Introduction: Galacto-oligosaccharides (GOS) are well-substantiated prebiotic substrates. Multiple studies have demonstrated a positive impact of GOS on gut microbiota composition and activity, so-far mainly related to Bifidobacterium. However, data on the beneficial impact at lower dosages in a healthy female population are limited. The primary aim of the current study was to reveal the effect of low dosages (1.3 and 2.0 g) of GOS on fecal Bifidobacterium abundance in healthy women. Other outcomes included the effect of low dosage of GOS on overall fecal microbiota composition and on self-perceived GI comfort, sleep quality and mental wellbeing.Method: Eighty-eight healthy women (42–70 years, BMI 18.7–30 kg/m²) were included in this randomized, parallel, double-blind study of 6 weeks. The participants were stratified for fiber intake, BMI and age and randomized to consume either 1.3 or 2.0 g of GOS per day for 3 weeks after a control period of 3 weeks without any intervention. Fecal samples were collected for shotgun metagenomics sequencing at the start (t = −3) and end (t = 0) of the control period and at the end of the intervention period (t = 3). Self-perceived gut comfort, sleep quality, and mental wellbeing were assessed weekly. Hierarchical clustering of principal components was applied to data collected from study participants.Results: The relative abundance of Bifidobacterium in feces increased significantly after 3 weeks of daily consumption of both 1.3 g (p < 0.01) and 2.0 g GOS (p < 0.01). This was accompanied by a significant shift in the overall microbiota composition for the dosage of 2.0 g GOS (p < 0.01). Participants that showed a larger increase in Bifidobacterium in the intervention period compared to the change in Bifidobacterium in the control period, defined as responders, showed a significant overall difference in initial fecal microbiota composition as compared to non-responders (p = 0.04) and a trend towards lower baseline levels of Bifidobacterium in responders (p = 0.10).Conclusion: Daily consumption of a low dose of GOS can lead to an increase in the relative abundance of Bifidobacterium in feces of healthy women. Additionally, with 2.0 g GOS, the enrichment of Bifidobacterium is accompanied with a shift in the overall microbiota composition.Clinical trial registration: clinicaltrials.gov, identifier NCT05762965.

The objective of the current study was to evaluate the potential of 2′-FL and GOS, individually and combined, in beneficially modulating the microbial composition of infant and toddler (12–18 months) feces using the micro-Matrix bioreactor. In addition, the impacts of GOS and 2′-FL, individually and combined, on the outgrowth of fecal bifidobacteria at (sub)species level was investigated using the baby M-SHIME^® model. For young toddlers, significant increases in the genera Bifidobacterium, Veillonella, and Streptococcus, and decreases in Enterobacteriaceae, Clostridium XIVa, and Roseburia were observed in all supplemented fermentations. In addition, GOS, and combinations of GOS and 2′-FL, increased Collinsella and decreased Salmonella, whereas 2′-FL, and combined GOS and 2′-FL, decreased Dorea. Alpha diversity increased significantly in infants with GOS and/or 2′-FL, as well as the relative abundances of the genera Veillonella and Akkermansia with 2′-FL, and Lactobacillus with GOS. Combinations of GOS and 2′-FL significantly stimulated Veillonella, Lactobacillus, Bifidobacterium, and Streptococcus. In all supplemented fermentations, Proteobacteria decreased, with the most profound decreases accomplished by the combination of GOS and 2′-FL. When zooming in on the different (sub)species of Bifidobacterium, GOS and 2’-FL were shown to be complementary in stimulating breast-fed infant-associated subspecies of Bifidobacterium longum in a dose-dependent manner: GOS stimulated Bifidobacterium longum subsp. longum, whereas 2′-FL supported outgrowth of Bifidobacterium longum subsp. infantis.

