Genomic Insights into Bifidobacteria

Abstract

SUMMARY Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.

Multi-Loci Gene Sequencing and Identification of Bifidobacteria Strains Isolated from Dairy and Pharmaceutical Sources in South Africa

“…The guanine-cytosine (G + C) content of the Bifidobacterium strains was in the range of 59-65.29%. The average G + C content for bifidobacteria is 55-67% (Lee and O'Sullivan, 2010), implying that the genes were not acquired recently. The three concatenated protein-coding genes (clpC, PurF, and dnaG) had a better selection potential than the 16S rRNA gene to purify the strains on the basis of a more negative Tajima test statistic (D).…”

Expression of Fluorescent Proteins in Bifidobacteria for Analysis of Host-Microbe Interactions

“…Natural habitats of the members of the genus Bifidobacterium include food, sewage, and oral cavities, but the most important ecological niche of bifidobacteria is the intestinal tract of humans and animals (2). Some strains of bifidobacteria have been associated with beneficial effects on the health status of the host and have thus attracted considerable interest by the food and dairy industries.…”

“…Some strains of bifidobacteria have been associated with beneficial effects on the health status of the host and have thus attracted considerable interest by the food and dairy industries. Some of the beneficial effects that have been claimed to be related to the presence or administration of bifidobacteria are cholesterol reduction, improvement of lactose intolerance, alleviation of constipation, and immunomodulation (2)(3)(4). Two of the more promising targets for bifidobacterial treatments are amelioration of chronic intestinal inflammation (5)(6)(7)(8)(9)(10) and protection against infections with enteric pathogens (11)(12)(13).…”

“…While some progress has been made in improving transformation efficiencies, directed gene inactivation, and transposon mutagenesis for single strains (19,20), the vast majority of strains of interest remain difficult if not impossible to modify genetically. Moreover, the available vector systems for bifidobacteria have a rather limited host range (i.e., replicons function only in some species of the genus Bifidobacterium but not in others), and expression systems are poorly developed (2,21).…”

Complete Genome Sequence of Bifidobacterium bifidum S17

“…In order to unravel the molecular mechanisms responsible for these beneficial effects, several bifidobacterial strains have recently been sequenced (17). However, while the genus Bifidobacterium comprises 31 species with nine subspecies, at present only nine whole-genome sequences of four species and two subspecies are publically available (9).…”