Intraspecies associations from strain-rich metagenome samples.

ABSTRACT: Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference-based approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutat

SUBMITTER: Qu EB 

PROVIDER: S-EPMC11839054 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature