Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data

• DOI: 10.7490/f1000research.1114648.1
• Publication Date: 2017-08-09
• Authors: Florian Plaza Oñate; Alessandra Cervino; Frédéric Magoulès; S. Dusko Ehrlich; Matthieu Pichaud
• Keywords: Shotgun; Sequence assembly

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 the extent reference genomes that far from covering all variability, as many species still not sequenced or have only few strains available. Binning co-abundant genes obtained de novo assembly is a powerful reference-free technique discovering and reconstituting repertoire species. While current methods accurately identify core genes, they miss accessory split them in small separated clusters. We introduce MSPminer, computationally efficient software tool reconstitutes Metagenomic Species Pan-genomes (MSPs) binning across large-scale metagenomic datasets. MSPminer relies on new robust measure grouping but also. In MSPs, an empirical classifier distinguishes shared genes. applied to largest publicly available abundance table which composed 9.9M quantified 1 267 stool samples. show successfully matter several hours > 1600 (some hitherto unknown) detects more than existing tools. By compiling information thousands samples, variability better accounted their quantification subsequently precise.