Abstract
Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects. Carbohydrates are considered key carbon sources for the gut microbiota, imposing strong selective pressure on the complex microbial consortium of the gut. Despite its importance, the genetic traits that facilitate carbohydrate utilization by gut microbiota members are still poorly characterized. Here, genome analyses of 47 representative Bifidobacterium (sub)species revealed the genes predicted to be required for the degradation and internalization of a wide range of carbohydrates, outnumbering those found in many other gut microbiota members. The glycan-degrading abilities of bifidobacteria are believed to reflect available carbon sources in the mammalian gut. Furthermore, transcriptome profiling of bifidobacterial genomes supported the involvement of various chromosomal loci in glycan metabolism. The widespread occurrence of bifidobacterial saccharolytic features is in line with metagenomic and metatranscriptomic datasets obtained from human adult/infant faecal samples, thereby supporting the notion that bifidobacteria expand the human glycobiome. This study also underscores the hypothesis of saccharidic resource sharing among bifidobacteria through species-specific metabolic specialization and cross feeding, thereby forging trophic relationships between members of the gut microbiota.
Highlights
Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects
Results showed that the average abundance of the carbohydrate metabolism functional family in Human Microbiome Project (HMP) metagenomic datasets is 8.0%, being 58% lower than the abundance detected in the bifidobacterial pan-genome, i.e. 13.7% (Fig. S1)
Comparison of the glycobiome identified in the genus Bifidobacterium with those identified in other members of the human gut microbiota revealed their unique and important contribution in terms of glycosyl hydrolases (GH) involved in the breakdown of complex plant carbohydrates such as arabinoxylan, galactan and starch
Summary
Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects. Genome analyses of 47 representative Bifidobacterium (sub)species revealed the genes predicted to be required for the degradation and internalization of a wide range of carbohydrates, outnumbering those found in many other gut microbiota members. Non-digestible carbohydrates derived from the diet, together with host-produced glycans found in the mammalian gut represent critical energy sources believed to be responsible for the survival and proliferation of many microbial components of the gut microbiota, including bifidobacteria[6]. We describe an analysis of the genomes and transcriptomes of representatives of all 47 (sub)species that are currently assigned to the Bifidobacterium genus, predicting bifidobacterial genome-based strategies for carbohydrate metabolism that impact on the overall glycobiome of the gut microbiota and host, while being pivotal for the establishment of trophic relationships between members of gut microbiota
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