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 · Nature · 2012 · biology · 10.1038/nature11234 · record huttenhower2012-structure-function-and-diversity-o
tag layer · index · concepts · authors · עברית

Where this record's text came from. 2026-08-20 schema-0.3 pass: every quote verified as an exact substring of the staged text and anchored at merge time; concept terms verified present; every edge endpoint an existing node.

How to read this page. The article itself is not reproduced here — this paper is not cleared for redistribution, so what follows is the tag layer alone. The evidence sentences are withheld with the article. The table at the foot lists every tag the record carries; each row names the facet it belongs to, and the whose words column says whether the tag records the paper's own wording or the tagger's sentence about the paper. Every tag links to each other paper in the corpus carrying it. The machine-readable edition of the same thing is the TEI file beside this one, where the tags live in standOff, and the article is at its publisher via the link below. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.

Other fields define these differently the same word, defined another way in another discipline
operational taxonomic units 5 fields · diversity 4 fields

Tags on this paper

Every tag the record carries, each linking to every other paper in the corpus that carries it. A tag appears here whether or not its words occur in the article — the spans below are only the ones a sentence in this paper licenses. Of the 12 concept tags on this paper, all 12 are grounded in a quoted sentence.

alpha diversity beta diversity diversity microbiome operational taxonomic units body habitat between-subject variation healthy exclusion criteria effect sizes internal controls Western population 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 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 omics-profiling

Method, as described: 16S rRNA profiling plus paired-end shotgun metagenomics across 18 habitats, with a second time point in 131 subjects

Legend

second reading	`alternatives`	an independent re-reading of a facet, recorded whether or not it agrees
claim type	`claim_type`	the shape of the claim: existence, mechanism, method, critique, prediction, null
concept edge	`concept_edges`	an asserted relation between two concepts, with the sentence asserting it
concept	`concepts`	an idea the paper works with, quoted where the paper uses it
contribution	`contribution`	what the paper claims to add
control	`controls`	an experiment run to eliminate a rival explanation
limitation	`limitations`	what the paper says its evidence cannot support
mechanism	`mechanisms`	how the reported effect is said to come about
method	`method`	how the paper produced its evidence
object of study	`object_of_study`	what the paper is about — the thing it investigates
phenomenon	`phenomenon`	the effect or regularity under study
research question	`research_question`	the question the paper sets itself
sense	`senses`	a distinct use of a term, quoted where the paper fixes it

The paper

The full text is not reproduced here. This article is not cleared for redistribution, so the page carries the tag layer only. Its evidence sentences are withheld; the grounding status remains with each tag, and the article itself is at https://doi.org/10.1038/nature11234. The reading view exists for the papers whose licence permits it.

Every tag on this page

alternatives 3 · claim_type 1 · concept_edges 1 · concepts 12 · contribution 1 · controls 1 · limitations 6 · mechanisms 2 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 3

Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; none of 1 relation here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.

This record holds no relations between claims. A layer is empty when the tagger recorded nothing in it — which is not the same as the paper having nothing to record.

facet	tag	field	conf.	whose words
object_of_study	the microbial communities of 18 body habitats in healthy Western adults, by 16S profiling and shotgun metagenomics Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`object_of_study`		the paper's words
research_question	what the normal range of structure and function is in the microbiome of people without disease Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`research_question`		the paper's words
contribution	a reference characterisation, and the finding that most microbiome variation is NOT explained by the phenotypes measured Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`contribution`		the paper's words
claim_type	existence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_type`		the paper's words
phenomenon	wide variation in the microbiota of healthy people, stable within a person and large between people Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`phenomenon`		the paper's words
method	omics-profiling Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: omics-profiling	`method`		the paper's words
mechanisms	mechanisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 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	`mechanisms[0]`	0.95	the tagger's words
mechanisms	mechanisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 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	`mechanisms[1]`	0.95	the tagger's words
limitations	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 — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[0]`	0.95	the tagger's words
limitations	'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 — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[1]`	0.95	the tagger's words
limitations	The characterisation is of a WESTERN population, stated in the paper's own first conclusion sentence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[2]`	0.95	the tagger's words
limitations	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 — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[3]`	0.95	the tagger's words
limitations	A remarkable fraction of the protein families found are functionally uncharacterised - 58% at the minimum, in the oral cavity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[4]`	0.95	the tagger's words
limitations	The catalogue does not remove the need for matched internal controls in later clinical studies, and the paper says so Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[5]`	0.95	the tagger's words
controls	131 of the subjects sampled again at a second time point, so within-subject change could be measured against between-subject spread Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: mistaking population-level variation for individual instability · outcome (stated by the tagger, no quotation): held	`controls[0]`	0.9	the tagger's words
concepts	alpha diversity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: alpha diversity	`concepts[0]`	0.95	the paper's words
concepts	beta diversity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: beta diversity	`concepts[1]`	0.95	the paper's words
concepts	diversity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: diversity	`concepts[2]`	0.95	the paper's words
concepts	microbiome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: microbiome	`concepts[3]`	0.95	the paper's words
concepts	operational taxonomic units Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: operational taxonomic units	`concepts[4]`	0.95	the paper's words
concepts	body habitat Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: body habitat	`concepts[5]`	0.95	the paper's words
concepts	between-subject variation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: between-subject variation	`concepts[6]`	0.95	the paper's words
concepts	healthy Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: healthy	`concepts[7]`	0.95	the paper's words
concepts	exclusion criteria Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: exclusion criteria	`concepts[8]`	0.95	the paper's words
concepts	effect sizes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: effect sizes	`concepts[9]`	0.95	the paper's words
concepts	internal controls Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: internal controls	`concepts[10]`	0.95	the paper's words
concepts	Western population Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Western population	`concepts[11]`	0.95	the paper's words
senses	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 — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[0]`	0.95	the tagger's words
senses	diversity - ALPHA, within a sample: how many kinds of organism and in what proportions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[1]`	0.95	the tagger's words
senses	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 — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[2]`	0.95	the tagger's words
alternatives	claim_type: existence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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).,	`alternatives.claim_type`	0.85	the tagger's words
alternatives	method: metagenomic-cohort-survey Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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).,	`alternatives.method`	0.8	the tagger's words
alternatives	phenomenon: the structure, function and diversity of the microbial communities of healthy humans across body habitats Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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).,	`alternatives.phenomenon`	0.9	the tagger's words
concept_edges	alpha diversity —distinct-from→ beta diversity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 1 also in: alpha diversity · beta diversity	`concept_edges[0]`		the tagger's words

Interpretive choices

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