{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T04:51:58Z","timestamp":1791348718173,"version":"4.3.1"},"reference-count":37,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Type 2 resistant starch (RS2) can be fermented by the gut microbiota and contribute to short-chain fatty acid (SCFA) production; however, microbial responses to resistant starch vary substantially across individuals and populations, and the role of baseline microbiota in this variability remains incompletely understood. In this study, we integrated four publicly available paired metagenomic datasets representing diverse experimental and host contexts and performed cross-dataset analyses of taxonomic and functional responses.\n                    <jats:italic>Faecalibacterium prausnitzii<\/jats:italic>\n                    was among the taxa consistently enriched after resistant starch-related intervention or exposure across multiple datasets. Exploratory baseline stratification further suggested that the presence of\n                    <jats:italic>F. prausnitzii<\/jats:italic>\n                    was associated with changes in selected SCFA- and carbohydrate metabolism-related pathways. We subsequently examined its relationships with the representative resistant starch degraders\n                    <jats:italic>Ruminococcus bromii<\/jats:italic>\n                    and\n                    <jats:italic>Bifidobacterium adolescentis<\/jats:italic>\n                    . Baseline association analyses identified a reproducible positive association between\n                    <jats:italic>R. bromii<\/jats:italic>\n                    and\n                    <jats:italic>F. prausnitzii<\/jats:italic>\n                    . In cohort-adjusted analyses of mutually exclusive microbial configurations, the Fp\u202f+\u202fRb configuration was associated with greater increases in the acetate\/lactate-related pathways P41-PWY and PWY-5100 than the Fp\u202f+\u202fRb\u202f+\u202fBa configuration, whereas no significant differences were observed for the other selected SCFA-related pathways. Continuous abundance analyses provided no significant evidence for abundance-dependent effects of Rb or Fp or for an Rb\u202f\u00d7\u202fFp interaction. These findings identify baseline Fp\u202f+\u202fRb co-occurrence as a hypothesis-generating microbial configuration associated with responses in selected SCFA-related pathways and provide a basis for independent experimental validation.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1959463","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T04:46:17Z","timestamp":1791348377000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Baseline co-occurrence of Faecalibacterium prausnitzii and Ruminococcus bromii is associated with greater increases in selected short-chain fatty acid-related pathways following resistant starch type 2 intervention across diverse populations"],"prefix":"10.3389","volume":"17","author":[{"given":"Yue","family":"Ma","sequence":"first","affiliation":[{"name":"Shandong Medical and Pharmaceutical University","place":["Yantai, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Lu","sequence":"additional","affiliation":[{"name":"Shandong Medical and Pharmaceutical University","place":["Yantai, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingyan","family":"Geng","sequence":"additional","affiliation":[{"name":"Shandong Medical and Pharmaceutical University","place":["Yantai, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Shandong Medical and Pharmaceutical University","place":["Yantai, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei-Hua","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology","place":["Wuhan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,10,7]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e65088","DOI":"10.7554\/elife.65088","article-title":"Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3","volume":"10","author":"Beghini","year":"2021","journal-title":"eLife"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.nutres.2020.02.009","article-title":"Conserved and variable responses of the gut microbiome to resistant starch type 2","volume":"77","author":"Bendiks","year":"2020","journal-title":"Nutr. 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