Human gut microbial metagenomic assembly

Identifying bacterial strains in metagenome and microbiome samples using computational analyses of short-read sequence remains a difficult problem. Here, we present an analysis of a human gut microbiome using Tru-seq synthetic long reads and computational tools for metagenomic long-read assembly, variant-calling and haplotyping (Nanoscope and Lens). Our analysis identifies 178 bacterial species, of which 51 were not found using short sequence reads alone. We recover bacterial contigs that comprise multiple operons, including 22 contigs of >1Mbp. Extensive intraspecies variation among microbial strains in the form of haplotypes that span up to hundreds of Kbp can be observed using our approach. Incorporation of synthetic long-read sequencing technology with standard short-read shotgun sequencing approaches enables more rapid and comprehensive analyses of metagenome and microbiome samples.