{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T13:02:32Z","timestamp":1790859752055,"version":"4.1.0"},"posted":{"date-parts":[[2026,8,13]]},"group-title":"Microbiology","reference-count":74,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["5R01AG075283-04"],"award-info":[{"award-number":["5R01AG075283-04"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["2R01AG067483-03"],"award-info":[{"award-number":["2R01AG067483-03"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,28]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Gut microbiome differences in Alzheimer\u2019s disease (AD) are typically cataloged taxon by taxon, yet bacterial competition and cross-feeding make species\u2019 roles dependent on the entire community. We analyzed 274 stool metagenomes from 119 older adults (18 with AD) as communities, retaining 22 recurring across 1,000 runs. Using our AI framework, we identified 15 species differing in abundance in AD, particularly the commensal\n                  <jats:italic>Phocaeicola vulgatus<\/jats:italic>\n                  (Cohen\u2019s\n                  <jats:italic>d<\/jats:italic>\n                  \u20130.91, 95% CI [-1.23, \u20130.59]), a finding robust to repeated sampling. It correlated negatively with its sister species,\n                  <jats:italic>Phocaeicola dorei<\/jats:italic>\n                  (\n                  <jats:italic>r<\/jats:italic>\n                  \u20130.57), suggesting possible niche competition; this replicated in an independent cohort (\n                  <jats:italic>r<\/jats:italic>\n                  \u20130.43).\n                  <jats:italic>P. vulgatus<\/jats:italic>\n                  was depleted in AD and the opportunistic pathogen\n                  <jats:italic>Bacteroides fragilis<\/jats:italic>\n                  enriched, shifting their balance toward\n                  <jats:italic>B. fragilis<\/jats:italic>\n                  (\n                  <jats:italic>d<\/jats:italic>\n                  \u20130.70), a modestly reproduced AD-associated pattern (\n                  <jats:italic>d<\/jats:italic>\n                  \u20130.24). Our findings suggest that AD-associated gut microbiome variation extends beyond taxon-specific abundance to the balance between specific species within a community matrix.\n                <\/jats:p>","DOI":"10.64898\/2026.08.12.743985","type":"posted-content","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T04:50:38Z","timestamp":1786683038000},"source":"Crossref","is-referenced-by-count":0,"title":["Gut community-level analysis reveals an altered balance between\n                  <i>Phocaeicola vulgatus<\/i>\n                  and\n                  <i>Bacteroides fragilis<\/i>\n                  in Alzheimer\u2019s disease"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2215-2473","authenticated-orcid":false,"given":"Ziyuan","family":"Huang","sequence":"first","affiliation":[{"name":"Department of Microbiology, UMass Chan Medical School, Worcester, MA 01655, USA"},{"name":"Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA 01655, USA"},{"name":"Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01655, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3460-010X","authenticated-orcid":false,"given":"Patrick M.","family":"McGrath","sequence":"additional","affiliation":[{"name":"Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA 01655, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5237-9538","authenticated-orcid":false,"given":"Danielle C.","family":"Ferdinand","sequence":"additional","affiliation":[{"name":"Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA 01655, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5992-2673","authenticated-orcid":false,"given":"Beth A.","family":"McCormick","sequence":"additional","affiliation":[{"name":"Department of Microbiology, UMass Chan Medical School, Worcester, MA 01655, USA"},{"name":"Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01655, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4952-824X","authenticated-orcid":false,"given":"Doyle V.","family":"Ward","sequence":"additional","affiliation":[{"name":"Department of Microbiology, UMass Chan Medical School, Worcester, MA 01655, USA"},{"name":"Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01655, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3257-2922","authenticated-orcid":false,"given":"Vanni","family":"Bucci","sequence":"additional","affiliation":[{"name":"Department of Microbiology, UMass Chan Medical School, Worcester, MA 01655, USA"},{"name":"Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01655, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7311-1121","authenticated-orcid":false,"given":"John P.","family":"Haran","sequence":"additional","affiliation":[{"name":"Department of Microbiology, UMass Chan Medical School, Worcester, MA 01655, USA"},{"name":"Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA 01655, USA"},{"name":"Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA 01655, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"issue":"5","key":"2026100105500752000_2026.08.12.743985v3.1","first-page":"872","article-title":"Alzheimer\u2019s Disease Facts and Figures","volume":"21","year":"2025","journal-title":"Alzheimer\u2019s C Dementia"},{"key":"2026100105500752000_2026.08.12.743985v3.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.neurobiolaging.2016.08.019"},{"key":"2026100105500752000_2026.08.12.743985v3.3","doi-asserted-by":"crossref","unstructured":"Shukla PK , Delotterie DF , Xiao J , Pierre JF , Rao R , McDonald MP , et al. 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