Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts.

BACKGROUND: The two subspecies of Bifidobacterium catenulatum, B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum, are usually from the infant and adult gut, respectively. However, the genomic analysis of their functional difference and genetic divergence has been rare. Here, 16 B. catenulatum strains, including 2 newly sequenced strains, were analysed through comparative genomics. RESULTS: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated. The comparison of genomic characteristics revealed that the two subspecies had significantly different genomic sizes (p < 0.05) but similar GC contents. The functional comparison revealed the most significant difference in genes of carbohydrate utilisation. Carbohydrate-active enzymes (CAZyme) present two clustering patterns in B. catenulatum. The B. catenulatum subsp. kashiwanohense specially including the glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51) families involved in the metabolism of human milk oligosaccharides (HMO) common in infants, also, the corresponding fucosylated HMO gene clusters were detected. Meanwhile, B. catenulatum subsp. catenulatum rich in GH3 may metabolise more plant-derived glycan in the adult intestine. CONCLUSIONS: These findings provide genomic evidence of carbohydrate utilisation bias, which may be a key cause of the genetic divergence of two B. catenulatum subspecies.

Characteristics of the gut microbiota in Bifidobacterium catenulatum LI10 pretreated rats with lower levels of D-galactosamine-induced liver damage.

AIMS: Liver damage has caused great illness in human beings. Bifidobacterium catenulatum LI10 has been determined with protective effect against D-galactosamine-induced liver damage. However, due to the sample limitation, the individual difference in its protective effect was not determined. The current study was designed to characterize the gut microbiota of LI10-pretreated rats with lower levels of liver damage. METHODS AND RESULTS: A series of experiments and bioinformatic analyses were carried out. Two rat cohorts with different levels of liver damage were determined, that is, Non-Severe and Severe cohorts. Six out of the seven measured liver function variables were lower in the Non-Severe cohort, while four cytokine variables also yielded differences between the two cohorts. The Non-Severe and Severe cohorts were determined with distinct gut microbiota, among which ASV14_Parabacteroides and ASV7_Bacteroides were most associated with Non-Severe and Severe cohorts, respectively. Five phylotypes were determined as structural gatekeepers in the microbiota network of Non-Severe cohort, ASV135_Lachnospiraceae_NK4A136 of which contributed most to the stability of the network. CONCLUSIONS: The relevant findings suggest that some gut bacteria could benefit the protective effect of LI10 on lowering the severity of rat liver damage. SIGNIFICANCE AND IMPACT OF THE STUDY: The bacteria benefiting the protective effects of potential probiotics could be further investigated for future clinical application.

Early gut colonization by Bifidobacterium breve and B. catenulatum differentially modulates eczema risk in children at high risk of developing allergic disease.

BACKGROUND: An altered compositional signature and reduced diversity of early gut microbiota are linked to development of allergic disease. We investigated the relationship between dominant Bifidobacterium species during the early post-natal period and subsequent development of allergic disease in the first year of life. METHODS: Faecal samples were collected at age 1 week, 1 month and 3 months from 117 infants at high risk of allergic disease. Bifidobacterium species were analysed by quantitative PCR and terminal restriction fragment length polymorphism. Infants were examined at 3, 6 and 12 months, and skin prick test was performed at 12 months. Eczema was diagnosed according to the UK Working Party criteria. RESULTS: The presence of B. catenulatum at 3 months was associated with a higher risk of developing eczema (ORadj = 4.5; 95% CI: 1.56-13.05, padj = 0.005). Infants colonized with B. breve at 1 week (ORadj = 0.29; 95% CI: 0.09-0.95, padj = 0.04) and 3 months (ORadj = 0.15; 95% CI: 0.05-0.44, padj = 0.00001) had a reduced risk of developing eczema. Furthermore, the presence of B. breve at 3 months was associated with a lower risk of atopic sensitization at 12 months (ORadj = 0.38; 95% CI: 0.15-0.98, padj = 0.05). B. breve colonization patterns were influenced by maternal allergic status, household pets and number of siblings. CONCLUSIONS: Temporal variations in Bifidobacterium colonization patterns early in life are associated with later development of eczema and/or atopic sensitization in infants at high risk of allergic disease. Modulation of the early microbiota may provide a means to prevent eczema in high-risk infants.

Co-Culture with Bifidobacterium catenulatum Improves the Growth, Gut Colonization, and Butyrate Production of Faecalibacterium prausnitzii: In Vitro and In Vivo Studies.

Faecalibacterium prausnitzii is a major commensal bacterium in the human gut. It produces short-chain fatty acids that promote intestinal health. However, the bacterium is extremely oxygen-sensitive, making it difficult to develop as a probiotic. To facilitate practical application of F. prausnitzii, we investigated factors that affect its growth and mammalian gut colonization. We evaluated cross-feeding interactions between F. prausnitzii and seven Bifidobacterium strains, and the anti-inflammatory properties of bacterial metabolites produced in co-culture, in vitro and in vivo. Co-culture of F. prausnitzii and Bifidobacterium catenulatum, with fructooligosaccharides as an energy source, resulted in the greatest viable cell-count and butyrate production increases. Further, the co-culture supernatant reduced the amount of proinflammatory cytokines produced by HT-29 cells and RAW 264.7 macrophages, an effect that was similar to that of butyrate. Furthermore, feeding mice both Faecalibacterium and Bifidobacterium enhanced F. prausnitzii gut colonization. Finally, feeding the co-culture supernatant decreased interleukin 8 levels in the colon and increased butyrate levels in the cecum in the dextran sodium sulfate-induced colitis mouse model. These observations indicate that the Faecalibacterium-Bifidobacterium co-culture exerts an anti-inflammatory effect by promoting F. prausnitzii survival and short-chain fatty acid production, with possible implications for the treatment of inflammatory bowel disease.

Complete genome sequence of Bifidobacterium catenulatum JCM 1194(T) isolated from human feces.

Bifidobacterium catenulatum JCM 1194(T) was isolated from human feces. This paper is the first report demonstrating the fully sequenced and completely annotated genome of a B. catenulatum strain.