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

Christopher Quince, Stephanie Connelly, Sébastien Raguideau, Johannes Alneberg, Seung Gu Shin, Gavin Collins, A. Murat Eren
doi: https://doi.org/10.1101/073825
Christopher Quince
1Warwick Medical School, University of Warwick, Coventry, UK
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Stephanie Connelly
2University of Glasgow, Glasgow, UK
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Sébastien Raguideau
3French National Institute for Agricultural Research, Mathématiques et Informatique Appliqués (MIA), Paris,France
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Johannes Alneberg
4KTH Royal Institute of Technology, Science for Life Laboratory,School of Biotechnology, Division of Gene Technology, Stockholm,Sweden
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Seung Gu Shin
5School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
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Gavin Collins
2University of Glasgow, Glasgow, UK
6Microbial Ecophysiology Laboratory, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
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A. Murat Eren
7Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, USA
8Department of Medicine, University of Chicago, Chicago, USA September 6, 2016
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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.

Footnotes

  • ↵* c.quince{at}warwick.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 06, 2016.
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De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning
Christopher Quince, Stephanie Connelly, Sébastien Raguideau, Johannes Alneberg, Seung Gu Shin, Gavin Collins, A. Murat Eren
bioRxiv 073825; doi: https://doi.org/10.1101/073825
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De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning
Christopher Quince, Stephanie Connelly, Sébastien Raguideau, Johannes Alneberg, Seung Gu Shin, Gavin Collins, A. Murat Eren
bioRxiv 073825; doi: https://doi.org/10.1101/073825

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