{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T13:36:48Z","timestamp":1781530608673,"version":"3.54.1"},"reference-count":134,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"}],"funder":[{"name":"BEAMER"},{"name":"Innovative Medicines Initiative 2 Joint Undertaking","award":["101034369"],"award-info":[{"award-number":["101034369"]}]},{"name":"European Union's Horizon 2020 Research and Innovation Program"},{"name":"the European Federation of Pharmaceutical Industries and Associations"},{"name":"Link2Trials BV"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE J. Biomed. Health Inform."],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1109\/jbhi.2025.3593198","type":"journal-article","created":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:54:35Z","timestamp":1760032475000},"page":"717-731","source":"Crossref","is-referenced-by-count":3,"title":["The Use of Machine Learning and Explainable Artificial Intelligence in Gut Microbiome Research: A Scoping Review"],"prefix":"10.1109","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0287-1232","authenticated-orcid":false,"given":"Hania","family":"Tourab","sequence":"first","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1536-1090","authenticated-orcid":false,"given":"Laura","family":"Lopez-Perez","sequence":"additional","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pe\u00f1a","family":"Arroyo-Gallego","sequence":"additional","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3607-0727","authenticated-orcid":false,"given":"Eleni","family":"Georga","sequence":"additional","affiliation":[{"name":"University of Ioannina, Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8198-3356","authenticated-orcid":false,"given":"Miguel","family":"Rujas","sequence":"additional","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5924-6238","authenticated-orcid":false,"given":"Francesca Romana","family":"Ponziani","sequence":"additional","affiliation":[{"name":"Universit&#x00E0; Cattolica del Sacro Cuore, Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8071-8976","authenticated-orcid":false,"given":"Macarena","family":"Torrego-Ellacur\u00eda","sequence":"additional","affiliation":[{"name":"Unidad de Apoyo a la Innovaci&#x00F3;n, San Carlos Clinical Hospital, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5070-4178","authenticated-orcid":false,"given":"Beatriz","family":"Merino-Barbancho","sequence":"additional","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4648-8852","authenticated-orcid":false,"given":"Neri Niccol\u00f2","family":"Dei","sequence":"additional","affiliation":[{"name":"Scuola Superiore Sant&#x2019;Anna, Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0855-7976","authenticated-orcid":false,"given":"Gastone","family":"Ciuti","sequence":"additional","affiliation":[{"name":"Scuola Superiore Sant&#x2019;Anna, Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5987-9350","authenticated-orcid":false,"given":"Dimitrios","family":"Fotiadis","sequence":"additional","affiliation":[{"name":"University of Ioannina, Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6230-1779","authenticated-orcid":false,"given":"Gasbarrini","family":"Antonio","sequence":"additional","affiliation":[{"name":"Universit&#x00E0; Cattolica del Sacro Cuore, Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9343-063X","authenticated-orcid":false,"given":"Mar\u00eda Fernanda","family":"Cabrera","sequence":"additional","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3113-3976","authenticated-orcid":false,"given":"Mar\u00eda Teresa","family":"Arredondo","sequence":"additional","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1551-4613","authenticated-orcid":false,"given":"Giuseppe","family":"Fico","sequence":"additional","affiliation":[{"name":"Life Supporting Technologies, Universidad Polit&#x00E9;cnica de Madrid, Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"263","reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v27.i41.7041"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007677"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.02868"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.1872323"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.635781"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1016\/j.inffus.2019.12.012"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1186\/s12916-019-1426-2"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2020.103655"},{"key":"ref9","article-title":"Towards a rigorous science of interpretable machine learning","author":"Doshi-Velez","year":"2017"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1016\/j.artint.2018.07.007"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa010"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01191-20"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1111\/jgh.15502"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1007\/s12553-020-00486-7"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1111\/jgh.15503"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1111\/jgh.15500"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2019-320065"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1111\/jgh.15501"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.634511"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.7326\/m18-0850"},{"issue":"3","key":"ref21","doi-asserted-by":"crossref","first-page":"A12","DOI":"10.7326\/ACPJC-1995-123-3-A12","article-title":"The