{"doi":"10.1016/j.cels.2024.12.008","title":"Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom","abstract":"The human gut microbiome contains many bacterial strains of the same species (\"strain-level variants\") that shape microbiome function. The tremendous scale and molecular resolution at which microbial communities are being interrogated motivates addressing how to describe strain-level variants. We introduce the \"Spectral Tree\"-an inferred tree of relatedness built from patterns of co-evolutionary constraint between greater than 7,000 diverse bacteria. Using the Spectral Tree to describe over 600 diverse gut commensal strains that we isolated, whole-genome sequenced, and metabolically profiled revealed (1) widespread phylogenetic structure among strain-level variants, (2) the origins of subspecies phylogeny as a shared history of phage infections across humans, and (3) the key role of inter-human strain variation in predicting strain-level metabolic qualities. Overall, our work demonstrates the existence and metabolic importance of structured phylogeny below the level of species for commensal gut bacteria, motivating a redefinition of individual strains according to their evolutionary context. A record of this paper's transparent peer review process is included in the supplemental information.","journal":"Cell Systems","year":2025,"id":542825,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9309,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","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":84,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:53:00.171379Z","pmid":"39826551","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":[]}