligation:

Article Title: Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products
Article Snippet: .. For Illumina sequencing, the KAPA HTP library preparation kit (KK8234, Kapa Biosystems, Pittsburgh, PA) was used for the ligation of NEXTflex adapters (Bioo Scientific, Austin, TX) to the 16S rRNA amplicons prior to 250-bp paired-end sequencing (with 7% PhiX control) on an Illumina MiSeq instrument at the University of California, Davis, Genome Center ( http://genomecenter.ucdavis.edu/ ). .. For Ion Torrent sequencing, non-barcoded Ion A and Ion P1 adapters were ligated to the pooled amplicons, followed by templating, enrichment, and sequencing on the One-Touch 2 and One-Touch ES systems and Ion PGM using the 400 sequencing kit and a 318 v2 chip (Life Technologies, Carlsbad, CA).

Next-Generation Sequencing:

Article Title: The Fecal Microbiome in Cats with Diarrhea
Article Snippet: .. In this study, we utilized Ion Torrent technology for sequencing of PCR amplicons, and it has been recently described that this technique has an increased error rate for 16S rRNA amplicons compared to traditional 454-pyrosequencing or Illumina next-generation sequencing [ ], although this technique has been used successfully in several microbiota studies [ , ]. ..

Sequencing:

Article Title: Comparison of Nitrate and Perchlorate in Controlling Sulfidogenesis in Heavy Oil-Containing Bioreactors
Article Snippet: .. Microbial Community Compositions in Batch Cultures With Oil Illumina sequencing of 16S rRNA amplicons and analysis of the sequences obtained indicated that communities in incubations with nitrate were less diverse than those in incubations without nitrate ( Supplementary Table : Shannon indices of 0.76–2.04 and 2.82–3.93, respectively). .. Likewise, comparison of microbial communities derived from these sequenced amplicons in a dendrogram indicated that communities in incubations without nitrate clustered separately from communities in incubations with nitrate ( Figure : clusters I and II, respectively).

Article Title: The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights
Article Snippet: .. Prokaryotic richness and diversity In total, 16S rRNA amplicons of fifteen samples, including three seawater samples and twelve sponge specimens that consisted of three replicates for each of the four sponge individuals, were subjected to Illumina sequencing. ..

Article Title: An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
Article Snippet: .. Sequencing low sequence diversity libraries such as 16S rRNA amplicons has been problematic on the Illumina MiSeq platform and often generates sequences of suboptimal quality. .. Here we present an improved dual-indexing amplification and sequencing approach to assess the composition of microbial communities from clinical samples using the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform.

Article Title: Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products
Article Snippet: .. For Illumina sequencing, the KAPA HTP library preparation kit (KK8234, Kapa Biosystems, Pittsburgh, PA) was used for the ligation of NEXTflex adapters (Bioo Scientific, Austin, TX) to the 16S rRNA amplicons prior to 250-bp paired-end sequencing (with 7% PhiX control) on an Illumina MiSeq instrument at the University of California, Davis, Genome Center ( http://genomecenter.ucdavis.edu/ ). .. For Ion Torrent sequencing, non-barcoded Ion A and Ion P1 adapters were ligated to the pooled amplicons, followed by templating, enrichment, and sequencing on the One-Touch 2 and One-Touch ES systems and Ion PGM using the 400 sequencing kit and a 318 v2 chip (Life Technologies, Carlsbad, CA).

Article Title: The Fecal Microbiome in Cats with Diarrhea
Article Snippet: .. In this study, we utilized Ion Torrent technology for sequencing of PCR amplicons, and it has been recently described that this technique has an increased error rate for 16S rRNA amplicons compared to traditional 454-pyrosequencing or Illumina next-generation sequencing [ ], although this technique has been used successfully in several microbiota studies [ , ]. ..

Article Title: Comprehensive evaluation of a cost-effective method of culturing Chlorella pyrenoidosa with unsterilized piggery wastewater for biofuel production
Article Snippet: .. The high-throughput sequencing of 16S rRNA amplicons was performed on the Illumina MiSeq platform at Novogene Bioinformatics Company (Beijing, China). .. Sequencing data analysis Paired-end reads were assigned based on the unique barcodes of samples, which were subsequently truncated by cutting off the barcode and primer sequence.

Polymerase Chain Reaction:

Article Title: The Fecal Microbiome in Cats with Diarrhea
Article Snippet: .. In this study, we utilized Ion Torrent technology for sequencing of PCR amplicons, and it has been recently described that this technique has an increased error rate for 16S rRNA amplicons compared to traditional 454-pyrosequencing or Illumina next-generation sequencing [ ], although this technique has been used successfully in several microbiota studies [ , ]. ..

High Throughput Screening Assay:

Article Title: Comprehensive evaluation of a cost-effective method of culturing Chlorella pyrenoidosa with unsterilized piggery wastewater for biofuel production
Article Snippet: .. The high-throughput sequencing of 16S rRNA amplicons was performed on the Illumina MiSeq platform at Novogene Bioinformatics Company (Beijing, China). .. Sequencing data analysis Paired-end reads were assigned based on the unique barcodes of samples, which were subsequently truncated by cutting off the barcode and primer sequence.

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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
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    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
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    Illumina Inc 16s rdna v4 region amplicon deep sequencing
    Comparison of the relative abundances of top 10 dominant genera in the rhizospheric soil between N698 and MD12. ( A ) Results revealed by <t>16S</t> <t>rDNA</t> V5–V7 hypervariable region <t>amplicon</t> deep sequencing. ( B ) Results revealed by 16S rDNA V4 hypervariable region amplicon deep sequencing. ( C ) Results revealed by shotgun metagenomic approaches (analyzed by One Codex). Error bars indicate standard errors; * p
    16s Rdna V4 Region Amplicon Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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:

    Comparison of the relative abundances of top 10 dominant genera in the rhizospheric soil between N698 and MD12. ( A ) Results revealed by 16S rDNA V5–V7 hypervariable region amplicon deep sequencing. ( B ) Results revealed by 16S rDNA V4 hypervariable region amplicon deep sequencing. ( C ) Results revealed by shotgun metagenomic approaches (analyzed by One Codex). Error bars indicate standard errors; * p

    Journal: Genes

    Article Title: Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach

    doi: 10.3390/genes9040214

    Figure Lengend Snippet: Comparison of the relative abundances of top 10 dominant genera in the rhizospheric soil between N698 and MD12. ( A ) Results revealed by 16S rDNA V5–V7 hypervariable region amplicon deep sequencing. ( B ) Results revealed by 16S rDNA V4 hypervariable region amplicon deep sequencing. ( C ) Results revealed by shotgun metagenomic approaches (analyzed by One Codex). Error bars indicate standard errors; * p

    Article Snippet: By contrast, Yersinia /Serratia , Pedobacter , Luteibacter and Flavisolibacter were detected only by 16S rDNA V4 region amplicon deep sequencing ( , ).

    Techniques: Amplification, Sequencing