Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing
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{"title"=>"Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Kathleen", "last_name"=>"Sim", "scopus_author_id"=>"55145175400"}, {"first_name"=>"Michael J.", "last_name"=>"Cox", "scopus_author_id"=>"55597087384"}, {"first_name"=>"Harm", "last_name"=>"Wopereis", "scopus_author_id"=>"51864832000"}, {"first_name"=>"Rocio", "last_name"=>"Martin", "scopus_author_id"=>"16069052600"}, {"first_name"=>"Jan", "last_name"=>"Knol", "scopus_author_id"=>"7005797980"}, {"first_name"=>"Ming Shi", "last_name"=>"Li", "scopus_author_id"=>"57193139880"}, {"first_name"=>"William O.C.M.", "last_name"=>"Cookson", "scopus_author_id"=>"35261536800"}, {"first_name"=>"Miriam F.", "last_name"=>"Moffatt", "scopus_author_id"=>"7004860467"}, {"first_name"=>"J. Simon", "last_name"=>"Kroll", "scopus_author_id"=>"7102160161"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84859014125", "pui"=>"364528349", "doi"=>"10.1371/journal.pone.0032543", "isbn"=>"doi:10.1371/journal.pone.0032543", "sgr"=>"84859014125", "pmid"=>"22470420"}, "id"=>"f6db417c-a947-3a18-810a-3b95235b9107", "abstract"=>"The 16S rRNA gene is conserved across all bacteria and as such is routinely targeted in PCR surveys of bacterial diversity. PCR primer design aims to amplify as many different 16S rRNA gene sequences from as wide a range of organisms as possible, though there are no suitable 100% conserved regions of the gene, leading to bias. In the gastrointestinal tract, bifidobacteria are a key genus, but are often under-represented in 16S rRNA surveys of diversity. We have designed modified, 'bifidobacteria-optimised' universal primers, which we have demonstrated detection of bifidobacterial sequence present in DNA mixtures at 2% abundance, the lowest proportion tested. Optimisation did not compromise the detection of other organisms in infant faecal samples. Separate validation using fluorescence in situ hybridisation (FISH) shows that the proportions of bifidobacteria detected in faecal samples were in agreement with those obtained using 16S rRNA based pyrosequencing. For future studies looking at faecal microbiota, careful selection of primers will be key in order to ensure effective detection of bifidobacteria.", "link"=>"http://www.mendeley.com/research/improved-detection-bifidobacteria-optimised-16s-rrnagene-based-pyrosequencing", "reader_count"=>118, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>34, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>2, "Student > Master"=>18, "Other"=>9, "Student > Bachelor"=>13, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>34, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>2, "Student > Master"=>18, "Other"=>9, "Student > Bachelor"=>13, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Nursing and Health Professions"=>1, "Mathematics"=>1, "Medicine and Dentistry"=>23, "Agricultural and Biological Sciences"=>70, "Arts and Humanities"=>1, "Sports and Recreations"=>1, "Immunology and Microbiology"=>5}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>23}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>70}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Canada"=>2, "United States"=>2, "Japan"=>1, "Brazil"=>1, "United Kingdom"=>4, "South Africa"=>2, "Germany"=>1, "India"=>1, "Spain"=>1}, "group_count"=>11}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/662477"], "description"=>"<p>Values in bold are different from 0 with a significance level alpha = 0.05.</p>", "links"=>[], "tags"=>["resulting", "bland-altman"], "article_id"=>332954, "categories"=>["Infectious Diseases", "Biochemistry", "Chemistry", "Ecology", "Medicine"], "users"=>["Kathleen Sim", "Michael J. Cox", "Harm Wopereis", "Rocío Martín", "Jan Knol", "Ming-Shi Li", "William O. C. M. Cookson", "Miriam F. Moffatt", "J. Simon Kroll"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0032543.t004", "stats"=>{"downloads"=>6, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_P_values_resulting_from_Bland_Altman_agreement_tests_/332954", "title"=>"<i>P</i>-values resulting from Bland-Altman agreement tests.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-28 00:49:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/662326"], "description"=>"<p>Proportions of DNA in each mixture.</p>", "links"=>[], "tags"=>["dna"], "article_id"=>332808, "categories"=>["Infectious Diseases", "Biochemistry", "Chemistry", "Ecology", "Medicine"], "users"=>["Kathleen Sim", "Michael J. Cox", "Harm Wopereis", "Rocío Martín", "Jan Knol", "Ming-Shi Li", "William O. C. M. Cookson", "Miriam F. Moffatt", "J. Simon Kroll"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0032543.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportions_of_DNA_in_each_mixture_/332808", "title"=>"Proportions of DNA in each mixture.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-28 00:46:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/662428"], "description"=>"<p>Relative proportions of faecal bifidobacteria in ten faecal samples as determined by FISH and 454-sequencing using ‘bifidobacteria-optimised’ universal primers (926Rb) or regular universal primers (926R).</p>", "links"=>[], "tags"=>["proportions", "faecal", "bifidobacteria", "samples", "454-sequencing", "primers"], "article_id"=>332899, "categories"=>["Infectious Diseases", "Biochemistry", "Chemistry", "Ecology", "Medicine"], "users"=>["Kathleen Sim", "Michael J. Cox", "Harm Wopereis", "Rocío Martín", "Jan Knol", "Ming-Shi Li", "William O. C. M. Cookson", "Miriam F. Moffatt", "J. Simon Kroll"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0032543.t002", "stats"=>{"downloads"=>3, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_proportions_of_faecal_bifidobacteria_in_ten_faecal_samples_as_determined_by_FISH_and_454_sequencing_using_8216_bifidobacteria_optimised_8217_universal_primers_926Rb_or_regular_universal_primers_926R_/332899", "title"=>"Relative proportions of faecal bifidobacteria in ten faecal samples as determined by FISH and 454-sequencing using ‘bifidobacteria-optimised’ universal primers (926Rb) or regular universal primers (926R).