well-built clinical question: A key to evidence-based decisions","volume":"123","author":"Richardson","year":"1995","journal-title":"ACP J. Club"},{"key":"ref22","volume-title":"Interpretable Machine Learning: A Guide for Making Black Box Models Explainable","author":"Molnar","year":"2022"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.g7594"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1109\/access.2018.2870052"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.3390\/electronics8080832"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.3233\/shti210591"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.3390\/app12094094"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2024.2375483"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-04182-y"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-022-04618-w"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-6652-7"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-31210-w"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics12102514"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2020.101199"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2297852"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36135-6"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-024-02823-z"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.2025016"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2023.106476"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-02858-4"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1348974"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines10082028"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2024.110709"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines10112998"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24119533"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2023.1170459"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2021.604584"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.3390\/ijms241713329"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0265756"},{"key":"ref50","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1371371"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1016\/j.ibmed.2024.100180"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2024.04.025"},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1101\/gr.278637.123"},{"key":"ref54","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00295-24"},{"key":"ref55","doi-asserted-by":"publisher","DOI":"10.1186\/s12916-024-03317-y"},{"key":"ref56","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2024.111442"},{"key":"ref57","doi-asserted-by":"publisher","DOI":"10.3390\/v16071054"},{"key":"ref58","doi-asserted-by":"publisher","DOI":"10.3389\/fnagi.2024.1444998"},{"key":"ref59","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2292254"},{"key":"ref60","doi-asserted-by":"publisher","DOI":"10.1016\/j.tjnut.2024.08.012"},{"key":"ref61","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-022-09087-2"},{"key":"ref62","doi-asserted-by":"publisher","DOI":"10.1111\/liv.15864"},{"key":"ref63","doi-asserted-by":"publisher","DOI":"10.1186\/s12911-020-01263-2"},{"key":"ref64","doi-asserted-by":"publisher","DOI":"10.1016\/j.critrevonc.2019.06.004"},{"key":"ref65","doi-asserted-by":"publisher","DOI":"10.3390\/biomedinformatics1030010"},{"key":"ref66","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2020.08.065"},{"key":"ref67","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02120-17"},{"key":"ref68","doi-asserted-by":"publisher","DOI":"10.1186\/s13040-021-00241-2"},{"key":"ref69","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2020.603740"},{"key":"ref70","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9102149"},{"key":"ref71","doi-asserted-by":"publisher","DOI":"10.1155\/2018\/2936257"},{"key":"ref72","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-46249-x"},{"key":"ref73","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2022.03.002"},{"key":"ref74","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.628426"},{"key":"ref75","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-018-0160-1"},{"key":"ref76","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.621310"},{"key":"ref77","doi-asserted-by":"publisher","DOI":"10.1016\/j.micres.2022.127198"},{"key":"ref78","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2021.01.028"},{"key":"ref79","doi-asserted-by":"publisher","DOI":"10.1109\/access.2021.3094529"},{"key":"ref80","doi-asserted-by":"publisher","DOI":"10.1093\/jamia\/ocz009"},{"key":"ref81","doi-asserted-by":"publisher","DOI":"10.1016\/j.compeleceng.2024.109370"},{"key":"ref82","doi-asserted-by":"publisher","DOI":"10.1136\/bmjhci-2023-100954"},{"key":"ref83","doi-asserted-by":"publisher","DOI":"10.1016\/j.imu.2024.101587"},{"key":"ref84","doi-asserted-by":"publisher","DOI":"10.1109\/access.2022.3196917"},{"key":"ref85","article-title":"Ethics