Background: Natural enrichment of sn-2 palmitate content of infant formulae by using bovine milk fat is known to reduce formation of faecal fatty acid soaps and to improve stool consistency, but effects on gut microbiota composition are unknown. The purpose of this study was to test the influence of milk fat-based formula high in sn-2 palmitate on the infants’ gut microbiota composition and to confirm the beneficial effects of the formula on formation of faecal fatty acid soaps and stool consistency. Methods: Twenty-two healthy term, formula-fed infants were enrolled in a single-blinded randomized, crossover, placebo-controlled trial. After a 2-week run-in period, infants received either a 50% milk fat-based formula containing 39% sn-2 palmitate (MF) or a vegetable fat-based formula (VF) containing 10% sn-2 palmitate in a 2 × 2-week crossover design. Faecal microbiota composition was the primary outcome of the study. Other outcomes included faecal fatty acid soap excretion, calcium excretion, gut comfort parameters and faecal metabolites. Results: Microbiota analysis showed that bifidobacteria dominated the gut microbiota of most infants. Neither alpha- nor beta-diversity was significantly influenced by the intervention. Also, abundance of metabolic pathways was independent of the intervention. The MF formula resulted in significantly lower faecal levels of palmitic acid soap (p = 0.0002) and total fatty acid soaps (p = 0.0001) than the VF formula. Additionally, calcium excretion and palmitic acid concentration were significantly (p = 0.0335) lower in stool samples after MF intervention. Furthermore, a significant physiological effect on softer stools was observed in the MF intervention compared to the VF intervention (p = 0.02). Of the 870 measured faecal metabolites, 190 were significantly different after MF and VF intervention (FDR corrected p < 0.05). Most of these were found at higher levels after MF intervention, potentially indicative of the complex structure of milk fat. Metabolites with more than twofold change between interventions were mostly lipid-derived and included several milk fat-specific fatty acids. Conclusions: Replacing part of the vegetable fat in infant formula with bovine milk fat with high sn-2 palmitate levels did not change the microbiota composition, although a reduction in faecal palmitate soaps, total fatty acid soaps and calcium excretion while improving stool consistency in the MF intervention was confirmed. In addition, 190 faecal metabolites were significantly different, many related to the fat source. Trial registration: Netherlands Trial Registry Identifier: NL7815 19/06/2019.

The integration and analysis of multi-omics modalities is an important challenge in bioinformatics and data science in general. A standard approach is to conduct a series of univariate tests to determine the significance for each parameter, but this underestimates the connected nature of biological data and thus increases the number of false-negative errors. To mitigate this issue and to understand how different omics’ data domains are jointly affected, we used the Stacked Regularization model with Bayesian optimization over its full parameter space. We applied this approach to a multi-omics data set consisting of microbiota, metabolites and clinical data from two recent clinical studies aimed at detecting the impact of replacing part of the vegetable fat in infant formula with bovine milk fat on healthy term infants. We demonstrate how our model achieves a high discriminative performance, show the advantages of univariate testing and discuss the detected outcome in its biological context.

Background and objectives: Globally, about 70% of the adult population is lactase non-persistent (LNP), lacking the enzyme required for lactose digestion. The main consequence of intolerance is withholding nutrient-rich dairy foods, while the literature shows that many LNPers are able to consume ≤12 g of lactose, comparable to 250 mL of milk, without experiencing gastrointestinal discomfort. Repetitive consumption of lactose may improve intolerance symptoms even further via colonic adaptation. This study aimed to assess the effects of daily consumption of incremental lactose doses on microbiota composition and function, and intolerance symptoms. Methods: Twenty-five healthy adults of Asian origin (age 22–44 yrs, BMI 19–28 kg/m²), carrying the LNP genotype and avoiding lactose in their habitual diet, were included in this 12-week single-blinded intervention trial. Participants consumed lactose twice daily, with doses being gradually increased from 3 to 6 g, to finally 12 g twice daily, each dose being provided for 4 consecutive weeks. Before and after the 12-week intervention, participants underwent a 25 g lactose challenge hydrogen breath test (HBT) and handed in stool samples. Daily gastrointestinal symptoms and acute intolerance symptoms during the HBT were recorded. Results: There was a significant increase in Bifidobacterium after 12 weeks of lactose consumption (p = 0.009), accompanied by a two-fold increase (p < 0.001) in fecal β-galactosidase activity. There was a 1.5-fold decrease (AUC; p = 0.01) in expired hydrogen during the second compared to the baseline HBT. There was a non-significant decrease in total symptom score (p = 0.09) during this second HBT, which was already relatively low during the baseline HBT. Daily consumption of lactose was generally well tolerated, with mild to no gastrointestinal complaints reported during the intervention. Discussion: Repetitive consumption of incremental doses of lactose increases lactose tolerance in LNP individuals via colonic adaptation, most likely through increasing the relative abundance of lactose-fermenting Bifidobacterium. Repetitive lactose consumption is well tolerated and able to reduce expired hydrogen during a 25 g lactose HBT. Here, we show that regular and incremental exposure to lactose in LNP individuals leads to colonic adaptation without any increase in gastrointestinal symptoms. This lifts the necessity to remove dairy foods completely from the diet.