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De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning
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Quince, Christopher, Connelly, Stephanie, Raguideau, Sebastien, Alneberg, Johannes, Shin, Seung Gu, Collins, Gavin and Eren, A. Murat (2016) De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning. Working Paper. bioRxiv: Cold Spring Harbour Laboratory. (Unpublished)
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Official URL: http://dx.doi.org/10.1101/073825
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: | Working or Discussion Paper (Working Paper) | ||||
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Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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Publisher: | Cold Spring Harbour Laboratory | ||||
Place of Publication: | bioRxiv | ||||
Book Title: | De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning | ||||
Official Date: | 6 September 2016 | ||||
Dates: |
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DOI: | 10.1101/073825 | ||||
Institution: | University of Warwick | ||||
Status: | Not Peer Reviewed | ||||
Publication Status: | Unpublished | ||||
Access rights to Published version: | Restricted or Subscription Access |
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