Structured Review

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
90/100 stars

Images

1) Product Images from "Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons"

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

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.00824

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.
Figure Legend 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.

Techniques Used: 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) .
Figure Legend 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) .

Techniques Used:

2) Product Images from "Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity"

Article Title: Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.00279

Phylogenetic tree based on alignment of 16S rRNA gene sequences showing the relationship of strain P5 (shown in bold print) within the genus Rhodovulum . The trees were constructed by the Neighbor-Joining method using MEGA version 6.0 software (closed circles represent the same tree branch using the algorithm of Maximum Likelihood and Maximum Parsimony) and rooted by using Rhodospirillum rubrum ATCC 11170 T as the outgroup. Numbers at nodes represent bootstrap values (based on 100 resamplings). Bootstrap values more than 50% are noted. The GenBank accession numbers for 16S rRNA gene sequences are shown in parentheses. Bar, 1 nt substitution per 100 nt.
Figure Legend Snippet: Phylogenetic tree based on alignment of 16S rRNA gene sequences showing the relationship of strain P5 (shown in bold print) within the genus Rhodovulum . The trees were constructed by the Neighbor-Joining method using MEGA version 6.0 software (closed circles represent the same tree branch using the algorithm of Maximum Likelihood and Maximum Parsimony) and rooted by using Rhodospirillum rubrum ATCC 11170 T as the outgroup. Numbers at nodes represent bootstrap values (based on 100 resamplings). Bootstrap values more than 50% are noted. The GenBank accession numbers for 16S rRNA gene sequences are shown in parentheses. Bar, 1 nt substitution per 100 nt.

Techniques Used: Construct, Software

Related Articles

Sequencing:

Article Title: The Role of Pseudomonas in Heterotrophic Nitrification: A Case Study on Shrimp Ponds (Litopenaeus vannamei) in Soc Trang Province
Article Snippet: .. Sequence Processing and Analysis At Macrogen (Seoul, South of Korea), bacterial 16S rRNA gene amplicons were sequenced on the Illumina MiSeq platform (Illumina, San Diego, CA, United States) (2 × 250 bp paired-end reads) and demultiplexed to remove all indexes, primers, and barcodes. ..

Article Title: Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity
Article Snippet: .. Amplification and Sequencing of the Bacterial 16S rRNA Gene Amplicons were generated using fusion degenerate primers 343F ( ) and 798R ( ) with ligated overhang Illumina adapter consensus sequences. .. The libraries were prepared in accordance with the instructions included with the Illumina Nextera XT Index kit (Illumina, United States).

Generated:

Article Title: Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity
Article Snippet: .. Amplification and Sequencing of the Bacterial 16S rRNA Gene Amplicons were generated using fusion degenerate primers 343F ( ) and 798R ( ) with ligated overhang Illumina adapter consensus sequences. .. The libraries were prepared in accordance with the instructions included with the Illumina Nextera XT Index kit (Illumina, United States).

Amplification:

Article Title: Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity
Article Snippet: .. Amplification and Sequencing of the Bacterial 16S rRNA Gene Amplicons were generated using fusion degenerate primers 343F ( ) and 798R ( ) with ligated overhang Illumina adapter consensus sequences. .. The libraries were prepared in accordance with the instructions included with the Illumina Nextera XT Index kit (Illumina, United States).

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 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 9 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 9 article reviews
    Price from $9.99 to $1999.99
    bacterial 16s rrna gene amplicons - by Bioz Stars, 2020-08
    90/100 stars
      Buy from Supplier

    90
    Illumina Inc bacterial microbial 16s rrna amplicons
    Sequence diversity among treatment groups. a Bar chart showing mean + standard deviation (SD) Chao1 a-diversity index of fecal microbiota in mice pre- and post-vaccination with the indicated antigens, as detected using <t>16S</t> <t>rRNA</t> amplicon sequencing. b Mean Shannon diversity indices. c Mean number of unique sequences in treatment groups
    Bacterial Microbial 16s Rrna Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bacterial microbial 16s rrna amplicons/product/Illumina Inc
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bacterial microbial 16s rrna amplicons - by Bioz Stars, 2020-08
    90/100 stars
      Buy from Supplier

    89
    Illumina Inc 16s rrna gene amplicon paired end sequencing
    Distribution of sequence lengths for matching barcodes. Once all the forward and reverse reads from the Illumina sequencer are joined one can see – in gray here – a pattern in the size of the fragments produced. Superposing in red the abundance of length variation found in the SILVAMOD database, one can see that the variation we uncovered follows closely the natural variation of the V3–V4 region of the <t>16S</t> <t>rRNA</t> gene. As shown in Fig. 3 , each of the three peaks are composed of characteristic phyla.
    16s Rrna Gene Amplicon Paired End Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/16s rrna gene amplicon paired end sequencing/product/Illumina Inc
    Average 89 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    16s rrna gene amplicon paired end sequencing - by Bioz Stars, 2020-08
    89/100 stars
      Buy from Supplier

