16s rrna gene amplification Search Results


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  • 88
    Illumina Inc bacterial 16s rrna gene amplification
    ( a ) Rarefaction curves showing the observed OTU richness (at 97% identity) of the <t>16S</t> <t>rRNA</t> gene with increasing sequencing depth. Mean values (n = 3) were shown for the two salinity treatments (S1 and S4) and two soil depths. ( b ) Comparison of the bacterial communities at the phylum level. Relative read abundance of different bacterial phyla in bacterial communities. Sequences that could not be classified into any known group were labeled “others”.
    Bacterial 16s Rrna Gene Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc 16s rrna gene amplification
    Host and symbiont phylogenies ( A ) Left: Midpoint-rooted, maximum likelihood (ML) phylogeny based on sponge ribosomal ITS-2 sequences from the current study (in bold) along with representative literature examples. Identical sequences are listed at a single branch tip, with symbols denoting dominant natural product chemistry. Bootstrap values ≥70 are shown; scale bar indicates substitutions per site. Matching superscripts indicate literature ITS-2 and <t>16S</t> <t>rRNA</t> sequences obtained from the same sponge specimen. Right: H. spongeliae ML tree of near-full length 16S rRNA gene sequences, including closest free-living relative Oscillatoria corallinae , and rooted on closest relative with a sequenced genome, Moorea producens 3L. One full-length 16S rRNA gene sequence (GUM098) was obtained from clone library (see Figure 3 ). Remaining Clade IV 16S rRNA sequences in this study, denoted in parentheses, are represented by 370 bp sequences obtained from high-throughput community data that are 100% identical to the GUM098 full-length sequence. ( B ) Chemical profiles, as monitored by absorbance at 280 nm by HPLC with in situ photographs of representative sponges for each clade.
    16s Rrna Gene Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 302 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Pacific Biosciences 16s rrna gene amplification
    Two-step generation of <t>16S</t> amplicons for PacBio sequencing using M13-tagged barcoded primers. The first round of PCR amplifies full-length 16S <t>rRNA</t> fragments using gene-specific primers tailed with universal M13 forward or reverse sequence. In the second step, a unique combination of barcode sequences is added to 16S amplicons from each sample using M13 forward and reverse primers tagged with 16-base PacBio barcodes at their 5′ ends. Barcoded amplicons are subsequently pooled for SMRTbell library construction and multiplexed sequencing.
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    Roche 16s rrna gene amplification
    Accuracy of <t>16S</t> <t>rRNA</t> gene copy determination using MYcrobiota. The expected number of 16S rRNA gene copies within the positive control (PC) was compared to the measured number of 16S rRNA gene copies using MYcrobiota (green dots). The PC contained 10,000 16S rRNA gene copies of four different bacterial species and was processed in three independent MYcrobiota experiments. The indirect estimation of the total bacterial biomass within 37 clinical samples using MYcrobiota was compared to the total 16S rRNA gene copies measured directly using a 16S rRNA gene qPCR (blue dots). The Staphylococcus OTU-specific biomass from 13 S . aureus culture-positive samples was compared to the S . aureus biomass detected directly using a S . aureus -specific qPCR (yellow dots). In order to compare the number of S . aureus genome copies estimated using qPCR to the number of 16S rRNA gene copies detected using MYcrobiota, the estimated S . aureus genome copies were first multiplied by a factor of 6 to correct for differences in copy numbers of the Martineau fragment and the 16S rRNA gene present on the S . aureus genome. The calculated differences between methods were plotted using a binary logarithmic scale
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    92
    Macrogen 16s rrna gene amplification
    Analysis of bacterial community’s structure and diversity of soil samples associated to spontaneous plants at SIN Caffaro. (A) Constraint (CAP) and (B) Unconstraint analysis of principal coordinates of the OTU 97 obtained from <t>16S</t> <t>rRNA</t> gene sequencing of the bacterial communities considering the different soil fractions (A) and the root-associated soil fractions according to the plant species (B) . (C) OTU 97 Richness, (D) OTU 97 Evenness and (E) OTU 97 diversity. Statistical analysis are indicated in within the plant species comparing each fraction while asterisks indicate the statistical significance among fractions (for details see the text). The letters R, S, and B indicate, respectively, the rhizosphere, root surrounding soil and non-vegetated bulk soil.
    16s Rrna Gene Amplification, supplied by Macrogen, used in various techniques. Bioz Stars score: 92/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc 16s rrna gene sequencing bacterial 16s rrna gene amplification
    Analysis of bacterial community’s structure and diversity of soil samples associated to spontaneous plants at SIN Caffaro. (A) Constraint (CAP) and (B) Unconstraint analysis of principal coordinates of the OTU 97 obtained from <t>16S</t> <t>rRNA</t> gene sequencing of the bacterial communities considering the different soil fractions (A) and the root-associated soil fractions according to the plant species (B) . (C) OTU 97 Richness, (D) OTU 97 Evenness and (E) OTU 97 diversity. Statistical analysis are indicated in within the plant species comparing each fraction while asterisks indicate the statistical significance among fractions (for details see the text). The letters R, S, and B indicate, respectively, the rhizosphere, root surrounding soil and non-vegetated bulk soil.
    16s Rrna Gene Sequencing Bacterial 16s Rrna Gene Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher 16s rrna gene amplification
    Phylogenetic tree displaying the full <t>16S</t> <t>rRNA</t> gene sequences of the three species of the genus Ignatzschineria , our sample (GenBank accession no. KT355688 ) and some related species. The tree was created with mega 6.0 software using the neighbour-joining method, Jukes–Cantor model, and 1000 bootstraps. Bar, 0.02 substitutions per nucleotide.
    16s Rrna Gene Amplification, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 151 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eurofins 16s rrna gene amplification
    Phylogenetic tree displaying the full <t>16S</t> <t>rRNA</t> gene sequences of the three species of the genus Ignatzschineria , our sample (GenBank accession no. KT355688 ) and some related species. The tree was created with mega 6.0 software using the neighbour-joining method, Jukes–Cantor model, and 1000 bootstraps. Bar, 0.02 substitutions per nucleotide.
