{"doi":"10.1101/2022.09.27.509746","title":"The TaxUMAP atlas: efficient display of large clinical microbiome data reveals ecological competition involved in protection against bacteremia","abstract":"SUMMARY The microbiome is associated with health and disease, but causal effects are hard to quantify— especially in humans where controlled experiments are nearly impossible. Akin to natural experiments, closely monitored patients offer an alternative to characterize microbiome effects. We present TaxUMAP, a taxonomically-informed visualization method to effectively display diverse microbiome states. TaxUMAP charts a microbiome atlas from 1,870 cancer patients as they progress through therapy-induced perturbations, and quantifies the microbiome contribution to patients’ risk for life-threatening bacteremia. We find that the lowest diversity states (gut dominations) that follow antibiotic treatments are stable, and that diverse communities harbor more diverse antimicrobial resistance genes than dominations. We reveal that certain Klebsiella species are associated with reduced risk for bacteremia, an effect driven by bacterial competition that we validate experimentally in vitro and in vivo . TaxUMAP effectively maps longitudinal microbiome data that can facilitate research into causal microbiome effects on human health. HIGHLIGHTS TaxUMAP charts an atlas of patients’ microbiome states and their clinical context to reveal new causal effects. Antibiotics deplete the biodiversity and reduce the number of different antimicrobial resistance genes in the gut microbiome. Certain Klebsiella species are associated with lower risk of bacteremia by other gut-borne pathogens. These Klebsiella outcompete other gram-negative pathogens in vivo .","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":304397,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9155,"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":778011,"name":"Ana Djuković","orcid":"0000-0001-8068-7188","position":1,"is_corresponding":false},{"id":669759,"name":"Bradford P. Taylor","orcid":"0000-0001-7808-955X","position":2,"is_corresponding":false},{"id":567676,"name":"Jinyuan Yan","orcid":"0000-0003-2046-5625","position":3,"is_corresponding":false},{"id":997238,"name":"Caichen Duan","orcid":"0000-0002-8634-2006","position":4,"is_corresponding":false},{"id":804267,"name":"Grant Hussey","orcid":"0000-0003-0544-8237","position":5,"is_corresponding":false},{"id":303729,"name":"Chen Liao","orcid":"0000-0001-8474-1196","position":6,"is_corresponding":false},{"id":997791,"name":"Sneh Sharma","orcid":null,"position":7,"is_corresponding":false},{"id":108855,"name":"Emily Fontana","orcid":"0000-0002-9060-5382","position":8,"is_corresponding":false},{"id":108856,"name":"Luigi A. Amoretti","orcid":"0000-0002-4625-5119","position":9,"is_corresponding":false},{"id":108857,"name":"Roberta J. Wright","orcid":"0000-0001-5299-0024","position":10,"is_corresponding":false},{"id":298456,"name":"Anqi Dai","orcid":"0000-0003-3106-4624","position":11,"is_corresponding":false},{"id":225648,"name":"Jonathan U. Peled","orcid":"0000-0002-4029-7625","position":12,"is_corresponding":false},{"id":108835,"name":"Ying Taur","orcid":"0000-0002-6601-8284","position":13,"is_corresponding":false},{"id":108873,"name":"Miguel‐Angel Perales","orcid":"0000-0002-5910-4571","position":14,"is_corresponding":false},{"id":282437,"name":"Benjamin A. Siranosian","orcid":"0000-0002-4935-8172","position":15,"is_corresponding":false},{"id":36377,"name":"Ami S. Bhatt","orcid":"0000-0001-8099-2975","position":16,"is_corresponding":false},{"id":108880,"name":"Marcel R.M. van den Brink","orcid":"0000-0003-0696-4401","position":17,"is_corresponding":false},{"id":108879,"name":"Eric G. Pamer","orcid":"0000-0002-6755-9904","position":18,"is_corresponding":false},{"id":108878,"name":"João B. Xavier","orcid":"0000-0003-3592-1689","position":19,"is_corresponding":false},{"id":804139,"name":"Jonas Schlüter","orcid":"0000-0002-6214-9367","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-19T00:32:32.651796Z","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":[]}