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However, microbiome disruption can enable its outgrowth, increasing the risk of life-threatening candidiasis. Restoring key protective microbes offer a therapeutic strategy, though their identification remains challenging. Using the M-SHIME\u00ae model simulating the human proximal colon, we investigated <jats:italic>C. albicans<\/jats:italic>-bacteriome interactions under eubiotic and dysbiotic conditions. We assessed how clindamycin, ciprofloxacin, and metronidazole modulate <jats:italic>C. albicans<\/jats:italic> colonization and evaluated associated microbial and metabolic shifts. The effects were antibiotic- and donor-specific: clindamycin facilitated colonization, ciprofloxacin had no impact, and metronidazole showed variable outcomes. Engraftment did not correlate with total bacterial concentration or \u03b1-diversity, but with the loss of specific taxa, notably <jats:italic>Lachnospiraceae<\/jats:italic> and <jats:italic>Bifidobacterium<\/jats:italic>. These correlations were supported functionally by reductions in acetate and butyrate, suggesting a metabolic mechanism of fungal suppression. This study highlights the role of dysbiosis in <jats:italic>C. albicans<\/jats:italic> outgrowth and supports targeted microbiome restoration strategies.<\/jats:p>","DOI":"10.1038\/s41522-025-00803-w","type":"journal-article","created":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T13:53:19Z","timestamp":1756216399000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Candida albicans colonization in the human colon correlates with a reduction in acetate- and butyrate-producing bacteria, as simulated using the M-SHIME\u00ae model"],"prefix":"10.1038","volume":"11","author":[{"given":"Beno\u00eet","family":"Marsaux","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Warre","family":"d\u2019Hoker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Moens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dries","family":"Van Elst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yorick","family":"Minnebo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Massimo","family":"Marzorati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom","family":"Van de Wiele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,8,26]]},"reference":[{"key":"803_CR1","doi-asserted-by":"publisher","first-page":"S38","DOI":"10.1111\/j.1753-4887.2012.00493.x","volume":"70","author":"LK Ursell","year":"2012","unstructured":"Ursell, L. 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