PT  - JOURNAL ARTICLE
AU  - Florian Plaza Oñate
AU  - Alessandra C. L. Cervino
AU  - Frédéric Magoulès
AU  - S. Dusko Ehrlich
AU  - Matthieu Pichaud
TI  - Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data
AID  - 10.1101/173203
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 173203
4099  - http://biorxiv.org/content/early/2017/10/04/173203.short
4100  - http://biorxiv.org/content/early/2017/10/04/173203.full
AB  - Analysis toolkits for whole-metagenome shotgun sequencing data achieved strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available.Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique for discovering and reconstituting gene repertoire of microbial species. While current methods accurately identify species core genes, they miss many accessory genes or split them in small separated clusters.We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across large-scale metagenomic datasets. MSPminer relies on a new robust measure for grouping not only species core genes but accessory genes also. In MSPs, an empirical classifier distinguishes core from accessory and shared genes.We applied MSPminer to the largest publicly available gene abundance table which is composed of 9.9M genes quantified in 1 267 stool samples. We show that MSPminer successfully reconstitutes in a matter of several hours gene repertoire of > 1600 microbial species (some hitherto unknown) and detects many more accessory genes than existing tools. By compiling the information from thousands of samples, species gene content variability is better accounted for and their quantification is subsequently more precise