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.

传统上，研究种内变异仅限于可培养的细菌分离株和低分辨率微生物群落指纹识别。宏基因组测序和技术进步使得能够在复杂环境中以高通量进行无培养、高分辨率菌株和亚种分析。这具有巨大的科学前景，但也导致了描述种内变异的大量方法和术语的出现。本综述旨在通过关注微生物组学背景下细菌和古菌物种的多样性来阐明这些进展。我们涵盖了与群体遗传学相关的基本微进化概念，并总结了如何在微生物群落内直接研究和分层物种内变异，重点关注宏基因组学。最后，我们描述了如何使用宏基因组数据实现种内变异的常见应用。我们的目标是指导选择适当的术语和分析方法，以帮助研究人员从日益增加的大型高分辨率微生物组基因测序数据中受益。