Structure, function and diversity of the healthy human microbiome

Structure, function and diversity of the healthy human microbiome Curtis Huttenhower J. Fah Sathirapongsasuti Nicola Segata Dirk Gevers Ashlee M. Earl Michael G. FitzGerald Sarah Young Qiandong Zeng Eric J. Alm Lucia Alvarado Scott Anderson Harindra Arachchi Toby Bloom Dawn Ciulla Rachel Erlich Michael Feldgarden Sheila Fisher Dennis C. Friedrich Georgia Giannoukos Jonathan M. Goldberg Allison Griggs Sharvari Gujja Brian J. Haas Theresa A. Hepburn Clinton Howarth Katherine Huang Cristyn Kells Niall J. Lennon Teena Mehta Chad Nusbaum M.A. Pearson Margaret Priest Carsten Russ Narmada Shenoy Sean M. Sykes Diana Tabbaa Doyle V. Ward Chandri Yandava Jeremy Zucker Bruce W. Birren Rob Knight José C. Clemente Catherine Lozupone Daniel McDonald Sahar Abubucker Asif Chinwalla Robert S. Fulton Kymberlie Hallsworth-Pepin Elizabeth A. Lobos Vincent Magrini John Martin Makedonka Mitreva Erica Sodergren Aye Wollam Elizabeth L. Appelbaum Veena Bhonagiri Lei Chen Sandra W. Clifton Kimberley D. Delehaunty David J. Dooling Candace N. Farmer Catrina C. Fronick Lucinda Fulton Hongyu Gao Brandi Herter Karthik Kota Elaine R. Mardis Kathie A. Mihindukulasuriya Patrick Minx Michelle O'Laughlin Craig Pohl Chad Tomlinson Jason Walker Zhengyuan Wang Wesley C. Warren Kristine M. Wylie Todd Wylie Ye Liang Yanjiao Zhou George M. Weinstock Richard K. Wilson Jonathan H. Badger Ramana Madupu Monika Bihan Dana Busam A. Scott Durkin Leslie Foster Johannes B. Goll Kelvin Li Jamison McCorrison Jason Miller Yu-Hui Rogers Ravi Sanka Indresh Singh Granger G. Sutton Mathangi Thiagarajan M A Torralba Barbara A. Methé Karen Nelson Heather H. Creasy Michelle Giglio Jennifer R. Wortman Olukemi O. Abolude Cesar Arze Brandi L. Cantarel Jonathan Crabtree Noam J. Davidovics Victor Felix Catherine Jordan Anup Mahurkar Joshua Orvis Jacques Ravel Lynn M. Schriml James R. White Owen White Donna M. Muzny Kim C. Worley Christian Buhay Yan Ding Shannon Dugan Michael Holder Huaiyang Jiang Vandita Joshi Christie Kovar Sandra L. Lee Lora Lewis Yue Liu Irene Newsham Xiang Qin Jeffrey G. Reid Katarzyna Wilczek-Boney Yuanqing Wu Lan Zhang Yiming Zhu Richard A. Gibbs Sarah K. Highlander Joseph F. Petrosino James Versalovic Kjersti M. Aagaard Emma Allen‐Vercoe Gary L. Andersen Armitage Gc Tulin Ayvaz Wendy A. Keitel Matthew C. Ross Bonnie P. Youmans Carl C. Baker Lisa Begg Tsegahiwot Belachew Joseph L. Campbell Carolyn Deal Valentina Di Francesco Christina Giblin Maria Y. Giovanni Martin J. Blaser Vivien Bonazzi Shaila Chhibba Jean E. McEwen Jane Peterson Lita M. Proctor Jeffery A. Schloss Lu Wang Christopher Wellington Kris A. Wetterstrand J. Paul Brooks Gregory A. Buck Maria C. Rivera Nihar U. Sheth Shane R. Canon Patrick Chain Jeffery A. Schloss Matthew Scholz Nikos C. Kyrpides Konstantinos Liolios Victor M. Markowitz Konstantinos Mavromatis Ioanna Pagani I-Min A. Chen Ken Chu Krishna Palaniappan Mary A. Cutting Holli Hamilton Emily Harris R. Dwayne Lunsford Pamela McInnes Catherine Davis Todd Z. DeSantis Floyd E. Dewhirst Jacques Izard Katherine P. Lemon Elena Deych Patricio S. La Rosa William D. Shannon W. Michael Dunne Mark A. Watson R. C. Edgar Ruth M. Farrell Richard R. Sharp Karoline Faust Jeroen Raes Anthony A. Fodor Larry J. Forney Jonathan Friedman Christopher S. Smillie Nathalia García Antonio González Dan Knights Susan Kinder Haake Diane E. Hoffmann Susan M. Huse Janet Jansson James A. Katancik Scott T. Kelley Beltran Rodriguez-Mueller Nicholas B. King Heidi H. Kong Omry Koren Ruth E. Ley Sergey Koren Bo Liu Mihai Pop Daniel Sommer Cecil M. Lewis Paul Spicer Tessa Madden Peter Mannon Amy L. McGuire Shital M. Patel Mircea Podar Tatiana A. Vishnivetskaya Katherine S. Pollard Thomas J. Sharpton Rebecca Truty Mina Rho Yuzhen Ye Rosamond Rhodes Kevin Riehle P Akshay Sankar Patrick D. Schloss Alyxandria M. Schubert Thomas M. Schmidt Gina A. Simone Jack D. Sobel Todd J. Treangen Shibu Yooseph LAURIE ZOLOTH Sean Conlan Julia A. Segre

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Structure, function and diversity of the healthy human microbiome 2012 Nature 10.1038/nature11234 huttenhower2012-structure-function-and-diversity-o huttenhower2012-structure-function-and-diversity-o.txt, the project's staged copy 4d9398e0b8e96c0ad9672dc61723f785c8e24625 cc-by-nc-sa biology

