De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning

Quince, C., Connelly, S. , Raguideau, S., Alneberg, J., Shin, S. G., Collins, G. and Eren, A. M. (2016) De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning. bioRxiv, (doi:10.1101/073825) (Submitted)

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Abstract

Background We introduce DESMAN for De novo Extraction of Strains from MetAgeNomes. Metagenome sequencing generates short reads from throughout the genomes of a microbial community. Increasingly large, multi-sample metagenomes, stratified in space and time are being generated from communities with thousands of species. Repeats result in fragmentary co-assemblies with potentially millions of contigs. Contigs can be binned into metagenome assembled genomes (MAGs) but strain level variation will remain. DESMAN identifies variants on core genes, then uses co-occurrence across samples to link variants into strain sequences and abundance profiles. These strain profiles are then searched for on non-core genes to determine the accessory genes present in each strain. Results We validated DESMAN on a synthetic twenty genome community with 64 samples. We could resolve the five E. coli strains present with 99.58% accuracy across core gene variable sites and their gene complement with 95.7% accuracy. Similarly, on real fecal metagenomes from the 2011 E. coli (STEC) O104:H4 outbreak, the outbreak strain was reconstructed with 99.8% core sequence accuracy. Application to an anaerobic digester metagenome time series reveals that strain level variation is endemic with 16 out of 26 MAGs (61.5%) examined exhibiting two strains. In almost all cases the strain proportions were not statistically different between replicate reactors, suggesting intra-species niche partitioning. The only exception being when the two strains had almost identical gene complement and, hence, functional capability. Conclusions DESMAN will provide a provide a powerful tool for de novo resolution of fine-scale variation in microbial communities. It is available as open source software from https://github.com/chrisquince/DESMAN.

Item Type:Articles
Status:Submitted
Refereed:No
Glasgow Author(s) Enlighten ID:Connelly, Dr Stephanie and Quince, Dr Christopher and Collins, Dr Gavin and Shin, Dr Seung Gu
Authors: Quince, C., Connelly, S., Raguideau, S., Alneberg, J., Shin, S. G., Collins, G., and Eren, A. M.
College/School:College of Science and Engineering > School of Engineering
College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:bioRxiv
Publisher:Cold Spring Harbor Laboratory
Copyright Holders:Copyright © 2016 The Authors
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
190371A Global Solution To Protect Water By Transforming WasteGavin CollinsEngineering and Physical Sciences Research Council (EPSRC)EP/J00538X/1ENG - Infrastructure & Environment