A human gut microbial gene catalogue established by metagenomic sequencing

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

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A human gut microbial gene catalogue established by metagenomic sequencing 2010 Nature 10.1038/nature08821 qin2010-a-human-gut-microbial-gene-catalog qin2010-a-human-gut-microbial-gene-catalog.txt, the project's staged copy fd6f669b99c1ec6b1016bcb37ec4ba8946929041 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 3.3 million non-redundant microbial genes from the faecal metagenomes of 124 European adults Quotation withheld because this record is not cleared for redistribution. what genes the human gut microbiome contains, and how much of that content people share Quotation withheld because this record is not cleared for redistribution. a reference gene catalogue, plus the minimal gut metagenome and minimal gut bacterial genome as defined terms Quotation withheld because this record is not cleared for redistribution. method Quotation withheld because this record is not cleared for redistribution. the genetic content of the gut microbial community and its overlap 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 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 Quotation withheld because this record is not cleared for redistribution. mechanisms 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 Quotation withheld because this record is not cleared for redistribution. The full bacterial gene complement of each individual was NOT sampled - the paper's own first sentence of caveat Quotation withheld because this record is not cleared for redistribution. The cohort is 124 European adults, Nordic and Mediterranean, and the paper states that scope in its own summary sentence 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. Quotation withheld because this record is not cleared for redistribution. 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 because this record is not cleared for redistribution. The sharing result is explicitly conditioned on the sequencing depth used Quotation withheld because this record is not cleared for redistribution. 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 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 Quotation withheld because this record is not cleared for redistribution. contigs from two samples mapped back to Sanger reads from those same samples 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 Quotation withheld because this record is not cleared for redistribution. minimal gut metagenome minimal gut metagenome Quotation withheld because this record is not cleared for redistribution. minimal gut bacterial genome minimal gut bacterial genome Quotation withheld because this record is not cleared for redistribution. gene catalogue gene catalogue Quotation withheld because this record is not cleared for redistribution. prevalent genes prevalent genes Quotation withheld because this record is not cleared for redistribution. metagenomic sequencing metagenomic sequencing Quotation withheld because this record is not cleared for redistribution. rRNA sequencing rRNA sequencing Quotation withheld because this record is not cleared for redistribution. proof of principle proof of principle Quotation withheld because this record is not cleared for redistribution. contigs contigs Quotation withheld because this record is not cleared for redistribution. gut microbiome gut microbiome Quotation withheld because this record is not cleared for redistribution. short-read metagenomic sequencing short-read metagenomic sequencing Quotation withheld because this record is not cleared for redistribution. 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 because this record is not cleared for redistribution. 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 because this record is not cleared for redistribution. minimal gut metagenome —distinct-from→ minimal gut bacterial genome minimal gut metagenome minimal gut bacterial genome strength of the relation: 1 Quotation withheld because this record is not cleared for redistribution. metagenomic sequencing —contrasted-with→ rRNA sequencing metagenomic sequencing rRNA sequencing 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/nature08821.