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0 spans located by searching the stored text for the quote's exact words, allowing any whitespace between them the microbial communities of 18 body habitats in healthy Western adults, by 16S profiling and shotgun metagenomics Quotation withheld because this record is not cleared for redistribution. what the normal range of structure and function is in the microbiome of people without disease Quotation withheld because this record is not cleared for redistribution. a reference characterisation, and the finding that most microbiome variation is NOT explained by the phenotypes measured Quotation withheld because this record is not cleared for redistribution. existence Quotation withheld because this record is not cleared for redistribution. wide variation in the microbiota of healthy people, stable within a person and large between people Quotation withheld because this record is not cleared for redistribution. omics-profiling omics-profiling Quotation withheld because this record is not cleared for redistribution. mechanisms EACH PERSON'S COMMUNITY IS MORE STABLE THAN THE POPULATION IS UNIFORM: variation within a subject over time is consistently smaller than variation between subjects, in composition and in function alike Quotation withheld because this record is not cleared for redistribution. mechanisms A DIVERSITY SPLIT THAT REVERSES BY HABITAT: saliva is among the richest within a person and among the most similar across people, while skin is the opposite - so one number for diversity would hide the pattern entirely Quotation withheld because this record is not cleared for redistribution. THE PAPER'S OWN NEGATIVE RESULT: most variation in the human microbiome is not well explained by the phenotypic metadata collected, and even the strongest associations carry low effect sizes and considerable unexplained variance Quotation withheld because this record is not cleared for redistribution. 'Healthy' is defined by an exclusion list rather than by a positive criterion, and the paper marks the word as its own stipulation Quotation withheld because this record is not cleared for redistribution. The characterisation is of a WESTERN population, stated in the paper's own first conclusion sentence Quotation withheld because this record is not cleared for redistribution. No taxon was found in every habitat and every individual at this sequencing depth - so the absence is bounded by the depth, not asserted of the biology Quotation withheld because this record is not cleared for redistribution. A remarkable fraction of the protein families found are functionally uncharacterised - 58% at the minimum, in the oral cavity Quotation withheld because this record is not cleared for redistribution. The catalogue does not remove the need for matched internal controls in later clinical studies, and the paper says so Quotation withheld because this record is not cleared for redistribution. 131 of the subjects sampled again at a second time point, so within-subject change could be measured against between-subject spread eliminates: mistaking population-level variation for individual instability · outcome (stated by the tagger, no quotation): held Quotation withheld because this record is not cleared for redistribution. alpha diversity alpha diversity Quotation withheld because this record is not cleared for redistribution. beta diversity beta diversity Quotation withheld because this record is not cleared for redistribution. diversity diversity Quotation withheld because this record is not cleared for redistribution. microbiome microbiome Quotation withheld because this record is not cleared for redistribution. operational taxonomic units operational taxonomic units Quotation withheld because this record is not cleared for redistribution. body habitat body habitat Quotation withheld because this record is not cleared for redistribution. between-subject variation between-subject variation Quotation withheld because this record is not cleared for