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Title: Recovering complete and draft population genomes from metagenome datasets

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
Authors:
 [1] ;  [2] ;  [3]
  1. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, IL (United States)
  2. Argonne National Lab. (ANL), Argonne, IL (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, IL (United States); Marine Biological Lab., Woods Hole, MA (United States)
Publication Date:
OSTI Identifier:
1258642
Grant/Contract Number:
AC02-06CH11357
Type:
Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 4; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Research Org:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES Metagenomics; Genotype; Assembly; Binning; Curation