    16s Rrna Gene Amplification, supplied by Eurofins, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Comeau Technique 16s rrna gene amplification
    Phylogenetic tree displaying the full <t>16S</t> <t>rRNA</t> gene sequences of the three species of the genus Ignatzschineria , our sample (GenBank accession no. KT355688 ) and some related species. The tree was created with mega 6.0 software using the neighbour-joining method, Jukes–Cantor model, and 1000 bootstraps. Bar, 0.02 substitutions per nucleotide.
    16s Rrna Gene Amplification, supplied by Comeau Technique, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa 16s rrna gene amplification
    Hybridization intensities of probes forming perfect-match (diamonds), one-mismatch (squares), and two-mismatch (circles) duplexes after hybridization with fluorescently labeled PCR-amplified <t>16S</t> <t>rRNA</t> gene fragments of Desulfovibrio halophilus at different stringencies. (A) Mean signal intensities (for 10 spots, with local background subtracted) for each probe and wash temperature. (B) Normalized mean signal intensity values for each probe and wash temperature. Mean intensity values were normalized for each probe separately by assuming that the highest value observed at the different wash temperatures had a value of 1.00. In panel B, probes which showed no hybridization signals at low stringencies are not shown.
    16s Rrna Gene Amplification, supplied by TaKaRa, used in various techniques. Bioz Stars score: 91/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad 16s rrna gene amplification
    <t>16S</t> <t>rRNA</t> gene abundance (qPCR quantification) of major phylogenetic groups from coastal bacterioplankton assemblages in 6 stations near Qinhuangdao coastal area. The symbols and lines in black, red, green, blue, cyan, and magenta represent stations W1, W2, W3, W4, W5, and W6. Values on Y -axis are plotted in log-scale.
    16s Rrna Gene Amplification, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 90/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Marine Biological Laboratory 16s rrna gene amplification
    <t>16S</t> <t>rRNA</t> gene abundance (qPCR quantification) of major phylogenetic groups from coastal bacterioplankton assemblages in 6 stations near Qinhuangdao coastal area. The symbols and lines in black, red, green, blue, cyan, and magenta represent stations W1, W2, W3, W4, W5, and W6. Values on Y -axis are plotted in log-scale.
    16s Rrna Gene Amplification, supplied by Marine Biological Laboratory, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eppendorf AG 16s rrna gene amplification
    <t>16S</t> <t>rRNA</t> gene abundance (qPCR quantification) of major phylogenetic groups from coastal bacterioplankton assemblages in 6 stations near Qinhuangdao coastal area. The symbols and lines in black, red, green, blue, cyan, and magenta represent stations W1, W2, W3, W4, W5, and W6. Values on Y -axis are plotted in log-scale.
    16s Rrna Gene Amplification, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 91/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ChunLab 16s rrna gene amplification
    <t>16S</t> <t>rRNA</t> gene abundance (qPCR quantification) of major phylogenetic groups from coastal bacterioplankton assemblages in 6 stations near Qinhuangdao coastal area. The symbols and lines in black, red, green, blue, cyan, and magenta represent stations W1, W2, W3, W4, W5, and W6. Values on Y -axis are plotted in log-scale.
    16s Rrna Gene Amplification, supplied by ChunLab, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc 16s rrna gene
    Relative abundance of OTUs from the Sponge Microbiome Project with ≥98% identity to <t>16S</t> <t>rRNA</t> sequences from strains isolated in this study. (A) Information relative to OTUs closely affiliated to isolate Cc27, (B) Information relative to OTUs closely affiliated with isolate Pv91. (C) Information relative to OTUs closely affiliated with isolates Pv86. Vertical bar represents the mean, the hinge represents SEM (Standard Error of Mean), and dots represent outlier values beyond mean.
    16s Rrna Gene, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 7251 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 16s rrna gene amplimers
    Analysis of PCR-RFLP patterns of 65-kDa HSP and <t>16S</t> <t>rRNA</t> genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .
    16s Rrna Gene Amplimers, supplied by Roche, used in various techniques. Bioz Stars score: 80/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BGI Shenzhen bacterial 16s rrna gene amplification
    Analysis of PCR-RFLP patterns of 65-kDa HSP and <t>16S</t> <t>rRNA</t> genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .
    Bacterial 16s Rrna Gene Amplification, supplied by BGI Shenzhen, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche bacterial 16s rrna gene amplification
    Analysis of PCR-RFLP patterns of 65-kDa HSP and <t>16S</t> <t>rRNA</t> genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .
    Bacterial 16s Rrna Gene Amplification, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher bacterial 16s rrna gene amplification
    Analysis of PCR-RFLP patterns of 65-kDa HSP and <t>16S</t> <t>rRNA</t> genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .
    Bacterial 16s Rrna Gene Amplification, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc microbial 16s rrna genes amplification
    Analysis of PCR-RFLP patterns of 65-kDa HSP and <t>16S</t> <t>rRNA</t> genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .
    Microbial 16s Rrna Genes Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc rrna gene amplification
    Analysis of PCR-RFLP patterns of 65-kDa HSP and <t>16S</t> <t>rRNA</t> genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .
    Rrna Gene Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc v3 v4 16s rrna gene amplification
    Analysis of PCR-RFLP patterns of 65-kDa HSP and <t>16S</t> <t>rRNA</t> genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .
    V3 V4 16s Rrna Gene Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    ( a ) Rarefaction curves showing the observed OTU richness (at 97% identity) of the 16S rRNA gene with increasing sequencing depth. Mean values (n = 3) were shown for the two salinity treatments (S1 and S4) and two soil depths. ( b ) Comparison of the bacterial communities at the phylum level. Relative read abundance of different bacterial phyla in bacterial communities. Sequences that could not be classified into any known group were labeled “others”.