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-28 00:48:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/662074"], "description"=>"<p>Samples are grouped by hierarchical cluster analysis on the x-axis and by neighbour-joining phylogenetic tree with nearest neighbour interchange on the y-axis. Samples amplified with ‘bifidobacteria-optimised’ primers are in red and with the standard primers in blue. Bifidobacterial OTUs are highlighted in the red box.</p>", "links"=>[], "tags"=>["displaying", "abundance", "otus"], "article_id"=>332555, "categories"=>["Infectious Diseases", "Biochemistry", "Chemistry", "Ecology", "Medicine"], "users"=>["Kathleen Sim", "Michael J. Cox", "Harm Wopereis", "Rocío Martín", "Jan Knol", "Ming-Shi Li", "William O. C. M. Cookson", "Miriam F. Moffatt", "J. Simon Kroll"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0032543.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_displaying_the_relative_abundance_of_OTUs_per_sample_/332555", "title"=>"Heatmap displaying the relative abundance of OTUs per sample.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-28 00:42:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/661898"], "description"=>"<p>Increased detection rate of <i>Bifidobacterium dentium</i> demonstrated using the ‘bifidobacteria-optimised’ universal primers (b) compared to regular universal primers (u).</p>", "links"=>[], "tags"=>["454", "sequencing", "reads", "primer"], "article_id"=>332375, "categories"=>["Infectious Diseases", "Biochemistry", "Chemistry", "Ecology", "Medicine"], "users"=>["Kathleen Sim", "Michael J. Cox", "Harm Wopereis", "Rocío Martín", "Jan Knol", "Ming-Shi Li", "William O. C. M. Cookson", "Miriam F. Moffatt", "J. Simon Kroll"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0032543.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportions_of_454_sequencing_reads_obtained_using_both_primer_sets_/332375", "title"=>"Proportions of 454 sequencing reads obtained using both primer sets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-28 00:39:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/339409"], "description"=>"<div><p>The 16S rRNA gene is conserved across all bacteria and as such is routinely targeted in PCR surveys of bacterial diversity. PCR primer design aims to amplify as many different 16S rRNA gene sequences from as wide a range of organisms as possible, though there are no suitable 100% conserved regions of the gene, leading to bias. In the gastrointestinal tract, bifidobacteria are a key genus, but are often under-represented in 16S rRNA surveys of diversity. We have designed modified, ‘bifidobacteria-optimised’ universal primers, which we have demonstrated detection of bifidobacterial sequence present in DNA mixtures at 2% abundance, the lowest proportion tested. Optimisation did not compromise the detection of other organisms in infant faecal samples. Separate validation using fluorescence <em>in situ</em> hybridisation (FISH) shows that the proportions of bifidobacteria detected in faecal samples were in agreement with those obtained using 16S rRNA based pyrosequencing. For future studies looking at faecal microbiota, careful selection of primers will be key in order to ensure effective detection of bifidobacteria.</p> </div>", "links"=>[], "tags"=>["detection", "bifidobacteria", "optimised", "16s", "rrna-gene", "based", "pyrosequencing"], "article_id"=>127094, "categories"=>["Biochemistry", "Cancer", "Chemistry", "Ecology", "Medicine"], "users"=>["Kathleen Sim", "Michael J. Cox", "Harm Wopereis", "Rocío Martín", "Jan Knol", "Ming-Shi Li", "William O. C. M. Cookson", "Miriam F. Moffatt", "J. Simon Kroll"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0032543", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Improved_Detection_of_Bifidobacteria_with_Optimised_16S_rRNA_Gene_Based_Pyrosequencing/127094", "title"=>"Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-28 01:58:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/662377"], "description"=>"<p>Values in bold are different from 0 with a significance level alpha = 0.05.</p>", "links"=>[], "tags"=>["matrix", "shows", "pearson", "coefficients"], "article_id"=>332851, "categories"=>["Infectious Diseases", "Biochemistry", "Chemistry", "Ecology", "Medicine"], "users"=>["Kathleen Sim", "Michael J. Cox", "Harm Wopereis", "Rocío Martín", "Jan Knol", "Ming-Shi Li", "William O. C. M. Cookson", "Miriam F. Moffatt", "J. Simon Kroll"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0032543.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_matrix_Pearson_shows_the_Pearson_correlation_coefficients_and_p_values_/332851", "title"=>"Correlation matrix (Pearson) shows the Pearson correlation coefficients and p-values.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-28 00:47:31"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"16", "full-text"=>"13", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"7"}
  • {"unique-ip"=>"16", "full-text"=>"14", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
  • {"unique-ip"=>"16", "full-text"=>"9", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
  • {"unique-ip"=>"17", "full-text"=>"14", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"13", "full-text"=>"10", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"20", "full-text"=>"20", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2014", "month"=>"12"}
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  • {"unique-ip"=>"20", "full-text"=>"17", "pdf"=>"10", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
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Relative Metric

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