Novel Bacterial Taxa in the Human Microbiome
Publication Date
June 13, 2012
Journal
PLOS ONE
Authors
Kristine M. Wylie, Rebecca M. Truty, Thomas J. Sharpton, Kathie A. Mihindukulasuriya, et al
Volume
7
Issue
6
Pages
e35294
DOI
https://dx.plos.org/10.1371/journal.pone.0035294
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0035294
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22719826
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374617
Europe PMC
http://europepmc.org/abstract/MED/22719826
Web of Science
000305341900008
Scopus
84862201019
Mendeley
http://www.mendeley.com/research/novel-bacterial-taxa-human-microbiome
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{"title"=>"Novel bacterial Taxa in the human microbiome", "type"=>"journal", "authors"=>[{"first_name"=>"Kristine M.", "last_name"=>"Wylie", "scopus_author_id"=>"7006257144"}, {"first_name"=>"Rebecca M.", "last_name"=>"Truty", "scopus_author_id"=>"56592878500"}, {"first_name"=>"Thomas J.", "last_name"=>"Sharpton", "scopus_author_id"=>"14018726100"}, {"first_name"=>"Kathie A.", "last_name"=>"Mihindukulasuriya", "scopus_author_id"=>"24174782100"}, {"first_name"=>"Yanjiao", "last_name"=>"Zhou", "scopus_author_id"=>"55249709400"}, {"first_name"=>"Hongyu", "last_name"=>"Gao", "scopus_author_id"=>"55249549600"}, {"first_name"=>"Erica", "last_name"=>"Sodergren", "scopus_author_id"=>"6701578232"}, {"first_name"=>"George M.", "last_name"=>"Weinstock", "scopus_author_id"=>"7005387907"}, {"first_name"=>"Katherine S.", "last_name"=>"Pollard", "scopus_author_id"=>"35235175500"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84862201019", "doi"=>"10.1371/journal.pone.0035294", "sgr"=>"84862201019", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22719826", "issn"=>"19326203", "pui"=>"364996232"}, "id"=>"a80e2560-2504-3029-a06f-e6c8fd6786d3", "abstract"=>"The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Consortium to determine if novel taxa remain to be discovered in stool samples from healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses sequence data from multiple platforms (Illumina GAIIX and Roche 454 FLX Titanium) and approaches (whole-genome shotgun and 16S rDNA amplicons) to validate novel taxa. We applied this approach to stool samples from 11 healthy subjects collected as part of the Human Microbiome Project. We discovered several low-abundance, novel bacterial taxa, which span three major phyla in the bacterial tree of life. We determined that these taxa are present in a larger set of Human Microbiome Project subjects and are found in two sampling sites (Houston and St. Louis). We show that the number of false-positive novel sequences (primarily chimeric sequences) would have been two orders of magnitude higher than the true number of novel taxa without validation using multiple datasets, highlighting the importance of establishing rigorous standards for the identification of novel taxa in metagenomic data. The majority of novel sequences are related to the recently discovered genus Barnesiella, further encouraging efforts to characterize the members of this genus and to study their roles in the microbial communities of the gut. A better understanding of the effects of less-abundant bacteria is important as we seek to understand the complex gut microbiome in healthy individuals and link changes in the microbiome to disease.", "link"=>"http://www.mendeley.com/research/novel-bacterial-taxa-human-microbiome", "reader_count"=>278, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>12, "Researcher"=>83, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>57, "Student > Postgraduate"=>10, "Student > Master"=>35, "Other"=>16, "Student > Bachelor"=>21, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>1, "Professor"=>18}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>12, "Researcher"=>83, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>57, "Student > Postgraduate"=>10, "Student > Master"=>35, "Other"=>16, "Student > Bachelor"=>21, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>1, "Professor"=>18}, "reader_count_by_subject_area"=>{"Unspecified"=>13, "Agricultural and Biological Sciences"=>186, "Arts and Humanities"=>2, "Veterinary Science and Veterinary Medicine"=>2, "Chemistry"=>1, "Computer Science"=>8, "Engineering"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>22, "Mathematics"=>3, "Medicine and Dentistry"=>20, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>3, "Sports and Recreations"=>1, "Physics and Astronomy"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>9}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>20}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>13}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>3}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>9}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>186}, "Computer Science"=>{"Computer Science"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>22}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United States"=>19, "Japan"=>1, "Egypt"=>1, "United Kingdom"=>3, "Thailand"=>1, "Portugal"=>1, "Spain"=>2, "Russia"=>1, "India"=>1, "Canada"=>7, "Sweden"=>2, "Czech Republic"=>1, "Taiwan"=>1, "Denmark"=>3, "Brazil"=>1, "Italy"=>2, "Mexico"=>1, "Chile"=>1, "France"=>2, "Australia"=>1, "Germany"=>1}, "group_count"=>19}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/623789"], "description"=>"<p>Green circles represent the data collected by the HMP, with the darkest green circles representing WGS read, and successively lighter green circles associated with 16S reads that show progressively more evidence of novelty. Blue squares represent external databases used to determine novelty. Major filtering steps in the pipeline are shown as yellow triangles.