Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota

Abstract

Phage predation is one of the key forces that shape genetic diversity in bacterial genomes. Phages are also believed to act as modulators of the microbiota composition and, consequently, as agents that drive bacterial speciation in complex bacterial communities. Very little is known about the occurrence and genetic variability of (pro)phages within the Bifidobacterium genus, a dominant bacterial group of the human infant microbiota. Here, we performed cataloguing of the predicted prophage sequences from the genomes of all currently recognized bifidobacterial type strains. We analysed their genetic diversity and deduced their evolutionary development, thereby highlighting an intriguing origin. Furthermore, we assessed infant gut microbiomes for the presence of (pro)phage sequences and found compelling evidence that these viral elements influence the composition of bifidobacterial communities in the infant gut microbiota.

The Sortase-Dependent Fimbriome of the Genus Bifidobacterium: Extracellular Structures with Potential To Modulate Microbe-Host Dialogue

“…The presence of bifidobacterial sequences within these samples has previously been evaluated, highlighting a higher abundance of bifidobacterial genes in healthy children compared to children treated with antibiotics and preterm infants (45,48). Our analyses demonstrated the presence of both bifidobacterial COPGs and PEL across these different metagenomic data sets (Fig.…”

Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission

“…Thus, we searched shotgun metagenomics data, obtained from stool samples of various mother and corresponding child and milk sample sets, for sequences that matched with known bacteriophages infecting bifidobacteria, i.e., bifidophages [24], focusing on datasets in which we had already identified bifidobacterial transmission. In order to identify the presence of both bifidophages as well as bifidoprophages, we scanned all obtained metagenomic datasets using a previously developed bioinformatics pipeline [11, 34].…”

“…Contigs attributed to bifidobacterial (sub)species, by means of the CoCla script, were screened for the presence of bifidobacterial phages/prophages using a custom database composed of previously identified bifidophages [24]. Identified phage sequences were further manually curated in order to unveil overlapping extremities within the contig sequences.…”

“…Currently, very little is known about the infant virome [21–23], although the existence and impact of phages specific for bifidobacteria, i.e., bifidophages, in the infant gut has recently been discribed [24]. …”

The Bacterial Microbiome and Virome Milestones of Infant Development

“…Bacteriophage predation has been observed in the infant gut between bifidobacteria species and bifidoprophages [74]. While the classical predator-prey model predicts that prey (bacteria) oscillations precede predator (bacteriophage) oscillations, bacteriophage-bacteria interactions during early infant development begin with the opposite dynamics.…”