    Image Search Results


    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 DGGE profiles of advanced IOB enrichments taken from liquid cultures with (+) and without (–) Fe 2+ addition (Step 5 in Figure 2 ) and phylogenetic tree of selected 16S rRNA gene sequences obtained from isolated DGGE bands. The tree was constructed using neighbor-joining method in ARB after 1000 bootstrap iterations. Closely related sequences, with respective GenBank accession numbers, are shown as reference. White, green, and yellow dots are sequences from bands that were solely detected in incubations with Fe 2+ , detected in both incubations with and without Fe 2+ , and solely detected in incubations without Fe 2+ , respectively. Scale bar indicates 10% sequence difference.

    Journal: Frontiers in Microbiology

    Article Title: Diversity of Iron Oxidizers in Groundwater-Fed Rapid Sand Filters: Evidence of Fe(II)-Dependent Growth by Curvibacter and Undibacterium spp.

    doi: 10.3389/fmicb.2018.02808

    Figure Lengend Snippet: 16S rRNA DGGE profiles of advanced IOB enrichments taken from liquid cultures with (+) and without (–) Fe 2+ addition (Step 5 in Figure 2 ) and phylogenetic tree of selected 16S rRNA gene sequences obtained from isolated DGGE bands. The tree was constructed using neighbor-joining method in ARB after 1000 bootstrap iterations. Closely related sequences, with respective GenBank accession numbers, are shown as reference. White, green, and yellow dots are sequences from bands that were solely detected in incubations with Fe 2+ , detected in both incubations with and without Fe 2+ , and solely detected in incubations without Fe 2+ , respectively. Scale bar indicates 10% sequence difference.

    Article Snippet: Finally, the relative abundance of the newly identified and well-known IOB in the full-scale RSFs was assessed by inspecting the community bacterial 16S rRNA gene amplicon libraries (Illumina MiSeq and 454) against FISH-verified full 16S rRNA clones from IOB enrichments.

    Techniques: Denaturing Gradient Gel Electrophoresis, Isolation, Construct, Sequencing

    Phylogenetic trees of bacterial 16S rRNA gene sequences retrieved from incubations with Fe(II) addition after 15 days incubation (Numbers as in Figure 3 ; see Figure 2 step 5). The tree was constructed using neighbor-joining method in ARB from full length sequences obtained via cloning and partial sequences (170 bp) obtained from excised DGGE bands. Percentages in parentheses correspond to the relative abundance of clones with identical ARDRA profiles; remaining clones represented as single OTU in corresponding ARDRA profiles. Thick branches on phylogenetic trees indicate high parsimony bootstrap support (≥70%) based on 1000 iterations. Scale bars indicate 10% sequence difference.

    Journal: Frontiers in Microbiology

    Article Title: Diversity of Iron Oxidizers in Groundwater-Fed Rapid Sand Filters: Evidence of Fe(II)-Dependent Growth by Curvibacter and Undibacterium spp.

    doi: 10.3389/fmicb.2018.02808

    Figure Lengend Snippet: Phylogenetic trees of bacterial 16S rRNA gene sequences retrieved from incubations with Fe(II) addition after 15 days incubation (Numbers as in Figure 3 ; see Figure 2 step 5). The tree was constructed using neighbor-joining method in ARB from full length sequences obtained via cloning and partial sequences (170 bp) obtained from excised DGGE bands. Percentages in parentheses correspond to the relative abundance of clones with identical ARDRA profiles; remaining clones represented as single OTU in corresponding ARDRA profiles. Thick branches on phylogenetic trees indicate high parsimony bootstrap support (≥70%) based on 1000 iterations. Scale bars indicate 10% sequence difference.

    Article Snippet: Finally, the relative abundance of the newly identified and well-known IOB in the full-scale RSFs was assessed by inspecting the community bacterial 16S rRNA gene amplicon libraries (Illumina MiSeq and 454) against FISH-verified full 16S rRNA clones from IOB enrichments.

    Techniques: Incubation, Construct, Clone Assay, Denaturing Gradient Gel Electrophoresis, Sequencing

    Sequence diversity among treatment groups. a Bar chart showing mean + standard deviation (SD) Chao1 a-diversity index of fecal microbiota in mice pre- and post-vaccination with the indicated antigens, as detected using 16S rRNA amplicon sequencing. b Mean Shannon diversity indices. c Mean number of unique sequences in treatment groups

    Journal: BMC Research Notes

    Article Title: Vaccinating with conserved Escherichia coli antigens does not alter the mouse intestinal microbiome

    doi: 10.1186/s13104-016-2208-y

    Figure Lengend Snippet: Sequence diversity among treatment groups. a Bar chart showing mean + standard deviation (SD) Chao1 a-diversity index of fecal microbiota in mice pre- and post-vaccination with the indicated antigens, as detected using 16S rRNA amplicon sequencing. b Mean Shannon diversity indices. c Mean number of unique sequences in treatment groups

    Article Snippet: Bacterial Microbial 16S rRNA amplicons were generated via amplification of the V4 hypervariable region of the 16S rRNA gene using single-indexed universal primers as described previously [U515F/806R; ] flanked by Illumina standard adapter sequences.