and governance of artificial intelligence for health: WHO guidance","year":"2021"},{"key":"ref86","article-title":"High-level expert group on artificial intelligence: Ethics guidelines for trustworthy AI","year":"2019"},{"key":"ref87","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1257002"},{"key":"ref88","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1250806"},{"key":"ref89","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1261889"},{"key":"ref90","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2019.20866"},{"key":"ref91","doi-asserted-by":"publisher","DOI":"10.1161\/circoutcomes.120.006556"},{"key":"ref92","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pdig.0000016"},{"key":"ref93","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00031-18"},{"key":"ref94","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq1019"},{"key":"ref95","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq967"},{"key":"ref96","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-7089-3_15"},{"key":"ref97","doi-asserted-by":"publisher","DOI":"10.7326\/m18-1376"},{"key":"ref98","doi-asserted-by":"publisher","DOI":"10.3390\/jcm9082403"},{"key":"ref99","doi-asserted-by":"publisher","DOI":"10.1136\/bmjgast-2019-000297"},{"key":"ref100","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-94007-9"},{"key":"ref101","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.794519"},{"key":"ref102","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-021-02414-9"},{"key":"ref103","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-04373-7"},{"key":"ref104","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.03.039"},{"key":"ref105","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-75515-6"},{"key":"ref106","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.711884"},{"key":"ref107","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0306-4"},{"key":"ref108","doi-asserted-by":"publisher","DOI":"10.1152\/ajpgi.00360.2020"},{"key":"ref109","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.13205"},{"key":"ref110","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2939"},{"key":"ref111","doi-asserted-by":"publisher","DOI":"10.1109\/ubmk.2018.8566487"},{"key":"ref112","doi-asserted-by":"publisher","DOI":"10.1109\/tcbb.2018.2831212"},{"key":"ref113","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.02.005"},{"key":"ref114","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(16)00081-7"},{"key":"ref115","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aax5727"},{"key":"ref116","doi-asserted-by":"publisher","DOI":"10.3892\/etm.2022.11234"},{"key":"ref117","doi-asserted-by":"publisher","DOI":"10.1038\/nature11450"},{"key":"ref118","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.711244"},{"key":"ref119","doi-asserted-by":"publisher","DOI":"10.1038\/nature15766"},{"key":"ref120","doi-asserted-by":"publisher","DOI":"10.1016\/j.eswa.2021.115648"},{"key":"ref121","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.03161-21","article-title":"A goldilocks principle for the gut microbiome: Taxonomic resolution matters for microbiome-based classification of colorectal cancer","author":"Armour","year":"2022"},{"key":"ref122","doi-asserted-by":"publisher","DOI":"10.1109\/tcbb.2018.2870124"},{"key":"ref123","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20145645"},{"key":"ref124","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.14498"},{"key":"ref125","doi-asserted-by":"publisher","DOI":"10.7150\/jca.46621"},{"key":"ref126","doi-asserted-by":"publisher","DOI":"10.3390\/brainsci10040242"},{"key":"ref127","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.00120"},{"key":"ref128","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1010050"},{"key":"ref129","doi-asserted-by":"publisher","DOI":"10.1093\/eurheartj\/ehaa704"},{"key":"ref130","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-76097-z"},{"key":"ref131","doi-asserted-by":"publisher","DOI":"10.1007\/s13300-021-01174-z"},{"key":"ref132","doi-asserted-by":"publisher","DOI":"10.3390\/nu12092695"},{"key":"ref133","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006693"},{"key":"ref134","doi-asserted-by":"publisher","DOI":"10.1161\/hypertensionaha.120.15885"}],"container-title":["IEEE Journal of Biomedical and Health Informatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx8\/6221020\/11338775\/11197657.pdf?arnumber=11197657","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T22:02:27Z","timestamp":1768255347000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/11197657\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":134,"journal-issue":{"issue":"1"},"URL":"https:\/\/doi.org\/10.1109\/jbhi.2025.3593198","relation":{"has-preprint":[{"id-type":"doi","id":"10.36227\/techrxiv.172902810.02756061\/v1","asserted-by":"object"}]},"ISSN":["2168-2194","2168-2208"],"issn-type":[{"value":"2168-2194","type":"print"},{"value":"2168-2208","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1]]}}}