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Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.

ABSTRACT: Identifying bacterial strains in metagenome and microbiome samples using computational analyses of short-read sequences remains a difficult problem. Here, we present an analysis of a human gut microbiome using TruSeq synthetic long reads combined with 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 shotgun reads alone. We recover bacterial contigs that comprise multiple operons, including 22 contigs of >1 Mbp. Furthermore, we observe extensive intraspecies variation within microbial strains in the form of haplotypes that span up to hundreds of Kbp. Incorporation of synthetic long-read sequencing technology with standard short-read approaches enables more precise and comprehensive analyses of metagenomic samples.

SUBMITTER: Kuleshov V

PROVIDER: S-EPMC4884093 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.

Kuleshov Volodymyr V Jiang Chao C Zhou Wenyu W Jahanbani Fereshteh F Batzoglou Serafim S Snyder Michael M

Nature biotechnology 20151214 1

Identifying bacterial strains in metagenome and microbiome samples using computational analyses of short-read sequences remains a difficult problem. Here, we present an analysis of a human gut microbiome using TruSeq synthetic long reads combined with 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 shotgun reads alone. We recover bacterial contigs that com ...[more]

PMID: 26655498

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