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. 2014 Aug;32(8):834-41.
doi: 10.1038/nbt.2942. Epub 2014 Jul 6.

An integrated catalog of reference genes in the human gut microbiome

Junhua Li  1 , Huijue Jia  2 , Xianghang Cai  2 , Huanzi Zhong  2 , Qiang Feng  3 , Shinichi Sunagawa  4 , Manimozhiyan Arumugam  5 , Jens Roat Kultima  4 , Edi Prifti  6 , Trine Nielsen  7 , Agnieszka Sierakowska Juncker  8 , Chaysavanh Manichanh  9 , Bing Chen  10 , Wenwei Zhang  10 , Florence Levenez  6 , Juan Wang  10 , Xun Xu  10 , Liang Xiao  10 , Suisha Liang  10 , Dongya Zhang  10 , Zhaoxi Zhang  10 , Weineng Chen  10 , Hailong Zhao  10 , Jumana Yousuf Al-Aama  11 , Sherif Edris  12 , Huanming Yang  13 , Jian Wang  14 , Torben Hansen  7 , Henrik Bjørn Nielsen  8 , Søren Brunak  8 , Karsten Kristiansen  15 , Francisco Guarner  9 , Oluf Pedersen  7 , Joel Doré  16 , S Dusko Ehrlich  17 ; MetaHIT Consortium; Peer Bork  18 , Jun Wang  19 ; MetaHIT Consortium
Collaborators, Affiliations

An integrated catalog of reference genes in the human gut microbiome

Junhua Li et al. Nat Biotechnol. 2014 Aug.

Abstract

Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.

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