    Journal: Scientific Reports

    Article Title: Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke

    doi: 10.1038/srep20687

    Figure Lengend Snippet: ( a ) Rarefaction curves showing the observed OTU richness (at 97% identity) of the 16S rRNA gene with increasing sequencing depth. Mean values (n = 3) were shown for the two salinity treatments (S1 and S4) and two soil depths. ( b ) Comparison of the bacterial communities at the phylum level. Relative read abundance of different bacterial phyla in bacterial communities. Sequences that could not be classified into any known group were labeled “others”.

    Article Snippet: Bacterial 16S rRNA gene amplification and Illumina Sequencing Primers 577F (5′-AYTGGGYDTAAAGNG-3′) and 926R (5′-CCGTCAATTCMTTTRAGT-3′) targeting the regions (V3-V4) of the 16S rRNA gene were used for PCR, because sequences in that regions provided the greatest diversity at the domain and bacterial phylum levels .

    Techniques: Sequencing, Labeling

    Host and symbiont phylogenies ( A ) Left: Midpoint-rooted, maximum likelihood (ML) phylogeny based on sponge ribosomal ITS-2 sequences from the current study (in bold) along with representative literature examples. Identical sequences are listed at a single branch tip, with symbols denoting dominant natural product chemistry. Bootstrap values ≥70 are shown; scale bar indicates substitutions per site. Matching superscripts indicate literature ITS-2 and 16S rRNA sequences obtained from the same sponge specimen. Right: H. spongeliae ML tree of near-full length 16S rRNA gene sequences, including closest free-living relative Oscillatoria corallinae , and rooted on closest relative with a sequenced genome, Moorea producens 3L. One full-length 16S rRNA gene sequence (GUM098) was obtained from clone library (see Figure 3 ). Remaining Clade IV 16S rRNA sequences in this study, denoted in parentheses, are represented by 370 bp sequences obtained from high-throughput community data that are 100% identical to the GUM098 full-length sequence. ( B ) Chemical profiles, as monitored by absorbance at 280 nm by HPLC with in situ photographs of representative sponges for each clade.

    Journal: Nature chemical biology

    Article Title: Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges

    doi: 10.1038/nchembio.2330

    Figure Lengend Snippet: Host and symbiont phylogenies ( A ) Left: Midpoint-rooted, maximum likelihood (ML) phylogeny based on sponge ribosomal ITS-2 sequences from the current study (in bold) along with representative literature examples. Identical sequences are listed at a single branch tip, with symbols denoting dominant natural product chemistry. Bootstrap values ≥70 are shown; scale bar indicates substitutions per site. Matching superscripts indicate literature ITS-2 and 16S rRNA sequences obtained from the same sponge specimen. Right: H. spongeliae ML tree of near-full length 16S rRNA gene sequences, including closest free-living relative Oscillatoria corallinae , and rooted on closest relative with a sequenced genome, Moorea producens 3L. One full-length 16S rRNA gene sequence (GUM098) was obtained from clone library (see Figure 3 ). Remaining Clade IV 16S rRNA sequences in this study, denoted in parentheses, are represented by 370 bp sequences obtained from high-throughput community data that are 100% identical to the GUM098 full-length sequence. ( B ) Chemical profiles, as monitored by absorbance at 280 nm by HPLC with in situ photographs of representative sponges for each clade.

