{"id":"https://openalex.org/W4412804298","doi":"https://doi.org/10.1371/journal.pcbi.1013299","title":"Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt","display_name":"Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt","publication_year":2025,"publication_date":"2025-07-31","ids":{"openalex":"https://openalex.org/W4412804298","doi":"https://doi.org/10.1371/journal.pcbi.1013299","pmid":"https://pubmed.ncbi.nlm.nih.gov/40743285"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013299","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013299","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013299","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088768904","display_name":"Chloe Herman","orcid":"https://orcid.org/0000-0003-2479-9710"},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chloe Herman","raw_affiliation_strings":["Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2479-9710","affiliations":[{"raw_affiliation_string":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]},{"raw_affiliation_string":"School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014309302","display_name":"Evan Bolyen","orcid":"https://orcid.org/0000-0002-5362-6782"},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Evan Bolyen","raw_affiliation_strings":["Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063248598","display_name":"Anthony Simard","orcid":"https://orcid.org/0000-0002-7394-1616"},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anthony Simard","raw_affiliation_strings":["Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114655557","display_name":"Liz Gehret","orcid":null},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Liz Gehret","raw_affiliation_strings":["Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038626201","display_name":"J. Gregory Caporaso","orcid":"https://orcid.org/0000-0002-8865-1670"},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. Gregory Caporaso","raw_affiliation_strings":["Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8865-1670","affiliations":[{"raw_affiliation_string":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]},{"raw_affiliation_string":"School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5014309302","https://openalex.org/A5038626201","https://openalex.org/A5063248598","https://openalex.org/A5088768904","https://openalex.org/A5114655557"],"corresponding_institution_ids":["https://openalex.org/I203172682"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1905,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.7953059,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"21","issue":"7","first_page":"e1013299","last_page":"e1013299"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11316","display_name":"Mycobacterium research and diagnosis","score":0.9817000031471252,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fecal-bacteriotherapy","display_name":"Fecal bacteriotherapy","score":0.8321866989135742},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.7311939001083374},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.7302389144897461},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.4968853294849396},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40300023555755615},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.34376221895217896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.27785345911979675},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23449477553367615},{"id":"https://openalex.org/keywords/clostridium-difficile","display_name":"Clostridium difficile","score":0.12386253476142883},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.12364190816879272}],"concepts":[{"id":"https://openalex.org/C137923570","wikidata":"https://www.wikidata.org/wiki/Q2121103","display_name":"Fecal bacteriotherapy","level":4,"score":0.8321866989135742},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.7311939001083374},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.7302389144897461},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.4968853294849396},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40300023555755615},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.34376221895217896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27785345911979675},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23449477553367615},{"id":"https://openalex.org/C2994496256","wikidata":"https://www.wikidata.org/wiki/Q27031090","display_name":"Clostridium difficile","level":3,"score":0.12386253476142883},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.12364190816879272},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069467","descriptor_name":"Fecal Microbiota Transplantation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000069467","descriptor_name":"Fecal Microbiota Transplantation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000069467","descriptor_name":"Fecal Microbiota Transplantation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000069467","descriptor_name":"Fecal Microbiota Transplantation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013299","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013299","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40743285","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40743285","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:b051e3cd0204419ebcb87021e2bca7d2","is_oa":true,"landing_page_url":"https://doaj.org/article/b051e3cd0204419ebcb87021e2bca7d2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 7, p e1013299 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12327600","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12327600","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013299","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013299","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4864707165","display_name":null,"funder_award_id":"1U24CA248454-01","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2086211531","https://openalex.org/W2893046185","https://openalex.org/W2936474142","https://openalex.org/W3202070756","https://openalex.org/W4389042312","https://openalex.org/W4412012601"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W47352601","https://openalex.org/W2013243191"],"abstract_inverted_index":{"We":[0],"present":[1],"q2-fmt,":[2],"a":[3,29,64],"QIIME":[4],"2":[5],"plugin":[6],"that":[7],"provides":[8],"diverse":[9],"methods":[10,23],"for":[11,35,54],"assessing":[12,36],"the":[13,71],"extent":[14],"of":[15,42],"microbiome":[16],"engraftment":[17,43],"following":[18],"fecal":[19],"microbiota":[20],"transplant.":[21],"The":[22],"implemented":[24],"here":[25],"were":[26],"informed":[27],"by":[28],"recent":[30],"literature":[31],"review":[32],"on":[33,63],"approaches":[34],"FMT":[37],"engraftment,":[38],"and":[39,49,57],"cover":[40],"aspects":[41],"including":[44],"Community":[45],"Coalescence,":[46],"Indicator":[47],"Features,":[48],"Resilience.":[50],"q2-fmt":[51],"is":[52],"free":[53],"all":[55],"use,":[56],"detailed":[58],"documentation":[59],"illustrating":[60],"worked":[61],"examples":[62],"real-world":[65],"data":[66],"set":[67],"are":[68],"provided":[69],"in":[70],"project's":[72],"documentation.":[73]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