</p>", "links"=>[], "tags"=>["describing", "pipeline"], "article_id"=>294273, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Microbiology", "Evolutionary Biology"], "users"=>["Kristine M. Wylie", "Rebecca M. Truty", "Thomas J. Sharpton", "Kathie A. Mihindukulasuriya", "Yanjiao Zhou", "Hongyu Gao", "Erica Sodergren", "George M. Weinstock", "Katherine S. Pollard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035294.g001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_chart_describing_the_pipeline_for_the_identification_of_novel_OTUs_/294273", "title"=>"Flow chart describing the pipeline for the identification of novel OTUs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-13 01:11:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/624221"], "description"=>"<p>(A) The number of reads assigned to each OTU (x-axis) across all the samples (y-axis) is represented by color on a scale from light yellow (few sequences) to dark red (many sequences). Within each dataset (“Roche V1–3”, “Roche V3–5”, and “WGS”), samples are organized by their source: the three smaller groups of samples labeled “11” contain the original reads (from 11 subjects) used to define the OTUs. Reads recruited to the OTUs from the extended Roche variable region datasets (“Roche V3–5” and “Roche V1–3”) and Illumina WGS dataset (additional samples, “AS”) are also shown. (B) The total number of reads assigned to each OTU (x-axis) across all subjects (y-axis) is represented by color on the same scale. These data include the original reads as well as reads from both extended variable region datasets and the Roche and Illumina WGS datasets. The subjects in the lower portion of the figure were sampled in St. Louis while those in the upper portion of the figure were sampled in Houston.</p>", "links"=>[], "tags"=>["abundance"], "article_id"=>294709, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Microbiology", "Evolutionary Biology"], "users"=>["Kristine M. Wylie", "Rebecca M. Truty", "Thomas J. Sharpton", "Kathie A. Mihindukulasuriya", "Yanjiao Zhou", "Hongyu Gao", "Erica Sodergren", "George M. Weinstock", "Katherine S. Pollard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035294.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_and_abundance_of_novel_OTUs_/294709", "title"=>"Distribution and abundance of novel OTUs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-13 01:18:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/323924", "https://ndownloader.figshare.com/files/323993", "https://ndownloader.figshare.com/files/324038", "https://ndownloader.figshare.com/files/324096", "https://ndownloader.figshare.com/files/324199", "https://ndownloader.figshare.com/files/324235", "https://ndownloader.figshare.com/files/324416"], "description"=>"<div><p>The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Consortium to determine if novel taxa remain to be discovered in stool samples from healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses sequence data from multiple platforms (Illumina GAIIX and Roche 454 FLX Titanium) and approaches (whole-genome shotgun and 16S rDNA amplicons) to validate novel taxa. We applied this approach to stool samples from 11 healthy subjects collected as part of the Human Microbiome Project. We discovered several low-abundance, novel bacterial taxa, which span three major phyla in the bacterial tree of life. We determined that these taxa are present in a larger set of Human Microbiome Project subjects and are found in two sampling sites (Houston and St. Louis). We show that the number of false-positive novel sequences (primarily chimeric sequences) would have been two orders of magnitude higher than the true number of novel taxa without validation using multiple datasets, highlighting the importance of establishing rigorous standards for the identification of novel taxa in metagenomic data. The majority of novel sequences are related to the recently discovered genus <em>Barnesiella</em>, further encouraging efforts to characterize the members of this genus and to study their roles in the microbial communities of the gut. A better understanding of the effects of less-abundant bacteria is important as we seek to understand the complex gut microbiome in healthy individuals and link changes in the microbiome to disease.