    Article Snippet: To gain insights into the microbial community composition of the different sponges, we inventoried the microbiomes of two specimens from each of Clades Ia, Ib, III, and IV by 16S rRNA gene amplification and deep Illumina sequencing, generating between 75,000-250,000 reads per sample ( ).

    Techniques: Sequencing, High Throughput Screening Assay, High Performance Liquid Chromatography, In Situ

    Representative 16S rRNA gene diversity profiles Genomic DNA for 16S amplification was isolated from cross sections of sponge tissues. Taxonomic groups are shown at the phylum level, with the exception of operational taxonomic units identified as H. spongeliae (dark green). For clarity, groups representing

    Journal: Nature chemical biology

    Article Title: Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges

    doi: 10.1038/nchembio.2330

    Figure Lengend Snippet: Representative 16S rRNA gene diversity profiles Genomic DNA for 16S amplification was isolated from cross sections of sponge tissues. Taxonomic groups are shown at the phylum level, with the exception of operational taxonomic units identified as H. spongeliae (dark green). For clarity, groups representing

    Article Snippet: To gain insights into the microbial community composition of the different sponges, we inventoried the microbiomes of two specimens from each of Clades Ia, Ib, III, and IV by 16S rRNA gene amplification and deep Illumina sequencing, generating between 75,000-250,000 reads per sample ( ).

    Techniques: Amplification, Isolation

    Quantitative PCR measurements of the 16S rRNA genes in each environment type/season using bacteria-specific primers. Units are 16S rRNA gene copies per m 2 of EDC (following 14 days of exposure). Each season/type box represents all 10 measurements made. Significance of the differences shown in this figure is demonstrated in the inset box containing results of the Wilcoxon rank sum test for various comparisons between seasons or environment types. P values in bold indicate values below 0.05 (significant). Values in parentheses are absolute values of Hodges–Lehmann estimators, showing the magnitude of the difference between the two sample types.

    Journal: Frontiers in Microbiology

    Article Title: Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

    doi: 10.3389/fmicb.2018.00870

    Figure Lengend Snippet: Quantitative PCR measurements of the 16S rRNA genes in each environment type/season using bacteria-specific primers. Units are 16S rRNA gene copies per m 2 of EDC (following 14 days of exposure). Each season/type box represents all 10 measurements made. Significance of the differences shown in this figure is demonstrated in the inset box containing results of the Wilcoxon rank sum test for various comparisons between seasons or environment types. P values in bold indicate values below 0.05 (significant). Values in parentheses are absolute values of Hodges–Lehmann estimators, showing the magnitude of the difference between the two sample types.

    Article Snippet: The 16S rRNA gene amplification steps were prepared as described by the Illumina protocol (16S Metagenomic Sequencing Library Preparation, Part # 15044223 Rev.

    Techniques: Real-time Polymerase Chain Reaction

    Two-step generation of 16S amplicons for PacBio sequencing using M13-tagged barcoded primers. The first round of PCR amplifies full-length 16S rRNA fragments using gene-specific primers tailed with universal M13 forward or reverse sequence. In the second step, a unique combination of barcode sequences is added to 16S amplicons from each sample using M13 forward and reverse primers tagged with 16-base PacBio barcodes at their 5′ ends. Barcoded amplicons are subsequently pooled for SMRTbell library construction and multiplexed sequencing.

    Journal: Scientific Reports

    Article Title: High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

    doi: 10.1038/s41598-017-03139-4

    Figure Lengend Snippet: Two-step generation of 16S amplicons for PacBio sequencing using M13-tagged barcoded primers. The first round of PCR amplifies full-length 16S rRNA fragments using gene-specific primers tailed with universal M13 forward or reverse sequence. In the second step, a unique combination of barcode sequences is added to 16S amplicons from each sample using M13 forward and reverse primers tagged with 16-base PacBio barcodes at their 5′ ends. Barcoded amplicons are subsequently pooled for SMRTbell library construction and multiplexed sequencing.

    Article Snippet: 16S rRNA gene amplification, sample barcoding and PacBio sequencing The diversity of bacterial communities associated with corals from various habitats was analyzed using single molecule real-time PacBio sequencing technology (Pacific Biosciences, Menlo Park, CA, USA).

