A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Sølvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada, Daniel R. Mende, Junhua Li, Junming Xu, Shaochuan Li, Dongfang Li, Jianjun Cao, Bo Wang, Huiqing Liang, Huisong Zheng, Yinlong Xie, Julien Tap, Patricia Lepage, Marcelo Bertalan, Jean-Michel Batto, Torben Hansen, Denis Le Paslier, Allan Linneberg, H. Bjørn Nielsen, Éric Pelletier, Pierre Renault, Thomas Sicheritz‐Pontén, A. Keith Turner, Hongmei Zhu, Chang Yu, Shengting Li, Min Jian, Yan Zhou, Rui Li, Xiuqing Zhang, Songgang Li, Nan Qin, Huanming Yang, Jian Wang, Jian Wang, Søren Brunak, Joël Doré, Francisco Guarner, Karsten Kristiansen, Oluf Pedersen, Julian Parkhill, Jean Weissenbach, Peer Bork, S. Dusko Ehrlich, Jun Wang, Jun Wang · Nature · 2010 · biology · 10.1038/nature08821 · record qin2010-a-human-gut-microbial-gene-catalog
tag layer · index · concepts · authors · עברית

Where this record's text came from. 2026-08-20 and 2026-08-25 schema-0.3 passes: 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.

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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 10 concept tags on this paper, all 10 are grounded in a quoted sentence.

minimal gut metagenome minimal gut bacterial genome gene catalogue prevalent genes metagenomic sequencing rRNA sequencing proof of principle contigs gut microbiome short-read metagenomic sequencing A CATALOGUE ARGUED TO BE GENERAL BY WHAT IT ALREADY CONTAINS: 70% of the reads from earlier American and Japanese studies map onto these contigs, so coverage is demonstrated against other cohorts rather than asserted of the population SHARING MEASURED AT A STATED DEPTH: almost 40% of each individual's genes are shared with at least half the cohort, and the sentence carries its own qualifier - AT THE PRESENT DEPTH OF SEQUENCING omics-profiling

Method, as described: Illumina short-read metagenomic sequencing of total faecal DNA, assembled into contigs

Legend

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/nature08821. The reading view exists for the papers whose licence permits it.

Every tag on this page

claim_type 1 · concept_edges 2 · concepts 10 · contribution 1 · controls 2 · limitations 4 · mechanisms 2 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 2

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 2 relations 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	3.3 million non-redundant microbial genes from the faecal metagenomes of 124 European adults 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 genes the human gut microbiome contains, and how much of that content people share 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 gene catalogue, plus the minimal gut metagenome and minimal gut bacterial genome as defined terms 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	method 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	the genetic content of the gut microbial community and its overlap 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: A CATALOGUE ARGUED TO BE GENERAL BY WHAT IT ALREADY CONTAINS: 70% of the reads from earlier American and Japanese studies map onto these contigs, so coverage is demonstrated against other cohorts rather than asserted of the population	`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: SHARING MEASURED AT A STATED DEPTH: almost 40% of each individual's genes are shared with at least half the cohort, and the sentence carries its own qualifier - AT THE PRESENT DEPTH OF SEQUENCING	`mechanisms[1]`	0.95	the tagger's words
limitations	The full bacterial gene complement of each individual was NOT sampled - the paper's own first sentence of caveat 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	The cohort is 124 European adults, Nordic and Mediterranean, and the paper states that scope in its own summary sentence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. about this quote: the quote carries an extractor fusion: the paper's “non-redundant” is staged as “nonredundant”. Verbatim against the staged text; the damage is mid-word and no re-slice avoids it. Confidence 0.85 under an earlier note of ours.	`limitations[1]`	0.85	the tagger's words
limitations	The proportion of shared genes is stated to be BOUNDED BY FUTURE WORK rather than settled here, which makes the sharing figure provisional by the authors' own account 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	The sharing result is explicitly conditioned on the sequencing depth used 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
controls	one of the two samples was ALSO sequenced on a different platform (Roche/454) and the assemblies compared - 97.9 per cent collinear over 99.5 per cent of mapped regions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: that the assembly is an artefact of the Illumina platform or of the assembler, rather than the biology - a second technology with different error modes should not reproduce a shared artefact · outcome (stated by the tagger, no quotation): held	`controls[0]`	0.95	the tagger's words
controls	contigs from two samples mapped back to Sanger reads from those same samples Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: that the short-read assembly has mis-joined or dropped sequence - Sanger reads are long and independently generated · outcome (stated by the tagger, no quotation): held	`controls[1]`	0.95	the tagger's words
concepts	minimal gut metagenome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: minimal gut metagenome	`concepts[0]`	0.95	the paper's words
concepts	minimal gut bacterial genome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: minimal gut bacterial genome	`concepts[1]`	0.95	the paper's words
concepts	gene catalogue Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene catalogue	`concepts[2]`	0.85	the paper's words
concepts	prevalent genes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: prevalent genes	`concepts[3]`	0.95	the paper's words
concepts	metagenomic sequencing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: metagenomic sequencing	`concepts[4]`	0.95	the paper's words
concepts	rRNA sequencing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: rRNA sequencing	`concepts[5]`	0.95	the paper's words
concepts	proof of principle Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: proof of principle	`concepts[6]`	0.95	the paper's words
concepts	contigs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: contigs	`concepts[7]`	0.95	the paper's words
concepts	gut microbiome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gut microbiome	`concepts[8]`	0.95	the paper's words
concepts	short-read metagenomic sequencing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: short-read metagenomic sequencing	`concepts[9]`	0.95	the paper's words
senses	minimal gut metagenome - defined by WHAT IS PRESENT IN ALL INDIVIDUALS, so the word minimal is about the intersection across people, not about a smallest viable set 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	minimal gut bacterial genome - the companion term, defined over MOST BACTERIA rather than over all individuals. TWO SENSES OF `minimal` COINED IN ONE SENTENCE, and the sentence marks which is which with `respectively` 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
concept_edges	minimal gut metagenome —distinct-from→ minimal gut bacterial genome 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: minimal gut metagenome · minimal gut bacterial genome	`concept_edges[0]`		the tagger's words
concept_edges	metagenomic sequencing —contrasted-with→ rRNA sequencing 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: metagenomic sequencing · rRNA sequencing	`concept_edges[1]`		the tagger's words

Interpretive choices

Tags that could not be placed in the text:

none — every tag was located in the text

What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.