</p> </div>", "links"=>[], "tags"=>["bacterial", "taxa", "microbiome"], "article_id"=>123937, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Microbiology", "Evolutionary Biology"], "users"=>["Kristine M. Wylie", "Rebecca M. Truty", "Thomas J. Sharpton", "Kathie A. Mihindukulasuriya", "Yanjiao Zhou", "Hongyu Gao", "Erica Sodergren", "George M. Weinstock", "Katherine S. Pollard"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0035294.s001", "https://dx.doi.org/10.1371/journal.pone.0035294.s002", "https://dx.doi.org/10.1371/journal.pone.0035294.s003", "https://dx.doi.org/10.1371/journal.pone.0035294.s004", "https://dx.doi.org/10.1371/journal.pone.0035294.s005", "https://dx.doi.org/10.1371/journal.pone.0035294.s006", "https://dx.doi.org/10.1371/journal.pone.0035294.s007"], "stats"=>{"downloads"=>6, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Novel_Bacterial_Taxa_in_the_Human_Microbiome/123937", "title"=>"Novel Bacterial Taxa in the Human Microbiome", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-13 01:05:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/624028"], "description"=>"<p>Novel reads from each dataset (dark colored branches, see legend) were inserted into the Silva reference tree with RAxML and are marked with a red box at the end of the leaf. Novel reads cluster into phyla that are typically found in stool samples (light colored branches, as labeled); all remaining phyla are shown in gray. The black arrow indicates the group of reads identified as the genus <i>Barnesiella</i>.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Computational biology", "Evolutionary biology", "pathology"], "article_id"=>294512, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Microbiology", "Evolutionary Biology"], "users"=>["Kristine M. Wylie", "Rebecca M. Truty", "Thomas J. Sharpton", "Kathie A. Mihindukulasuriya", "Yanjiao Zhou", "Hongyu Gao", "Erica Sodergren", "George M. Weinstock", "Katherine S. Pollard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035294.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxonomic_distribution_of_novel_reads_/294512", "title"=>"Taxonomic distribution of novel reads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-13 01:15:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/624292"], "description"=>"*<p>not applicable.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Computational biology", "Evolutionary biology", "pathology"], "article_id"=>294776, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Microbiology", "Evolutionary Biology"], "users"=>["Kristine M. Wylie", "Rebecca M. Truty", "Thomas J. Sharpton", "Kathie A. Mihindukulasuriya", "Yanjiao Zhou", "Hongyu Gao", "Erica Sodergren", "George M. Weinstock", "Katherine S. Pollard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035294.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_statistics_/294776", "title"=>"Sequence statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-13 01:19:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/624141"], "description"=>"<p>(A) Distribution of novel OTUs as a function of the maximum percent identity of a constituent read to a nearest neighbor for (black) all reads in the RDP and NT databases and (red) cultured reads. (B) The distribution of novel OTUs as a function of the lowest taxonomic rank that was confidently (with a bootstrap value of >0.5) assigned to a constituent read.</p>", "links"=>[], "tags"=>["taxonomic"], "article_id"=>294629, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Microbiology", "Evolutionary Biology"], "users"=>["Kristine M. Wylie", "Rebecca M. Truty", "Thomas J. Sharpton", "Kathie A. Mihindukulasuriya", "Yanjiao Zhou", "Hongyu Gao", "Erica Sodergren", "George M. Weinstock", "Katherine S. Pollard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035294.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Novelty_at_different_taxonomic_levels_/294629", "title"=>"Novelty at different taxonomic levels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-13 01:17:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/623880"], "description"=>"<p>(A) This flow chart describes the removal of Roche WGS and variable region sequences based on characteristics of the Illumina alignments, resulting in a final set of high-quality novel sequences. Possible problems listed in red indicate errors in the Roche sequence, and possible problems listed in black indicate situations in which the Roche read may be of high quality but could not be confirmed by aligned Illumina sequences. The inset plot shows an example of a Roche variable region sequence with a progressive shortening of aligned Illumina sequences. The base position of the Roche sequence at which the Illumina alignment begins is plotted on the x-axis, and the maximum length of aligned Illumina reads with the given start position is plotted on the y-axis. In the middle of the Roche sequence, the Illumina sequences decrease to approximately 60 bp before returning to 100 bp in length. Characteristics of the Illumina alignments associated with specific problems with the Roche WGS and variable region reads are illustrated in B–D.</p>", "links"=>[], "tags"=>["illumina", "chimeras", "sequencing"], "article_id"=>294369, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Microbiology", "Evolutionary Biology"], "users"=>["Kristine M. Wylie", "Rebecca M. Truty", "Thomas J. Sharpton", "Kathie A. Mihindukulasuriya", "Yanjiao Zhou", "Hongyu Gao", "Erica Sodergren", "George M. Weinstock", "Katherine S. Pollard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035294.g002", "stats"=>{"downloads"=>1, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Irregularities_in_Illumina_coverage_used_to_identify_chimeras_and_sequencing_error_/294369", "title"=>"Irregularities in Illumina coverage used to identify chimeras and sequencing error.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-13 01:12:49"}

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Relative Metric

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