Recent studies suggest that the dietary intake of human milk oligosaccharides (HMOs) provides health benefits from infancy up to adulthood. Thus far, beneficial changes in the adult gut microbiome have been observed at oral doses of 5–20 g/day of HMOs. Efficacy of lower doses has rarely been tested. We assessed four HMO molecular species—2′Fucosyllactose (2′FL), Lacto-N-neotetraose (LNnT), 3′Sialyllactose (3′SL), and 6′Sialyllactose (6′SL)—at predicted doses from 0.3 to 5 g/day for 6-year-old children and adults (n = 6 each), using ex vivo SIFR^® technology (Cryptobiotix, Ghent, Belgium). This technology employing bioreactor fermentation on fecal samples enables us to investigate microbial fermentation products that are intractable in vivo given their rapid absorption/consumption in the human gut. We found that HMOs significantly increased short-chain fatty acids (SCFAs), acetate, propionate (in children/adults), and butyrate (in adults) from predicted doses of 0.3–0.5 g/day onwards, with stronger effects as dosing increased. The fermentation of 6′SL had the greatest effect on propionate, LNnT most strongly increased butyrate, and 2′FL and 3′SL most strongly increased acetate. An untargeted metabolomic analysis revealed that HMOs enhanced immune-related metabolites beyond SCFAs, such as aromatic lactic acids (indole-3-lactic acid/3-phenyllactic acid) and 2-hydroxyisocaproic acid, as well as gut–brain-axis-related metabolites (γ-aminobutyric acid/3-hydroxybutyric acid/acetylcholine) and vitamins. The effects of low doses of HMOs potentially originate from the highly specific stimulation of keystone species belonging to, for example, the Bifidobacteriaceae family, which had already significantly increased at doses of only 0.5 g/day LNnT (adults) and 1 g/day 2′FL (children/adults).

The prevalence of pediatric inflammatory bowel disease (pIBD) has been increasing over the last two decades. Yet, treatment strategies are still limited, in part due to the multifactorial nature of the disease and the complex interplay between genetic, environmental, dietary, immune, and gut microbial factors in its etiology. With their direct and indirect anti-inflammatory properties, human milk oligosaccharides (HMOs) are a promising treatment and management strategy for IBD. However, to date there are no insights into how HMOs may affect pIBD microbiota. Here, we compared the effects of 2′fucosyllactose (2′FL), difucosyllactose (DFL), 3′sialyllactose (3′SL), and blends thereof with fructooligosaccharide (FOS) on microbiota functionality (short- and branched-chain fatty acids, pH, and gas production) and composition (quantitative shallow shotgun sequencing) using fecal material from eight different pediatric Crohn’s disease patients inoculated in the SIFR^® technology. In general, all HMO treatments significantly increased total short-chain fatty acid production when compared with FOS, despite equal gas production. We found that 2′FL, either alone or in combination with DFL and 3′SL, exhibited a strong acetogenic and propiogenic effect, and 3′SL an acetogenic effect that surpassed the effects observed with FOS. No differences in overall community diversity between HMO- and FOS-treated pIBD microbiota were observed. There was, however, a stronger bifidogenic effect of 2′FL, 3′SL, 2′FL/DFL, and 2′FL/DFL + 3′SL when compared with FOS. In general, 3′SL and HMO blends enriched a broader species profile, including taxa with potentially anti-inflammatory properties, such as Faecalibacterium prausnitzii and Blautia species. This study suggests HMOs as a promising strategy to beneficially alter the gut microbial profile in pIBD.

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. We investigated how β-carotene (BC), lutein (LU), lycopene (LY) and zeaxanthin (ZE), at biological relevant doses (between 1 and 60 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). We observed phenotype-specific microbiota characteristics for each cohort at baseline. Carotenoids alone had only minor effects but in combination with prebiotic inulin significantly altered community composition (Bray-Curtis dissimilarity, P < 0.05) and enhanced short-chain fatty acid (SCFA) production. Most 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 (p_adjusted<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%, p_adjusted<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 (p_adjusted<0.20). Antioxidant carotenoids may support anaerobic gut microbes including dominant butyrate producers and counteract phenotype-specific dysbiosis, potentially offering novel dietary approaches for IBS and obesity-associated 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.