Open AccessDiversity within species: interpreting strains in microbiomes
Author(s) -
Thea Van Rossum,
Pamela Ferretti,
Oleksandr M Maistrenko,
Peer Bork
Publication year - 2020
Publication title -
nature reviews. microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 11.496
H-Index - 300
eISSN - 1740-1534
pISSN - 1740-1526
DOI - 10.1038/s41579-020-0368-1
Subject(s) - metagenomics , biology , microbiome , context (archaeology) , evolutionary biology , subspecies , genetic diversity , ecology , variation (astronomy) , population genetics , population , computational biology , genetics , gene , sociology , paleontology , demography , physics , astrophysics
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.