An integrated catalog of reference genes in the human gut microbiome

Research output: Contribution to journalJournal articleResearchpeer-review

  • Junhua Li
  • Huijue Jia
  • Xianghang Cai
  • Huanzi Zhong
  • Qiang Feng
  • Shinichi Sunagawa
  • Jens Roat Kultima
  • Edi Prifti
  • Trine Nielsen
  • Agnieszka Juncker
  • Chaysavanh Manichanh
  • Bing Chen
  • Wenwei Zhang
  • Florence Levenez
  • Juan Wang
  • Xun Xu
  • Liang Xiao
  • Suisha Liang
  • Dongya Zhang
  • Zhaoxi Zhang
  • Weineng Chen
  • Hailong Zhao
  • Jumana Yousuf Al-Aama
  • Sherif Edris
  • Huanming Yang
  • Jian Wang
  • Henrik Bjørn Nielsen
  • Søren Brunak
  • Francisco Guarner
  • Joel Doré
  • S Dusko Ehrlich
  • Peer Bork
  • Jun Wang

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.

Original languageEnglish
JournalNature Biotechnology
Issue number8
Pages (from-to)834-845
Number of pages12
Publication statusPublished - 2014

ID: 119293288