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

Decreased Taxon-Specific IgA Response in Relation to the Changes of Gut Microbiota Composition in the Elderly

Gut microbiota is known to change with aging; however, the underlying mechanisms have not been well elucidated. Immunoglobulin A (IgA) is the dominant class of antibody secreted by the intestinal mucosa, and are thought to play a key role in the regulation of the gut microbiota. T cells regulate the magnitude and nature of microbiota-specific IgA responses. However, it is also known that T cells become senescent in elderly people. Therefore, we speculated that the age-related changes of IgA response against the gut microbiota might be one of the mechanisms causing the age-associated changes of gut microbiota composition. To prove our hypothesis, faecal samples from 40 healthy subjects (adult group: n = 20, an average of 35 years old; elderly group: n = 20, an average of 76 years old) were collected, and the gut microbiota composition and the response of IgA to gut microbiota were investigated. The relative abundance of Bifidobacteriaceae was significantly lower, whereas those of Clostridiaceae, Clostridiales;f__ and Enterobacteriaceae were significantly higher in the elderly group than in the adult group. There was no significant difference in the faecal IgA concentration between the adult and elderly groups. However, the taxon-specific IgA response to some bacterial taxa was different between the adult and elderly groups. To evaluate inter-group differences in the taxon-specific IgA response to each bacterial taxon, the IgA-indices were calculated, and the IgA-indices of Clostridiaceae and Enterobacteriaceae were found to be significantly lower in the elderly group than the adult group. In addition, Clostridiales;f__ and Enterobacteriaceae were significantly enriched in the IgA+ fraction in the adult group but not in the elderly group, whereas Clostridiaceae was significantly enriched in the IgA- fraction in the elderly group but not in the adult group. Some species assigned to Clostridiaceae or Enterobacteriaceae are known to be pathogenic bacteria. Our results suggest the possible contribution of decreased IgA response in the increased abundance of bacterial taxa with potential pathogenicity in the intestinal environment of the elderly. Our findings contribute to the understanding of the regulatory factor for the changes in the gut microbiota composition with aging

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

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 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