Genomic insights into the beneficial potential of Bifidobacterium and Enterococcus strains isolated from Cameroonian infants

A healthy early-life gut microbiota plays an important role in maintaining immediate and long-term health. Perturbations, particularly in low-to middle-income communities, are associated with increased infection risk. Thus, a promising avenue for restoring a healthy infant microbiota is to select key beneficial bacterial candidates from underexplored microbiomes for developing new probiotic-based therapies. This study aimed to recover bifidobacteria and lactic acid bacteria from the faeces of healthy Cameroonian infants and unravel the genetic basis of their beneficial properties. Faecal samples were collected from 26 infants aged 0–5 months recruited in Dschang (Cameroon). Recovered bacterial isolates were subjected to whole-genome sequencing and in silico analysis to assess their potential for carbohydrate utilization, their antimicrobial capacities, host-adaptation capabilities and their safety. From the range of infant-associated Bifidobacterium and Enterococcus strains identified, Bifidobacterium species were found to harbour putative gene clusters implicated in human milk oligosaccharide metabolism. Genes linked to the production of antimicrobial peptides such as class IV lanthipeptides were found in Bifidobacterium pseu-docatenulatum, while those implicated in biosynthesis of cytolysins, enterolysins, enterocins and propeptins, among others, were identified in enterococci. Bifidobacterial isolates did not contain genes associated with virulence; however, we detected the presence of putative tetracycline resistance genes in several strains belonging to Bifidobacterium animalis subsp. lactis and Bifidobacterium longum subsp. longum. Among the enterococci, Enterococcus mundtii PM10 did not carry any genes associated with antimicrobial resistance or virulence. The latter, together with all the Bifidobacterium strains, also encoded several putative adaptive and stress-response-related genes, suggesting robust gastroinstestinal tract colonization potential. This work provides the first genomic characterization of Bifidobacterium and Enterococcus isolates from Cameroonian infants. Several strains showed the genomic potential to confer beneficial properties. Further phenotypic and clinical investigations are needed to confirm their suitability as customized probiotics.