Recovering complete and draft population genomes from metagenome datasets. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack
• Is Part Of: Microbiome. Volume 4:Issue 1(2016)
• Page Start: 1
• Page End: 11
• Publication Date: 2016-12
• Subjects: Metagenomics -- Genotype -- Assembly -- Binning -- Curation; Microbiology -- Periodicals; Microorganisms -- Periodicals; Medical microbiology -- Periodicals; Soil microbiology -- Periodicals; Microbiological Phenomena -- Periodicals; Environmental Microbiology -- Periodicals; Medical microbiology; Microbiology; Microorganisms; Soil microbiology; Periodicals; Electronic journals; 579.17
• DOI: 10.1186/s40168-016-0154-5
• Languages: English
• ISSNs: 2049-2618

Abstract

Abstract 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.