Fructooligosaccharides (FOS) are a well-known class of prebiotic and are considered to selectively stimulate the growth of bifidobacteria in the gut. Previous studies focused on the growth stimulation of Bifidobacterium, but they did not further investigate the bifidobacterial composition and the specific species that were stimulated. In this study, mice were fed with FOS in different doses for four weeks and the composition of fecal microbiota, in particular Bifidobacterium, was analyzed by sequencing the V3–V4 region and the groEL gene on the MiSeq platform, respectively. In the high-dose group, the relative abundance of Actinobacteria was significantly increased, which was mainly contributed by Bifidobacterium. At the genus level, the relative abundances of Blautia and Coprococcus were also significantly increased. Through the groEL sequencing, 14 species of Bifidobacterium were identified, among which B. pseudolongum was most abundant. After FOS treatment, B. pseudolongum became almost the sole bifidobacterial species (>95%). B. pseudolongum strains were isolated and demonstrated their ability to metabolize FOS by high performance liquid chromatography (HPLC). Therefore, we inferred that FOS significantly stimulated the growth of B. pseudolongum in mice. Further investigations are needed to reveal the mechanism of selectiveness between FOS and B. pseudolongum, which would aid our understanding of the basic principles between dietary carbohydrates and host health.

The rat is an important model animal used frequently in biological researches exploring the correlations between gut microbiome and a wide array of diseases. In this study, we used an extended ancestral-state reconstruction algorithm to predict the functional capabilities of the rat gastrointestinal microbiome. Our results indicate an apparent tendency toward metabolic heterogeneity along the longitudinal and transverse axes of the rat gastrointestinal tract (GIT). This heterogeneity was suggested by the enriched small-molecule transport activity and amino acid metabolism in the upper GIT, the aerobic energy metabolism in the stomach and the mucolysis-related metabolism in the lower GIT mucus layer. In contrast to prior results, many functional overlaps were observed when the gastrointestinal microbiomes of different hosts were compared. These overlaps implied that although both the biogeographic location and host genotype were prominent driving forces in shaping the gastrointestinal microbiota, the microbiome functions were similar across hosts when observed under similar physicochemical conditions at identical anatomical sites. Our work effectively complements the rat microbial biogeography dataset we released in 2017 and, thus, contributes to a better understanding and prediction of disease-related alterations in microbial community function.