Carotenoids modulate fermentation of inulin ex vivo in IBS and overweight adult gut microbiota

BMC Microbiology https://doi.org/10.1186/s12866-026-05271-6 Article in Press Carotenoids modulate fermentation of inulin ex vivo in IBS and overweight adult gut microbiota Robert E. Steinert, Pieter Abbeele, Christian Schaefer, Jonas Poppe, Lam Dai Vu & Danica Bajic Received: 3 July 2025 Accepted: 2 June 2026 Cite this article as: Steinert R.E., Abbeele P., Schaefer C. et al. Carotenoids modulate fermentation of inulin ex vivo in IBS and overweight adult gut microbiota. BMC Microbiol (2026). https://doi.org/10.1186/ s12866-026-05271-6 A We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply. E R P S S If this paper is publishing under a Transparent Peer Review model then Peer Review reports will publish with the final article. I T R E L C IN © The Author(s) 2026. 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To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. ACCEPTED ARTICLEMANUSCRIPT IN PRESS CAROTENOIDS MODULATE FERMENTATION OF INULIN EX VIVO IN IBS AND OVERWEIGHT ADULT GUT MICROBIOTA Robert E. Steinert1,2*, Pieter Van den Abbeele3, Christian Schaefer1, Jonas Poppe3, Lam Dai Vu3, Danica Bajic1* 1 Health, Nutrition & Care (HNC), DSM-Firmenich, Kaiseraugst, Switzerland; (R.E.S), danica.bajic@dsm- firmenich.com (D.B.), (CS). 2. Adelaide Medical School, Faculty of Health and Medical Sciences, CRE in Translating Nutritional Science to Good Health, The University of Adelaide. Australia 3 S S E R P Cryptobiotix SA, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; IN E L C I T R A (P.V.d.A.), (J.P.); (L.D.V.). * Corresponding authors: Robert E. Steinert, DSM-Firmenich, Wurmisweg 576, 4303 Kaiseraugst, Switzerland, , Tel.: +41793091212 Danica Bajic, DSM-Firmenich, Wurmisweg 576, 4303 Kaiseraugst, Switzerland, , Tel.:+4531765536 ABSTRACT Background: Carotenoids have direct antioxidant and anti- inflammatory health benefits. Owing to their low bioavailability, they also reach the colon, yet their microbiome interactions remain poorly characterized. Methods: We investigated how β-carotene (BC), lutein (LU), ACCEPTED ARTICLEMANUSCRIPT IN PRESS lycopene (LY) and zeaxanthin (ZE), at biological relevant doses (between 160 mg/d), impact composition and metabolite production of irritable bowel syndrome (IBS) and overweight (OW) adult gut microbiota using the ex vivo SIFR® fermentation system (systemic intestinal fermentation research). Fresh fecal samples were collected from 12 donors (n = 6 per cohort) and incubated for 24 h under anaerobic conditions, with carotenoids administered alone or in combination with prebiotic inulin (IN, tested at 2.5 g/day). Results: We observed phenotype-specific microbiota characteristics for each cohort at baseline. Carotenoids alone had only minor effects but in combination with prebiotic inulin S S E R P significantly altered community composition (Bray-Curtis dissimilarity, P<0.05) and enhanced short-chain fatty acid (SCFA) production. IN Most E L C I T R A carotenoids increased butyrate production vs. inulin alone with ZE (at 2 mg/d) in IBS (+7.6%) and LU (at 60 mg/d) in OW (+8.0%) showing the strongest effects (padjusted<0.10). In contrast, LY (at 45 mg/d) uniquely increased acetate (+3.5%) and propionate (+8.0%) at the expense of butyrate (-7.5%, padjusted<0.10) when compared vs. inulin only. Changes in SCFA correlated with carotenoid- and cohort-specific shifts in the abundance of Bifidobacterium, Alistipes, Akkermansia, Faecalibacterium and Coprococcus. ZE also enhanced the effect of inulin on the health-related metabolites 3-phenyllactic acid (PLA) and 2- hydroxyisocaproic acid (HICA), particularly IBS subjects (padjusted<0.20). Conclusions: Antioxidant carotenoids may support anaerobic gut microbes including dominant butyrate producers and counteract phenotype-specific ACCEPTED ARTICLEMANUSCRIPT IN PRESS dysbiosis, potentially offering novel dietary approaches for IBS and obesityassociated dysbiosis. As these effects were observed when carotenoids were combined with inulin, carotenoids may have greater impacts when consumed as part of a fiber-rich diet, reflecting their natural occurrence in plant-based foods. Keywords: SCFA, microbiota, ex vivo, carotenoid, prebiotic, SIFR® BACKGROUND The gut microbiome comprises trillions of microorganisms essential for host health notably by fermenting dietary and host-derived glycans into short- S S E R P chain fatty acids (SCFA) such as acetate, propionate, and butyrate with broad health benefits [1] [2] [3]. An imbalanced microbiome (‘dysbiosis’) has been IN increasingly linked to conditions such as Irritable Bowel Syndrome (IBS) [4] and obesity [5]. E L C I T R A IBS is a highly prevalent functional bowel disorder in which recurrent abdominal pain is associated with irregular defecation or other changes in bowel habits [6]. Despite some inter-study variability, a consistent dysbiotic pattern is observed in IBS, characterized by reduced fecal Lactobacillus and Bifidobacterium and increased Escherichia coli abundance [7]. Other changes include an increase of Ruminococcus gnavus at the expense of Coprococcus spp. [8], the latter which is also observed in patients with depression [9]. Moreover, increased Alistipes spp. have been reported in IBS patients responding to fecal microbiota transplantation. As SCFA-producing ACCEPTED ARTICLEMANUSCRIPT IN PRESS taxa, Coprococcus and Alistipes may therefore exert protective effects in IBS [10] [11]. Also obesity is highly prevalent [5] and linked to an altered gut microbiome [12, 13]. Obesity-associated microbiota typically exhibit reduced richness and diversity, with increased Ruminococcus gnavus and Roseburia, and decreased Eubacterium eligens and Akkermansia muciniphila, compared with lean individuals [12, 14]. In obesity, fecal SCFA levels (...truncated)