Bifidobacteria: General Overview of Ecology, Taxonomy, and Genomics

Bifidobacteria were originally identified from stool samples of breast-fed infants in 1899 by Tissier, and termed Bacillus bifidus. Glycobiomes of bifidobacterial species typical of the infant gut are enriched in growth hormone families that are essential for host-glycan degradation, such as those representing exo-sialidases, fucosidases, hexosaminidase, and lacto-N-biosidase activities. Commensals such as bifidobacteria must coexist with their host and must evade or survive the diversity of responses that the host will generate to combat and eradicate unwanted and pathogenic bacteria. Focusing on the human intestine, it is now widely accepted that there is also a specialization of bifidobacterial species according to an individual’s age. Milk-mediated transmission of certain bifidobacterial strains may be supported by their ability to utilize human milk oligosaccharides (HMOs) and/or HMO-derived glycans. The availability of large amounts of information obtained from comparative genomic studies, allowed the prediction of complete metabolic pathways in the so far know bifidobacterial (sub)species through the use of Pathway tools software.