ReviewNature reviews. Microbiology2020
Diversity within species: interpreting strains in microbiomes.
Review in Nature reviews. Microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 242 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
242 citing papers in PubMed, 2 syntheses or guidelines pooled it, 454 citations in OpenAlex.
- Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.NPJ biofilms and microbiomes · 2025Pooled it
- Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.Nature medicine · 2022Pooled it
- Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.Gut microbes · 2026Review
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.Cell reports · 2026Article
- Article
- Large-scale benchmarking of prokaryotic annotation tools across thousands of species.Genome biology · 2026Article
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.Nature communications · 2026Article
- Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes.bioRxiv : the preprint server for biology · 2026Article
- Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils.Nature microbiology · 2026Article
- Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources.Environmental microbiology · 2026Article
- Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.NPJ biofilms and microbiomes · 2026Article
- Biocontrol of Mycotoxin-Producing Fungi by Lactic Acid Bacteria.Foods (Basel, Switzerland) · 2026Review
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- Antioxidant capacity, and probiotic properties of Enterococcus faecium strains isolated from raw milk of indigenous brown atlas cows.Antonie van Leeuwenhoek · 2026Article
- Draft genome sequences of 180 bacterial strains recovered from ground beef in retail markets in Fort Collins, Colorado.Microbiology resource announcements · 2026Article
- StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.Bioinformatics (Oxford, England) · 2026Article
- Gut Microbiota and Extraintestinal Cancers: Mechanistic Insights and Microbiome-Targeted Interventions.JGH open : an open access journal of gastroenterology and hepatology · 2026Review
- Article
182 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.