Whole-Genome Analysis and Tolerance Assessment on Bifidobacteria-like Bacteria Isolated from Breast Milk and Infant Fecal Samples in Indonesia

Probiotics are living microorganisms that can provide health benefits to the host when administered in sufficient quantities. To exert their health effects, probiotics must first be capable of surviving the harsh conditions of the gastrointestinal tract. We decided to sequence whole genomes of Bifidobacteria-like isolates (i.e., BS2-PS1, BS2-PS2, BS2-PB5, and BR2-12) and assess their abilities to resist low pH and bile salt. Molecular identification through whole genome sequencing indicated that the bacteria isolated from human breast milk were identified as Bifidobacterium breve (BS2-PS1 and BS2-PS2) and Lacticaseibacillus paracasei subspecies paracasei (BS2-PB5), whereas the bacteria isolated from infant feces was identified as Lactiplantibacillus plantarum (BR-12). All isolates exhibited resilience upon exposure to bile salts at concentrations of 0%, 0.3%, and 0.5%, with survival observed even at the highest concentration (0.5%) after three hours of incubation. The ability to withstand bile salt was presumably mediated by various genes that encode the resistance, e.g., bsh, cbh, dps, glf, cfa, or nagB, found in genomes of tested isolates. Upon exposure to pH 2 and 5 for three hours, BS2-PS1, BS2-PS2, and BR-12 exhibited acid resistance as well. The ability to withstand low pH could be mediated by the presence of relevant genes, e.g., argC, argH, dapA, pyk, pyrG, as well as genes that encode F0F1-ATPase enzyme, such as atpC, atpB, atpE, atpF, atpH, atpA, atpG, and atpD in their genomes. In summary, these results indicated the potential of all isolates to be further developed as probiotic candidates.