Analyses of the stability and core taxonomic memberships of the human microbiome.

Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core"), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by qua...

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Autores principales:	Kelvin Li, Monika Bihan, Barbara A Methé
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9dd3cd38b145458da2beafea4bc20ce4
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spelling	oai:doaj.org-article:9dd3cd38b145458da2beafea4bc20ce42021-11-18T07:46:47ZAnalyses of the stability and core taxonomic memberships of the human microbiome.1932-620310.1371/journal.pone.0063139https://doaj.org/article/9dd3cd38b145458da2beafea4bc20ce42013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23671663/?tool=EBIhttps://doaj.org/toc/1932-6203Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core"), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat's microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of "minor" oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region.Kelvin LiMonika BihanBarbara A MethéPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e63139 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kelvin Li Monika Bihan Barbara A Methé Analyses of the stability and core taxonomic memberships of the human microbiome.
description	Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core"), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat's microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of "minor" oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region.
format	article
author	Kelvin Li Monika Bihan Barbara A Methé
author_facet	Kelvin Li Monika Bihan Barbara A Methé
author_sort	Kelvin Li
title	Analyses of the stability and core taxonomic memberships of the human microbiome.
title_short	Analyses of the stability and core taxonomic memberships of the human microbiome.
title_full	Analyses of the stability and core taxonomic memberships of the human microbiome.
title_fullStr	Analyses of the stability and core taxonomic memberships of the human microbiome.
title_full_unstemmed	Analyses of the stability and core taxonomic memberships of the human microbiome.
title_sort	analyses of the stability and core taxonomic memberships of the human microbiome.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/9dd3cd38b145458da2beafea4bc20ce4
work_keys_str_mv	AT kelvinli analysesofthestabilityandcoretaxonomicmembershipsofthehumanmicrobiome AT monikabihan analysesofthestabilityandcoretaxonomicmembershipsofthehumanmicrobiome AT barbaraamethe analysesofthestabilityandcoretaxonomicmembershipsofthehumanmicrobiome
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Analyses of the stability and core taxonomic memberships of the human microbiome.

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