Isolation and Characterization of Bifidobacterium longum A1, an Isolate from Faeces of an Exclusively Breast-fed Infant with Probiotic Potential

Microbial colonization of the newborn (primocolonization) plays a crucial role in the development of digestive, metabolic, and immune systems. Disruptions may impair intestinal barrier function and raise the risk of chronic diseases like inflammatory bowel disease, allergies, and obesity. Recent evidence suggests probiotic supplementation in infants may help counter or prevent these effects. This study isolates and characterizes potential probiotic candidates from the gut microbiota of exclusively breastfed infants. Bifidobacterium and Lacticaseibacillus strains were selectively isolated and initially characterized in vitro. To evaluate their ability to reach the colon intact, we assessed their growth and bile tolerance. Strains safety was evaluated in vitro by determining antibiotic resistance profiles, DNase, and β-hemolytic activities. Additionally, their potential effects on the intestinal barrier and their ability to modulate the immune response were assessed in order to highlight potential probiotic functionality. The most promising strains underwent further characterizations. We performed whole genome sequencing (WGS) analysis to examine transferable antibiotic resistance, virulence factors, toxicity, and biogenic amine formation, thereby confirming the safety of the strains. Bile salt hydrolase (BSH) and glycoside hydrolase (GH) genes were also investigated. Furthermore, we explored the ability of certain strains to ferment human milk oligosaccharides (HMOs) and engage in cross-feeding interactions. The study showed that isolated strains exhibit probiotic traits such as acid and bile resistance, immunomodulatory potential, and strong safety with no detected virulence or resistance genes. Bifidobacterium longum A1 stood out for its metabolic strength, safety, ability to degrade human milk oligosaccharides, and support beneficial cross-feeding.