DESMAN: A new tool for de novo extraction of strains from metagenomes

Christopher Quince; Tom O. Delmont; Sébastien Raguideau; Johannes Alneberg; Aaron E. Darling; Gavin Collins; A. Murat Eren

doi:10.1186/s13059-017-1309-9

DESMAN: A new tool for de novo extraction of strains from metagenomes

Christopher Quince, Tom O. Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E. Darling, Gavin Collins, A. Murat Eren

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

113 Citations (Scopus)

Abstract

We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.

Original language	English
Article number	181
Journal	Genome Biology
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s13059-017-1309-9
Publication status	Published - 21 Sep 2017

Keywords

Metagenomes
Niche
Strain

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10.1186/s13059-017-1309-9Licence: CC BY

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title = "DESMAN: A new tool for de novo extraction of strains from metagenomes",

abstract = "We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.",

keywords = "Metagenomes, Niche, Strain",

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note = "Funding Information: CQ is funded through a Medical Research Council fellowship (MR/M50161X/1) as part of the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) consortium (MR/L015080/1). GC was supported by a European Research Council Starting Grant (3C-BIOTECH 261330). AME was supported by a Frank R. Lillie Research Innovation Award. Publisher Copyright: {\textcopyright} 2017 The Author(s).",

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doi = "10.1186/s13059-017-1309-9",

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AU - Alneberg, Johannes

AU - Darling, Aaron E.

AU - Collins, Gavin

AU - Eren, A. Murat

N1 - Funding Information: CQ is funded through a Medical Research Council fellowship (MR/M50161X/1) as part of the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) consortium (MR/L015080/1). GC was supported by a European Research Council Starting Grant (3C-BIOTECH 261330). AME was supported by a Frank R. Lillie Research Innovation Award. Publisher Copyright: © 2017 The Author(s).

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N2 - We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.

AB - We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.

KW - Metagenomes

KW - Niche

KW - Strain

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DESMAN: A new tool for de novo extraction of strains from metagenomes

Abstract

Keywords

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