Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon

Abstract

Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum , B. longum subsp. infantis and B. longum subsp. suis . Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.

Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants

“…suis . This designation still stands today confirmed by numerous pangenomic analysis of the clade 57 , 58 . Although the shortened term “ B. infantis ” is still routinely used in the scientific literature to refer to the subspecies, the official name is Bifidobacterium longum subsp.…”

Gut microbe metabolism of small molecules supports human development across the early stages of life

“…Notably, among the microbial metabolic activities almost exclusively present in the first year after birth (age groups A, B, and C), we found enzymes for the metabolism of milk-derived compounds, such as D-tagatose (monosaccharide; EC number 4.1.2.40), ethanolamine (amino alcohol; EC number 4.3.1.7), N-Acteylglucosamine and Lacto-N-biose (Nglycans; EC numbers 3.2.1.52 and 3.2.1.140) (Figure 1B and Supplementary Table 3). On average, their abundances progressively decreased from 0.011% in age group A to 0.0053% in age group C, in accordance with the presence of a 1-year-lasting milk-adapted microbiota (Zhou et al, 2018;Tarracchini et al, 2021b;Campbell et al, 2022). Otherwise, microbial functions involved in amino acids metabolism, including L-threonine, L-isoleucine, L-valine, and L-methionine biosynthesis (EC numbers 4.2.3.1, 4.2.1.9, and 2.5.1.48), as well as L-tryptophan catabolism with indole biosynthesis (EC number 4.2.1.20) were highly represented in the growing infants (mainly from a few days to 1 year of age) while maintaining their relevance also in the adult population (Figure 1B and Supplementary Table 3).…”

The Integrated Probiotic Database: a genomic compendium of bifidobacterial health-promoting strains

“…Subsequently, for each bifidobacterial chromosome, the genomic regions flanking the putative pGTF were investigated to identify EPS-encoding key genes (such as glycosyltransferases, flippases, ABC transporters, and carbohydrate precursor biosynthesis/modification enzymes). The presence of putative virulence genes and bile salt hydrolases were identified through sequence similarity (homology) search in the Virulence Factor Database [28] and in the protein sequence NCBI database, respectively (cutoff E value of 1 × 10 -5 ). Thus, the resulting hits were manually inspected to remove false positives.…”