Journal
NATURE REVIEWS MICROBIOLOGY
Volume 18, Issue 9, Pages 491-506Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41579-020-0368-1
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Funding
- European Research Council (ERC) [ERC-AdG-669830 MicrobioS]
- European Union [825694 MICROB-PREDICT]
- German Federal Ministry of Education and Research (Bundesministerium fur Bildung und Forschung, BMBF) [01GL1746B PRIMAL]
- European Molecular Biology Laboratory (EMBL)
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Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data. Large-scale metagenomic analyses are vastly increasing the rate of discovery of variation within species but they are also leading to scientific and semantic challenges. Bork and colleagues highlight the advances and challenges that are resulting from the use of metagenomic data to study within-species diversity.
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