Comparative Genomics Revealed Genetic Diversity and Species/Strain-Level Differences in Carbohydrate Metabolism of Three Probiotic Bifidobacterial Species

Strains of Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium animalis are widely used as probiotics in the food industry. Although numerous studies have revealed the properties and functionality of these strains, it is uncertain whether these characteristics are species common or strain specific. To address this issue, we performed a comparative genomic analysis of 49 strains belonging to these three bifidobacterial species to describe their genetic diversity and to evaluate species-level differences. There were 166 common clusters between strains of B. breve and B. longum, whereas there were nine common clusters between strains of B. animalis and B. longum and four common clusters between strains of B. animalis and B. breve. Further analysis focused on carbohydrate metabolism revealed the existence of certain strain-dependent genes, such as those encoding enzymes for host glycan utilisation or certain membrane transporters, and many genes commonly distributed at the species level, as was previously reported in studies with limited strains. As B. longum and B. breve are human-residential bifidobacteria (HRB), whereas B. animalis is a non-HRB species, several of the differences in these species’ gene distributions might be the result of their adaptations to the nutrient environment. This information may aid both in selecting probiotic candidates and in understanding their potential function as probiotics

Additional file 13: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Hierarchical Ward’s linkage clustering based on the proportion of transporter genes predicted by PICRUSt. Age-related groups (adult-enriched and infant/elderly-enriched clusters) were revealed by Ward’s linkage clustering using the squared Euclidean distance. The population densities (z-score) of the transporters scaled by color are displayed together with a dendrogram of the transporters in a heat map. The colors within the horizontal clustering represent the age-segmented groups as shown in Fig. 1 The color code for the vertical clustering indicates KEGG Orthology (KO) as follows: white, ABC Transporters, Eukaryotic Type; yellow, ABC Transporters, Prokaryotic Type; blue, Solute Carrier Family (SLC); orange, Major Facilitator Superfamily (MFS); red, Phosphotransferase System (PTS); and green, Other Transporters. (PDF 209 kb

Additional file 10: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Taxa that are found in more than 50 % of the subjects in any cluster (shown in Additional file 8) with significantly difference between adult 1 and adult 2 clusters. (XLSX 857 kb

Additional file 14: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Relative abundance of predicted D-Xylose transporter (KEGG module: M00215). The KEGG module M00215 consists of three KO entries, K10543, K10544 and K10545. Each number indicates a group as shown in Table 1. Box-plots show the interquartile range (IQR) of the relative abundance of the predicted D-Xylose transporter. Open circles indicate outliers from 1.5- to 3.0-fold IQR. (PDF 96 kb