{"doi":"10.1101/2023.12.04.569969","title":"An evolution-based framework for describing human gut bacteria","abstract":"The human gut microbiome contains many bacterial strains of the same species ('strain-level variants'). Describing strains in a biologically meaningful way rather than purely taxonomically is an important goal but challenging due to the genetic complexity of strain-level variation. Here, we measured patterns of co-evolution across >7,000 strains spanning the bacterial tree-of-life. Using these patterns as a prior for studying hundreds of gut commensal strains that we isolated, sequenced, and metabolically profiled revealed widespread structure beneath the phylogenetic level of species. Defining strains by their co-evolutionary signatures enabled predicting their metabolic phenotypes and engineering consortia from strain genome content alone. Our findings demonstrate a biologically relevant organization to strain-level variation and motivate a new schema for describing bacterial strains based on their evolutionary history.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":395445,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8516,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":629693,"name":"Robert Y. Chen","orcid":"0000-0002-3680-2609","position":1,"is_corresponding":false},{"id":1171069,"name":"Hannah Giba","orcid":null,"position":2,"is_corresponding":false},{"id":1170705,"name":"Vivek Behera","orcid":"0000-0001-6013-5706","position":3,"is_corresponding":false},{"id":554213,"name":"Bidisha Barat","orcid":"0000-0002-6883-4517","position":4,"is_corresponding":false},{"id":406633,"name":"Anitha Sundararajan","orcid":"0000-0001-9550-3644","position":5,"is_corresponding":false},{"id":348145,"name":"Huaiying Lin","orcid":"0000-0003-2339-9491","position":6,"is_corresponding":false},{"id":262010,"name":"Ashley M. Sidebottom","orcid":"0000-0002-8670-9090","position":7,"is_corresponding":false},{"id":108879,"name":"Eric G. Pamer","orcid":"0000-0002-6755-9904","position":8,"is_corresponding":false},{"id":326795,"name":"Arjun S. Raman","orcid":"0000-0002-7303-7272","position":9,"is_corresponding":false},{"id":104326,"name":"Benjamin A. Doran","orcid":"0000-0003-4713-5562","position":0,"is_corresponding":true}],"reference_count":59,"raw_metadata":null,"created_at":"2026-07-19T01:19:22.857556Z","pmid":"38105970","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}