    Techniques: Sequencing, Polymerase Chain Reaction

    Comparison of species detection between full-length and partial 16S rRNA sequences. A neighbor-joining phylogenetic tree of 20 species identified in coral-associated microbiome generated using MEGA7. Reference type strain sequences were obtained from the RDP database. The clustering of the sequences was tested by a bootstrap approach using 1,000 replications. Orange, green and blue boxes indicate species that are classifiable based on sequence information from full-length, V3-V4 and V5-V6 regions of the 16S rRNA genes, respectively.

    Journal: Scientific Reports

    Article Title: High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

    doi: 10.1038/s41598-017-03139-4

    Figure Lengend Snippet: Comparison of species detection between full-length and partial 16S rRNA sequences. A neighbor-joining phylogenetic tree of 20 species identified in coral-associated microbiome generated using MEGA7. Reference type strain sequences were obtained from the RDP database. The clustering of the sequences was tested by a bootstrap approach using 1,000 replications. Orange, green and blue boxes indicate species that are classifiable based on sequence information from full-length, V3-V4 and V5-V6 regions of the 16S rRNA genes, respectively.

    Article Snippet: 16S rRNA gene amplification, sample barcoding and PacBio sequencing The diversity of bacterial communities associated with corals from various habitats was analyzed using single molecule real-time PacBio sequencing technology (Pacific Biosciences, Menlo Park, CA, USA).

    Techniques: Generated, Sequencing

    A histogram illustrating proportions of sequence reads from each sampling site that are classifiable at the species level using full-length (orange) or partial 16S rRNA gene fragments (V3-V4, green; V5-V6, blue).

    Journal: Scientific Reports

    Article Title: High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

    doi: 10.1038/s41598-017-03139-4

    Figure Lengend Snippet: A histogram illustrating proportions of sequence reads from each sampling site that are classifiable at the species level using full-length (orange) or partial 16S rRNA gene fragments (V3-V4, green; V5-V6, blue).

    Article Snippet: 16S rRNA gene amplification, sample barcoding and PacBio sequencing The diversity of bacterial communities associated with corals from various habitats was analyzed using single molecule real-time PacBio sequencing technology (Pacific Biosciences, Menlo Park, CA, USA).

    Techniques: Sequencing, Sampling

    Accuracy of 16S rRNA gene copy determination using MYcrobiota. The expected number of 16S rRNA gene copies within the positive control (PC) was compared to the measured number of 16S rRNA gene copies using MYcrobiota (green dots). The PC contained 10,000 16S rRNA gene copies of four different bacterial species and was processed in three independent MYcrobiota experiments. The indirect estimation of the total bacterial biomass within 37 clinical samples using MYcrobiota was compared to the total 16S rRNA gene copies measured directly using a 16S rRNA gene qPCR (blue dots). The Staphylococcus OTU-specific biomass from 13 S . aureus culture-positive samples was compared to the S . aureus biomass detected directly using a S . aureus -specific qPCR (yellow dots). In order to compare the number of S . aureus genome copies estimated using qPCR to the number of 16S rRNA gene copies detected using MYcrobiota, the estimated S . aureus genome copies were first multiplied by a factor of 6 to correct for differences in copy numbers of the Martineau fragment and the 16S rRNA gene present on the S . aureus genome. The calculated differences between methods were plotted using a binary logarithmic scale

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    Article Title: Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics

    doi: 10.1007/s10096-018-3220-z

    Figure Lengend Snippet: Accuracy of 16S rRNA gene copy determination using MYcrobiota. The expected number of 16S rRNA gene copies within the positive control (PC) was compared to the measured number of 16S rRNA gene copies using MYcrobiota (green dots). The PC contained 10,000 16S rRNA gene copies of four different bacterial species and was processed in three independent MYcrobiota experiments. The indirect estimation of the total bacterial biomass within 37 clinical samples using MYcrobiota was compared to the total 16S rRNA gene copies measured directly using a 16S rRNA gene qPCR (blue dots). The Staphylococcus OTU-specific biomass from 13 S . aureus culture-positive samples was compared to the S . aureus biomass detected directly using a S . aureus -specific qPCR (yellow dots). In order to compare the number of S . aureus genome copies estimated using qPCR to the number of 16S rRNA gene copies detected using MYcrobiota, the estimated S . aureus genome copies were first multiplied by a factor of 6 to correct for differences in copy numbers of the Martineau fragment and the 16S rRNA gene present on the S . aureus genome. The calculated differences between methods were plotted using a binary logarithmic scale

    Article Snippet: Also, 0.25 μM of a Fam-labeled probe was added for the real-time detection of the 16S rRNA gene amplification, and 1× Resolight Dye (Roche) was added to the S . aureus qPCR in order to measure the S . aureus DNA amplification.

    Techniques: Positive Control, Real-time Polymerase Chain Reaction

    Analysis of bacterial community’s structure and diversity of soil samples associated to spontaneous plants at SIN Caffaro. (A) Constraint (CAP) and (B) Unconstraint analysis of principal coordinates of the OTU 97 obtained from 16S rRNA gene sequencing of the bacterial communities considering the different soil fractions (A) and the root-associated soil fractions according to the plant species (B) . (C) OTU 97 Richness, (D) OTU 97 Evenness and (E) OTU 97 diversity. Statistical analysis are indicated in within the plant species comparing each fraction while asterisks indicate the statistical significance among fractions (for details see the text). The letters R, S, and B indicate, respectively, the rhizosphere, root surrounding soil and non-vegetated bulk soil.

