Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum

Abstract

Members of genus Bifidobacterium are Gram-positive bacteria, representing a large part of the human infant microbiota and moderately common in adults. However, our knowledge about their diversity, intraspecific phylogeny and long-term persistence in humans is still limited. Bifidobacterium longum is generally considered to be the most common and prevalent species in the intestinal microbiota. In this work we studied whole genome sequences of 28 strains of B. longum, including 8 sequences described in this paper. Part of these strains were isolated from healthy children during a long observation period (up to 10 years between isolation from the same patient). The three known subspecies (longum, infantis and suis) could be clearly divided using sequence-based phylogenetic methods, gene content and the average nucleotide identity. The profiles of glycoside hydrolase genes reflected the different ecological specializations of these three subspecies. The high impact of horizontal gene transfer on genomic diversity was observed, which is possibly due to a large number of prophages and rapidly spreading plasmids. The pan-genome characteristics of the subspecies longum corresponded to the open pan-genome model. While the major part of the strain-specific genetic loci represented transposons and phage-derived regions, a large number of cell envelope synthesis genes were also observed within this category, representing high variability of cell surface molecules. We observed the cases of isolation of high genetically similar strains of B. longum from the same patients after long periods of time, however, we didn’t succeed in the isolation of genetically identical bacteria: a fact, reflecting the high plasticity of microbiota in children.

Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum

“…longum revealed a common origin for the 12 strains and also reflected divergent evolution into four distinct clusters based on iterative spacer acquisition events (Figure 5B ). Noteworthy, cluster i includes two closely related strains, B longum 44B and 1-6B, isolated from the same Russian infant (child 1) during the first year of life and 5 years later, respectively (Shkoporov et al, 2013 ; Chaplin et al, 2015 ). These two strains share ancestral and recently acquired spacers in their type II-C CRISPR systems (Figure 5 ) and also in Type I-E, though there are differences in recently acquired spacers in the latest timepoint (Figure 6 ).…”

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

“…This can directly influence the degree by which phylogenetic relatedness conveys competitive interactions among members of the human gut microbiome. Most bacterial species, including B. longum, possess pan-genomes with individual strains displaying variation in genomic content (Chaplin et al, 2015;O'Callaghan et al, 2015). Horizontal gene transfer can further lead to similar genetic information being shared among bacterial taxa that are not closely related, resulting in phylogenetically distant taxa with similar traits (Boto, 2010).…”

Bifidobacteria and Their Role as Members of the Human Gut Microbiota

“…Although, they do not encode the same HMO catabolic arsenal found in B. bifidum and B. longum subsp. infantis, they can degrade certain HMOs and may also scavenge on carbohydrates that are released by other (bifido)bacteria (Egan et al, 2014a ; Chaplin et al, 2015 ). After weaning the composition of the bifidobacterial population changes toward species capable of adapting to the metabolism of plant-derived sugars.…”