{"doi":"10.1101/2022.05.30.494065","title":"Resource competition predicts assembly of <i>in vitro</i> gut bacterial communities","abstract":"ABSTRACT Members of microbial communities interact via a plethora of mechanisms, including resource competition, cross-feeding, and pH modulation. However, the relative contributions of these mechanisms to community dynamics remain uncharacterized. Here, we develop a framework to distinguish the effects of resource competition from other interaction mechanisms by integrating data from growth measurements in spent media, synthetic community assembly, and metabolomics with consumer-resource models. When applied to human gut commensals, our framework revealed that resource competition alone could explain most pairwise interactions. The resource-competition landscape inferred from metabolomic profiles of individual species predicted assembly compositions, demonstrating that resource competition is a dominant driver of in vitro community assembly. Moreover, the identification and incorporation of interactions other than resource competition, including pH-mediated effects and cross-feeding, improved model predictions. Our work provides an experimental and modeling framework to characterize and quantify interspecies interactions in vitro that should advance mechanistically principled engineering of microbial communities.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":296993,"datarank":0.40620753016533157,"base_score":2.70805020110221,"endowment":2.70805020110221,"self_citation_contribution":0.40620753016533157,"citation_network_contribution":0.0,"self_endowment_contribution":0.40620753016533157,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":14,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9481,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":343791,"name":"Taylor H. Nguyen","orcid":"0000-0002-1288-8882","position":1,"is_corresponding":false},{"id":616357,"name":"Juan M. Sánchez","orcid":"0000-0002-4139-7273","position":2,"is_corresponding":false},{"id":500512,"name":"Brian C. DeFelice","orcid":"0000-0001-8243-0300","position":3,"is_corresponding":false},{"id":74113,"name":"Kerwyn Casey Huang","orcid":"0000-0002-8043-8138","position":4,"is_corresponding":false},{"id":74103,"name":"Po-Yi Ho","orcid":"0000-0002-0160-0425","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:31:21.257700Z","pmid":null,"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":[]}