Cited by 441Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyGut microbiota and health

Diversity within Species: Interpreting Strains in Microbiomes

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Van Rossum, Thea, Ferretti, Pamela, Maistrenko, Oleksandr M., Bork, Peer·2020·Nature Reviews Microbiology

Abstract

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.

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Authors
Van Rossum, T., Ferretti, P., Maistrenko, O. M., & Bork, P.
Affiliations
European Molecular Biology Laboratory (DE)
Venue
Nature Reviews Microbiology
Published
2020-06-04
Volume
18
Issue
9
Pages
491-506
ISSN
  • 1740-1526 (ISSN-L)
  • 1740-1534
OpenAlex
W3034087136
Cited by
441
References
193
Citations by year
2026: 59 · 2025: 92 · 2024: 80 · 2023: 64 · 2022: 62 · 2021: 70 · 2020: 14
FWCI
5.16
Type
journal article
Language
en
Open access
Locations
  • Nature Reviews Microbiology (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
bacterial strain, infraspecific variation, metagenomics, microbial communities, strain typing, population genetics, terminology
MeSH terms
Bacteria, Evolution, Molecular, Metagenomics, Microbiota

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