Dynamic response of different types of gut microbiota to fructooligosaccharides and inulin.

Fructooligosaccharides (FOS) and inulin are beneficial for human health. However, their benefits differ in individuals who consume prebiotics. Several factors contribute to this variation, including host genetics and differences in the gut microbiota. Bifidobacterium and Bacteroides are strong carbohydrate-utilizing bacteria in the gut, and the level of the Bacteroides/Bifidobacterium (Ba/Bi) ratio in the gut is closely related to the body's ability to utilize prebiotics. However, how to select the type of prebiotics more beneficial for populations with specific Ba/Bi backgrounds and the underlying regulatory mechanisms remain unclear. Here, we explored the dynamics of the gut microbiota and metabolic functions during the in vitro fermentation of FOS and inulin in two different groups: Bacteroides/Bifidobacterium high (H) and Bacteroides/Bifidobacterium low (L). This study revealed that the baseline Ba/Bi ratio had a greater impact on the gut microbiota compared to prebiotic species. Noticeable differences were observed between the two groups after prebiotic intervention, with the H group being more likely to benefit from the prebiotic intervention. Compared to the L group, the H group exhibited significantly higher microbial α-diversity; the co-abundance response group 1 (CARG1) members Ruminococcus gnavus and Blautia involved in the synthesis of propionic and butyric acids increased significantly, the abundance of pathogenic bacteria such as Escherichia Shigella decreased significantly, and the ability to degrade carbohydrates and synthesize fatty acids was greater. Regression modeling showed that the key microbiota could predict the short-chain fatty acid (SCFA) levels, with FOS associated with the ecological roles of CARG2 and CARG7 and inulin associated with CARG4, which provides the basis for the use of prebiotics in nutritional applications and the stratification of populations based on pertinent microbiota profiles to explain the incongruent health effects in human intervention studies.

Response differences of gut microbiota in oligofructose and inulin are determined by the initial gut Bacteroides/Bifidobacterium ratios.

Prebiotics are known to modulate the gut microbiota, but there is host variability, mainly due to differences in carbohydrate-utilisation by gut microbiota. Bifidobacterium and Bacteroides are powerful carbohydrate-utilising bacteria, and the ratio of both is closely related to the utilisation of prebiotics. However, the differential impact of prebiotics on the composition and function of the gut microbiota and its metabolites in participants with different Bacteroides/Bifidobacterium (Ba/Bi) ratios have not been studied. Here, we conducted a 4-week randomised double-blind, parallel four-arm trial using two prebiotics (oligofructose and inulin) in two populations with high Ba/Bi (H) and low Ba/Bi (L). The response to prebiotics in both populations was influenced by the baseline microbiota background specificity. Notably, at an overall level, FOS was slightly better than inulin in modulating the gut microbiota. Difference in gut microbiota regulation by FOS across microbiota contexts were significant between the two groups. Butyric acid-producing bacteria were significantly more abundant in H and further elevated butyric acid and related metabolite levels, with H more likely to benefit from the FOS intervention. The two groups showed only metabolic differences in their response to inulin, with L showing a significant increase in propionic acid and being enriched in glycolysis functions, whereas H was enriched in amino acids and aminoglycolysis functions. Overall, these results provide a basis for selecting appropriate prebiotics for participants with different gut backgrounds.

Compositional and functional features of the intestinal lactobacilli associated with different long-term diet types.

It is well known that diet is one of the most important factors in shaping the host's intestinal microbiota. Lactobacillus, a common group of probiotic bacteria, is widely distributed in the host gut, and studies have linked changes in lactobacilli in the gut to differences in dietary habits. Different dietary habits may affect not only the structural composition but also the function of lactobacilli in the intestine. Therefore, we dissected 283 metagenomes from samples collected from individuals with different dietary habits, investigating the presence of different species of lactobacilli. We demonstrated that the highest abundance of lactobacilli was found in stool samples from omnivorous populations and that Ligilactobacillus ruminis (L. ruminis) and Lactiplantibacillus plantarum (L. plantarum) were more prevalent in these samples than in vegetarian and vegan samples. In addition, we determined that different dietary structures affected the functional potential of lactobacilli by reconstructing the metagenome-assembled genomes (MAGs) of L. ruminis (highest abundance) in the samples. L. ruminis strains associated with a vegetarian diet had a higher "replication, recombination and repair" functional potential and may also have a greater capacity for glutathione (GSH) synthesis and metabolism. The results of our analysis provide evidence for the possibility of a specific selection of lactobacillus strains for people with different dietary habits.

Meta-analysis reveals different functional characteristics of human gut Bifidobacteria associated with habitual diet.

Dietary habits contribute to the composition and function of the gut microbiota. Different dietary structures, including vegan, vegetarian, and omnivorous diets, affect intestinal Bifidobacteria; however, the relationship between Bifidobacterial function and host metabolism in subjects with different dietary patterns is unclear. Here, we analyzed five metagenomics studies and six 16S sequencing studies, including 206 vegetarians (VG), 249 omnivores (O), and 270 vegans (V), through an unbiased theme-level meta-analysis framework and discovered that diet significantly affects the composition and functionality of intestinal Bifidobacteria. The relative abundance of Bifidobacterium pseudocatenulatum was significantly higher in V than in O and Bifidobacterium longum, Bifidobacterium adolescentis, and B. pseudocatenulatum differed significantly in carbohydrate transport and metabolism in subjects with different diet types. Diets high in fiber were associated with B. longum with increased capacity for carbohydrate catabolism and genes encoding GH29 and GH43_27 were significantly enriched in V. Bifidobacterium adolescentis and B. pseudocatenulatum, associated with O, had a higher prevalence of the genes related to carbohydrate transport and metabolism, which showed the enrichment of GH26 and GH27 families. The same Bifidobacterium species has different functions in subjects with different diet types, resulting in different physiological significance. The diversification and functionalities of Bifidobacterial species in the gut microbiome can be influenced by the host diet and this aspect should be considered when studying host-microbe associations.

Integrative analysis of the metabolome and transcriptome reveals the influence of Lactobacillus plantarum CCFM8610 on germ-free mice.

This study describes the influence of Lactobacillus plantarum CCFM8610 on the host by employing transcriptome and untargeted metabolomics. According to the enrichment analysis, three pathways, including the complement and coagulation cascade pathway, antigen processing and presentation pathways, and protein processing in the endoplasmic reticulum pathway, were affected by L. plantarum CCFM8610 colonization. According to partial least squares-discriminant analysis, five metabolites, L-methionine, D-tryptophan, indoleacrylic acid, DL-acetylcarnitine, and L-norleucine, were identified as key metabolites in the serum. Furthermore, integrative analysis of the metabolome and transcriptome revealed connections between enriched pathways and differential metabolites, and the regulation strategy of choline by affecting gene expression was proposed. Overall, the effects of L. plantarum CCFM8610 on host health were investigated after excluding the influence of gut microbes, which provides a valuable reference for studying the potential mechanisms of the effect of probiotics on host health.