Metagenomic Species (MGS) and Co-Abundance gene Groups (CAGs) of the Mouse Gut

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A catalog of the mouse gut metagenome

Abstract
We established a catalog of the mouse gut metagenome comprising ~2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.

Liang Xiao, Qiang Feng, Suisha Liang, Si Brask Sonne, Zhongkui Xia, Xinmin Qiu, Xiaoping Li, Hua Long, Jianfeng Zhang, Dongya Zhang, Chuan Liu, Zhiwei Fang, Joyce Chou, Jacob Glanville, Qin Hao, Dorota Kotowska, Camilla Colding, Tine Rask Licht, Donghai Wu, Jun Yu, Joseph Jao Yiu Sung, Qiaoyi Liang, Junhua Li, Huijue Jia, Zhou Lan, Valentina Tremaroli, Piotr Dworzynski, H Bjørn Nielsen, Fredrik Bäckhed, Joël Doré, Emmanuelle Le Chatelier, S Dusko Ehrlich, John C Lin, Manimozhiyan Arumugam, Jun Wang, Lise Madsen & Karsten Kristiansen

Nature Biotechnology (2015) Oct;33(10):1103-8 .

MGS and CAGs

R object describing the CAGs and MGS
This file contains an R object that describes all the CAGs and the MGS. The object is a list containing the elements:

sets: vectors of gene identifiers [list]
profiles: 75% quantile abundance profiles for each CAG based
attributes: a table containing attributed for the CAGs, inc. size, number of sample-wise observations, internal correlation to the profile, GC content and more [data.frame]
Tax: taxonomy statistics at species, genus, family, order, class and phylum level [list of data.frames]
sampleInfo: sample information [data.frame]

Co-Abundance gene Groups (CAG) table
Table linking the mouse CAG and MGS identifiers to the mouse gene catalog

CAG abundance profiles
Abundance profiles of the CAG and MGS throughout 184 mouse fecal samples. The gene abundances were based on Illumina sequence reads counts. Here the abundances are the 75% gene quantile signal.

Software

The canopy clustering software version 1.2 used for the mouse gene catalogue can be found at the bitbucket repository

Mouse gene catalogue

Mouse gene catalog (fasta zipped, 847 MB)
Sequences of the 2.6M non-redundant mouse gut microbiome gene catalog