    Journal: Frontiers in Microbiology

    Article Title: Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation

    doi: 10.3389/fmicb.2017.01385

    Figure Lengend Snippet: Analysis of bacterial community’s structure and diversity of soil samples associated to spontaneous plants at SIN Caffaro. (A) Constraint (CAP) and (B) Unconstraint analysis of principal coordinates of the OTU 97 obtained from 16S rRNA gene sequencing of the bacterial communities considering the different soil fractions (A) and the root-associated soil fractions according to the plant species (B) . (C) OTU 97 Richness, (D) OTU 97 Evenness and (E) OTU 97 diversity. Statistical analysis are indicated in within the plant species comparing each fraction while asterisks indicate the statistical significance among fractions (for details see the text). The letters R, S, and B indicate, respectively, the rhizosphere, root surrounding soil and non-vegetated bulk soil.

    Article Snippet: Bacterial strains were identified through 16S rRNA gene amplification and partial sequencing (Macrogen, Rep. of South Korea) as described by .

    Techniques: Sequencing

    Phylogenetic tree displaying the full 16S rRNA gene sequences of the three species of the genus Ignatzschineria , our sample (GenBank accession no. KT355688 ) and some related species. The tree was created with mega 6.0 software using the neighbour-joining method, Jukes–Cantor model, and 1000 bootstraps. Bar, 0.02 substitutions per nucleotide.

    Journal: JMM Case Reports

    Article Title: A case of Ignatzschineria bacteraemia in an unconscious man from the Netherlands

    doi: 10.1099/jmmcr.0.005043

    Figure Lengend Snippet: Phylogenetic tree displaying the full 16S rRNA gene sequences of the three species of the genus Ignatzschineria , our sample (GenBank accession no. KT355688 ) and some related species. The tree was created with mega 6.0 software using the neighbour-joining method, Jukes–Cantor model, and 1000 bootstraps. Bar, 0.02 substitutions per nucleotide.

    Article Snippet: We offered the strain to an external laboratory (BaseClear, Leiden, The Netherlands) for identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (VITEK MS; bioMérieux) and MicroSEQ analysis, a 16S rRNA gene amplification and sequencing method (Life Technologies).

    Techniques: Software

    Hybridization intensities of probes forming perfect-match (diamonds), one-mismatch (squares), and two-mismatch (circles) duplexes after hybridization with fluorescently labeled PCR-amplified 16S rRNA gene fragments of Desulfovibrio halophilus at different stringencies. (A) Mean signal intensities (for 10 spots, with local background subtracted) for each probe and wash temperature. (B) Normalized mean signal intensity values for each probe and wash temperature. Mean intensity values were normalized for each probe separately by assuming that the highest value observed at the different wash temperatures had a value of 1.00. In panel B, probes which showed no hybridization signals at low stringencies are not shown.

    Journal: Applied and Environmental Microbiology

    Article Title: Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment

    doi: 10.1128/AEM.68.10.5064-5081.2002

    Figure Lengend Snippet: Hybridization intensities of probes forming perfect-match (diamonds), one-mismatch (squares), and two-mismatch (circles) duplexes after hybridization with fluorescently labeled PCR-amplified 16S rRNA gene fragments of Desulfovibrio halophilus at different stringencies. (A) Mean signal intensities (for 10 spots, with local background subtracted) for each probe and wash temperature. (B) Normalized mean signal intensity values for each probe and wash temperature. Mean intensity values were normalized for each probe separately by assuming that the highest value observed at the different wash temperatures had a value of 1.00. In panel B, probes which showed no hybridization signals at low stringencies are not shown.

    Article Snippet: For 16S rRNA gene amplification, reaction mixtures (total volume, 50 μl) containing each primer at a concentration of 25 pM were prepared by using 10× Ex Taq reaction buffer and 2.5 U of Ex Taq polymerase (Takara Biomedicals, Otsu, Shiga, Japan).

    Techniques: Hybridization, Labeling, Polymerase Chain Reaction, Amplification

    Phylogenetic affiliations of SRPs belonging to the orders “ Desulfobacterales ” and “ Syntrophobacterales ” of the class “ Deltaproteobacteria .” The 16S rRNA consensus tree was constructed from comparative sequence analysis data by using maximum-parsimony, maximum-likelihood, and neighbor-joining methods and applying filters excluding all alignment positions which are not conserved in at least 50% of all bacterial and deltaproteobacterial 16S rRNA sequences. A collection of organisms representing all major lineages of the Archaea and Bacteria was used as an outgroup. Multifurcations connect branches for which a relative order could not be determined unambiguously. Non-SRPs are underlined. Parsimony bootstrap values (1,000 resamplings) for branches are indicated by solid circles ( > 90%) or an open circle (75 to 90%). Branches without circles had bootstrap values of less than 75%. The bar indicates 10% estimated sequence divergence (distance inferred by neighbor joining by using a 50% bacterial conservation filter). The colored boxes show the specificities (perfect-match target organisms) of the SRP-PhyloChip probes (indicated by short names). The numbers of probes with identical specificities for the target organisms are indicated in parentheses. Probes SRB385Db, DSS658, DSR651, and DSB804 are not shown to enhance clarity.