redistribution. healthy healthy Quotation withheld because this record is not cleared for redistribution. exclusion criteria exclusion criteria Quotation withheld because this record is not cleared for redistribution. effect sizes effect sizes Quotation withheld because this record is not cleared for redistribution. internal controls internal controls Quotation withheld because this record is not cleared for redistribution. Western population Western population Quotation withheld because this record is not cleared for redistribution. healthy - A STIPULATED TERM IN THIS PAPER, flagged as such in the sentence that introduces it: not a clinical judgement but the absence of anything on a list of exclusion criteria, and the authors put the word in quotation marks Quotation withheld because this record is not cleared for redistribution. diversity - ALPHA, within a sample: how many kinds of organism and in what proportions Quotation withheld because this record is not cleared for redistribution. diversity - BETA, between samples from the same habitat in different people. The paper's saliva case is the reason the split matters: HIGHEST alpha and one of the LOWEST betas - each mouth is rich, and every mouth is rich in the same way Quotation withheld because this record is not cleared for redistribution. claim_type: existence a second reading reaching the same value. Recorded: existence — note: A BLIND second reading by the project on 2026-08-25: the record's own claim type/method/phenomenon were not looked at until every value here was written and substring-verified. Not applied - a person decides. Sampling frame: the 504 staged records carrying no alternatives block, so this never re-measures the 202. All 11 records with 130+ tags were taken as a census and 19 more spread one per discipline across 22 disciplines - the dense non-neuroscience cell is the one the 202 do not contain (inside them, 94-100% of the densest bands are neuroscience; among these 11, one is)., Quotation withheld because this record is not cleared for redistribution. method: metagenomic-cohort-survey a second reading DIFFERING from the recorded value. Recorded: omics-profiling — note: A BLIND second reading by the project on 2026-08-25: the record's own claim type/method/phenomenon were not looked at until every value here was written and substring-verified. Not applied - a person decides. Sampling frame: the 504 staged records carrying no alternatives block, so this never re-measures the 202. All 11 records with 130+ tags were taken as a census and 19 more spread one per discipline across 22 disciplines - the dense non-neuroscience cell is the one the 202 do not contain (inside them, 94-100% of the densest bands are neuroscience; among these 11, one is)., Quotation withheld because this record is not cleared for redistribution. phenomenon: the structure, function and diversity of the microbial communities of healthy humans across body habitats a second reading DIFFERING from the recorded value. Recorded: wide variation in the microbiota of healthy people, stable within a person and large between people — note: A BLIND second reading by the project on 2026-08-25: the record's own claim type/method/phenomenon were not looked at until every value here was written and substring-verified. Not applied - a person decides. Sampling frame: the 504 staged records carrying no alternatives block, so this never re-measures the 202. All 11 records with 130+ tags were taken as a census and 19 more spread one per discipline across 22 disciplines - the dense non-neuroscience cell is the one the 202 do not contain (inside them, 94-100% of the densest bands are neuroscience; among these 11, one is)., Quotation withheld because this record is not cleared for redistribution. alpha diversity —distinct-from→ beta diversity alpha diversity beta diversity strength of the relation: 1 Quotation withheld because this record is not cleared for redistribution.

The full text of this article is not redistributable, so it is not included here. The evidence sentences are withheld with it; the tag layer and its grounding status remain. The article itself is at https://doi.org/10.1038/nature11234.