    Techniques: Sequencing, Standard Deviation, Mouse Assay, Amplification

    Principal component analyses and UniFrac distances. a Unweighted principal component analyses showing β-diversity of fecal microbiota in mice pre- and post-vaccination with the indicated antigens, as detected via 16S rRNA amplicon sequencing. Principal component 1 (PC1) versus PC2 ( left ) and PC1 versus PC3 ( right ) are shown. Color-coding is identical to Fig. 2 , with open symbols representing pre-vaccination and closed symbols representing post-vaccination samples. b Mean intragroup unweighted UniFrac distances between pre- and post-vaccination samples

    Journal: BMC Research Notes

    Article Title: Vaccinating with conserved Escherichia coli antigens does not alter the mouse intestinal microbiome

    doi: 10.1186/s13104-016-2208-y

    Figure Lengend Snippet: Principal component analyses and UniFrac distances. a Unweighted principal component analyses showing β-diversity of fecal microbiota in mice pre- and post-vaccination with the indicated antigens, as detected via 16S rRNA amplicon sequencing. Principal component 1 (PC1) versus PC2 ( left ) and PC1 versus PC3 ( right ) are shown. Color-coding is identical to Fig. 2 , with open symbols representing pre-vaccination and closed symbols representing post-vaccination samples. b Mean intragroup unweighted UniFrac distances between pre- and post-vaccination samples

    Article Snippet: Bacterial Microbial 16S rRNA amplicons were generated via amplification of the V4 hypervariable region of the 16S rRNA gene using single-indexed universal primers as described previously [U515F/806R; ] flanked by Illumina standard adapter sequences.

    Techniques: Mouse Assay, Amplification, Sequencing

    Vaccination with ETEC MipA, Skp, and ETEC_2479. a Serum IgG responses in mice. Data are plotted as the fold-change in serum IgG after immunization with the indicated antigens, n = 5/group. b Bar chart showing relative abundance of all operational taxonomic units (OTUs) detected in the feces of mice prior to (pre) and 6 weeks after (post) vaccination with the indicated antigens, as detected using 16S rRNA amplicon sequencing. The identities of dominant taxa are shown at the right. c Mean number + standard deviation (SD) of sequence reads that were specific to Bacteriodales or Proteobacteria in indicated treatment groups

    Journal: BMC Research Notes

    Article Title: Vaccinating with conserved Escherichia coli antigens does not alter the mouse intestinal microbiome

    doi: 10.1186/s13104-016-2208-y

    Figure Lengend Snippet: Vaccination with ETEC MipA, Skp, and ETEC_2479. a Serum IgG responses in mice. Data are plotted as the fold-change in serum IgG after immunization with the indicated antigens, n = 5/group. b Bar chart showing relative abundance of all operational taxonomic units (OTUs) detected in the feces of mice prior to (pre) and 6 weeks after (post) vaccination with the indicated antigens, as detected using 16S rRNA amplicon sequencing. The identities of dominant taxa are shown at the right. c Mean number + standard deviation (SD) of sequence reads that were specific to Bacteriodales or Proteobacteria in indicated treatment groups

    Article Snippet: Bacterial Microbial 16S rRNA amplicons were generated via amplification of the V4 hypervariable region of the 16S rRNA gene using single-indexed universal primers as described previously [U515F/806R; ] flanked by Illumina standard adapter sequences.

    Techniques: Mouse Assay, Amplification, Sequencing, Standard Deviation

    Distribution of sequence lengths for matching barcodes. Once all the forward and reverse reads from the Illumina sequencer are joined one can see – in gray here – a pattern in the size of the fragments produced. Superposing in red the abundance of length variation found in the SILVAMOD database, one can see that the variation we uncovered follows closely the natural variation of the V3–V4 region of the 16S rRNA gene. As shown in Fig. 3 , each of the three peaks are composed of characteristic phyla.

    Journal: PLoS ONE

    Article Title: Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform

    doi: 10.1371/journal.pone.0116955

    Figure Lengend Snippet: Distribution of sequence lengths for matching barcodes. Once all the forward and reverse reads from the Illumina sequencer are joined one can see – in gray here – a pattern in the size of the fragments produced. Superposing in red the abundance of length variation found in the SILVAMOD database, one can see that the variation we uncovered follows closely the natural variation of the V3–V4 region of the 16S rRNA gene. As shown in Fig. 3 , each of the three peaks are composed of characteristic phyla.

    Article Snippet: Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform.

    Techniques: Sequencing, Produced