    Journal: Applied and Environmental Microbiology

    Article Title: Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment

    doi: 10.1128/AEM.68.10.5064-5081.2002

    Figure Lengend Snippet: Phylogenetic affiliations of SRPs belonging to the orders “ Desulfobacterales ” and “ Syntrophobacterales ” of the class “ Deltaproteobacteria .” The 16S rRNA consensus tree was constructed from comparative sequence analysis data by using maximum-parsimony, maximum-likelihood, and neighbor-joining methods and applying filters excluding all alignment positions which are not conserved in at least 50% of all bacterial and deltaproteobacterial 16S rRNA sequences. A collection of organisms representing all major lineages of the Archaea and Bacteria was used as an outgroup. Multifurcations connect branches for which a relative order could not be determined unambiguously. Non-SRPs are underlined. Parsimony bootstrap values (1,000 resamplings) for branches are indicated by solid circles ( > 90%) or an open circle (75 to 90%). Branches without circles had bootstrap values of less than 75%. The bar indicates 10% estimated sequence divergence (distance inferred by neighbor joining by using a 50% bacterial conservation filter). The colored boxes show the specificities (perfect-match target organisms) of the SRP-PhyloChip probes (indicated by short names). The numbers of probes with identical specificities for the target organisms are indicated in parentheses. Probes SRB385Db, DSS658, DSR651, and DSB804 are not shown to enhance clarity.

    Article Snippet: For 16S rRNA gene amplification, reaction mixtures (total volume, 50 μl) containing each primer at a concentration of 25 pM were prepared by using 10× Ex Taq reaction buffer and 2.5 U of Ex Taq polymerase (Takara Biomedicals, Otsu, Shiga, Japan).

    Techniques: Construct, Sequencing

    Melting curves for probe SRB385 (A), probe DSV698 (B), and probe EUB338 (C) after hybridization with fluorescently labeled PCR-amplified 16S rRNA gene fragments of Desulfovibrio halophilus , Desulfomicrobium aspheronum , and Desulfohalobium retbaense . For each probe the difference alignment with these reference SRPs is shown. The observed dissociation temperature (T d ) is indicated for each probe. Each data point represents the mean signal intensity value for 10 probe spots (local background was subtracted for each measurement). The error bars indicate the standard deviations. For each wash temperature and reference organism a separate microarray hybridization was performed. a.u., arbitrary units.

    Journal: Applied and Environmental Microbiology

    Article Title: Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment

    doi: 10.1128/AEM.68.10.5064-5081.2002

    Figure Lengend Snippet: Melting curves for probe SRB385 (A), probe DSV698 (B), and probe EUB338 (C) after hybridization with fluorescently labeled PCR-amplified 16S rRNA gene fragments of Desulfovibrio halophilus , Desulfomicrobium aspheronum , and Desulfohalobium retbaense . For each probe the difference alignment with these reference SRPs is shown. The observed dissociation temperature (T d ) is indicated for each probe. Each data point represents the mean signal intensity value for 10 probe spots (local background was subtracted for each measurement). The error bars indicate the standard deviations. For each wash temperature and reference organism a separate microarray hybridization was performed. a.u., arbitrary units.

    Article Snippet: For 16S rRNA gene amplification, reaction mixtures (total volume, 50 μl) containing each primer at a concentration of 25 pM were prepared by using 10× Ex Taq reaction buffer and 2.5 U of Ex Taq polymerase (Takara Biomedicals, Otsu, Shiga, Japan).

    Techniques: Hybridization, Labeling, Polymerase Chain Reaction, Amplification, Microarray

    16S rRNA gene abundance (qPCR quantification) of major phylogenetic groups from coastal bacterioplankton assemblages in 6 stations near Qinhuangdao coastal area. The symbols and lines in black, red, green, blue, cyan, and magenta represent stations W1, W2, W3, W4, W5, and W6. Values on Y -axis are plotted in log-scale.

    Journal: Frontiers in Microbiology

    Article Title: Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea

    doi: 10.3389/fmicb.2017.01579

    Figure Lengend Snippet: 16S rRNA gene abundance (qPCR quantification) of major phylogenetic groups from coastal bacterioplankton assemblages in 6 stations near Qinhuangdao coastal area. The symbols and lines in black, red, green, blue, cyan, and magenta represent stations W1, W2, W3, W4, W5, and W6. Values on Y -axis are plotted in log-scale.

