ArticleGenome biology2020
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 3 of them syntheses that pooled it.
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Who cites it
79 citing papers in PubMed, 3 syntheses or guidelines pooled it, 124 citations in OpenAlex.
- Dietary interventions and the gut microbiota: a systematic literature review of 80 controlled clinical trials.Journal of translational medicine · 2026Pooled it
- Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.Nature communications · 2025Pooled it
- Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.Cell host & microbe · 2023Pooled it
- Trial
- Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance.Nature communications · 2021Trial
- Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.Gut microbes · 2026Review
- Extensive genomic diversity in Desulfovibrio reveals species-specific functional traits associated with disease.Nature communications · 2026Article
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.Cell reports. Medicine · 2026Article
- A roadmap to create FAIR collections of microbial strains.Nature microbiology · 2026Review
- Article
- Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery.Microbiome · 2026Article
- De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.PLoS computational biology · 2026Article
- The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health.Nature reviews. Gastroenterology & hepatology · 2026Article
- A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.bioRxiv : the preprint server for biology · 2026Article
- Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.Microorganisms · 2026Review
- Genome-scale insights into the metabolic landscape and evolutionary development ofMicrobiome research reports · 2026Article
- High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.Gut microbes · 2025Article
- Host transcriptional responses to gut microbiome variation arising from urbanism.bioRxiv : the preprint server for biology · 2025Article
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
- Human microbiome acquisition and transmission.Nature reviews. Microbiology · 2025Review
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
22 authors at 10 institutions in 5 countries.
Funding
Abstract
backgroundEubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out.
resultsHere, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis.
conclusionsOur study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.
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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.