ArticleMicrobiome2025
Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.
Article in Microbiome, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.Gut microbes · 2026Review
- The cervicovaginal gut microbiota axis as a key determinant of systemic physiology.Gut microbes · 2026Review
- Strain-level analyses of public sequencing data to characterizeOne health (Amsterdam, Netherlands) · 2026Article
- Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.bioRxiv : the preprint server for biology · 2026Article
- Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.bioRxiv : the preprint server for biology · 2025Article
- A comprehensive atlas of the bonobo gut bacteriome and its associated host and exposome factors.Cell reports · 2025Article
- Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.Microbiome · 2025Article
- Eco-evolutionary robustness of wild bacterial communities to experimental perturbation.The ISME journal · 2025Article
- Differential microbial community assembly following co-housing versus microbiota transplant.The ISME journal · 2025Article
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Abstract
backgroundIn humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmission per se, is not well understood.
resultsHere, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners.
conclusionsWe conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms of strain sharing and resolving true social transmission network. Video Abstract.
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