{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Qu EB"],"funding":["National Science Foundation Graduate Research Fellowship Program","National Institutes of Health Office of the Director","National Institutes of Health","NIGMS NIH HHS","DSM","National Science Foundation"],"pagination":["116134"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12452263"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["44(8)"],"pubmed_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 database approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-"],"journal":["Cell reports"],"pubmed_title":["Intraspecies associations from strain-rich metagenome samples."],"pmcid":["PMC12452263"],"funding_grant_id":["R35 GM156282","1DP2GM140922","R35GM156282","DP2 GM140922"],"pubmed_authors":["Mancuso C","Lieberman TD","Qu EB","Baker JS","Khadka V","Tripp AD","Markey L"],"additional_accession":[]},"is_claimable":false,"name":"Intraspecies associations from strain-rich metagenome samples.","description":"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 database approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Aug","modification":"2026-06-03T19:31:47.182Z","creation":"2026-04-30T03:12:08.97Z"},"accession":"S-EPMC12452263","cross_references":{"pubmed":["40811063"],"doi":["10.1016/j.celrep.2025.116134"]}}