    Article Snippet: The isolated DNA was used as template for bacterial 16S rRNA gene amplification using universal primers 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′) on Bio-Rad S1000 thermal cycler (Bio-Rad Laboratories Inc., United States) using the following protocol: 95°C 5 min; 94°C 45 s, 55°C 45 s, 72°C 1 min; 35 cycles; 72°C 10 min. PCR amplification for each sample was performed in triplicates and the triplicate PCR products were mixed to obtain the final sample for clone library construction.

    Techniques: Real-time Polymerase Chain Reaction

    Biplot of redundancy analysis (RDA) showing relationship between the environmental variables and 16S rRNA gene abundance (qPCR quantification) of major phylogenetic groups in six stations near Qinhuangdao coastal area. The two RDA axes (RDA1 and RDA2) explained 70.35% of total variation in abundance data, and the significant ( p

    Journal: Frontiers in Microbiology

    Article Title: Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea

    doi: 10.3389/fmicb.2017.01579

    Figure Lengend Snippet: Biplot of redundancy analysis (RDA) showing relationship between the environmental variables and 16S rRNA gene abundance (qPCR quantification) of major phylogenetic groups in six stations near Qinhuangdao coastal area. The two RDA axes (RDA1 and RDA2) explained 70.35% of total variation in abundance data, and the significant ( p

    Article Snippet: The isolated DNA was used as template for bacterial 16S rRNA gene amplification using universal primers 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′) on Bio-Rad S1000 thermal cycler (Bio-Rad Laboratories Inc., United States) using the following protocol: 95°C 5 min; 94°C 45 s, 55°C 45 s, 72°C 1 min; 35 cycles; 72°C 10 min. PCR amplification for each sample was performed in triplicates and the triplicate PCR products were mixed to obtain the final sample for clone library construction.

    Techniques: Real-time Polymerase Chain Reaction

    Composition and distribution of bacterioplankton assemblages at the 6 stations near Qinhuangdao coastal area. Percentage distribution of the 16S rRNA gene sequences at the (A) phylum level and (B) class level indicates higher relative abundance of subgroups Proteobacteria, Cyanobacteria, Bacteroidetes , and Actinobacteria .

    Journal: Frontiers in Microbiology

    Article Title: Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea

    doi: 10.3389/fmicb.2017.01579

    Figure Lengend Snippet: Composition and distribution of bacterioplankton assemblages at the 6 stations near Qinhuangdao coastal area. Percentage distribution of the 16S rRNA gene sequences at the (A) phylum level and (B) class level indicates higher relative abundance of subgroups Proteobacteria, Cyanobacteria, Bacteroidetes , and Actinobacteria .

    Article Snippet: The isolated DNA was used as template for bacterial 16S rRNA gene amplification using universal primers 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′) on Bio-Rad S1000 thermal cycler (Bio-Rad Laboratories Inc., United States) using the following protocol: 95°C 5 min; 94°C 45 s, 55°C 45 s, 72°C 1 min; 35 cycles; 72°C 10 min. PCR amplification for each sample was performed in triplicates and the triplicate PCR products were mixed to obtain the final sample for clone library construction.

    Techniques:

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

    Journal: Frontiers in Microbiology

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

    doi: 10.3389/fmicb.2016.00416

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

    Article Snippet: The V4 region of the 16S rRNA gene was amplified using the primers 515F and 806R and sequenced using the HiSeq2500 platform (Illumina) (Caporaso et al., ).

    Techniques: Isolation

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

    Journal: Frontiers in Microbiology

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

    doi: 10.3389/fmicb.2016.00416

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

    Article Snippet: The V4 region of the 16S rRNA gene was amplified using the primers 515F and 806R and sequenced using the HiSeq2500 platform (Illumina) (Caporaso et al., ).

    Techniques: Isolation

    Analysis of PCR-RFLP patterns of 65-kDa HSP and 16S rRNA genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .

    Journal: Journal of Clinical Microbiology

    Article Title: Identification of Mycobacterium Species by PCR-Restriction Fragment Length Polymorphism Analyses Using Fluorescence Capillary Electrophoresis

    doi:

    Figure Lengend Snippet: Analysis of PCR-RFLP patterns of 65-kDa HSP and 16S rRNA genes of six Mycobacterium species using FCE. Terminal Bst EII and Hae III restriction fragments of the 439-bp 65-kDa HSP gene amplimer are labeled with TET (green), and Cfo I and Hae III fragments of the 475-bp 16S rRNA gene amplimer are labeled with FAM (blue). A, M. tuberculosis ; B, M. microti ; C, M. avium ; D, M. intracellulare ; E, M. gordonae ; F, M. kansasii .

    Article Snippet: The 16S rRNA gene amplimers were similarly divided and digested with Hae III and Cfo I (Roche-Boehringer Mannheim).

    Techniques: Polymerase Chain Reaction, Labeling