Intraspecies associations from strain-rich metagenome samples

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 8, 2025

Abstract Genetically distinct strains of a species can vary widely in phenotype, reducing the utility species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all sample, current strain-resolved analysis methods face tradeoff: de novo genotyping approaches detect novel but struggle when applied to strain-rich low-coverage samples, while reference database work robustly across sample types are insensitive diversity. We present PHLAME, method that bridges this divide by combining advantages reference-based novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces probabilistic, mutation-based, framework accurately quantify from nearest reference. By applying publicly available human skin vaginal metagenomes, we uncover previously undetected clade coexisting species, geography, host age. The ability characterize intraspecies dynamics inaccessible environments will propel new mechanistic insights accumulating metagenomic data.

Language: Английский

Mixing microbiomes in vitro reveals rules of community assembly

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(15)

Published: April 7, 2025

Language: Английский

Intraspecies warfare restricts strain coexistence in human skin microbiomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 7, 2024

Determining why only a fraction of encountered or applied bacterial strains engraft in given person's microbiome is crucial for understanding and engineering these communities

Language: Английский