Recovering complete and draft population genomes from metagenome datasets

Microbiome
Naseer SangwanJack A Gilbert

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.

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Related Concepts

Sequence Determinations, DNA
Contig Mapping
Metagenome
Metagenomics
Genome, Microbial
Datasets as Topic
Biological Evolution
Genome
Metabolism
In Situ

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