Exploratory In Vitro Evaluation of Maternal–Infant Bifidobacterium Strains for Microbiota Modulation in a Pediatric Cystic Fibrosis Context

This study explores the potential of novel <i>Bifidobacterium</i> isolates as targeted probiotic supplements for children with cystic fibrosis (CF), a condition often associated with gut dysbiosis. Five strains of <i>Bifidobacterium</i> genus (<i>B</i>. <i>animalis</i> IATA01, <i>B</i>. <i>pseudocatenulatum</i> IATA35, <i>B</i>. <i>longum</i> IATA02, <i>B</i>. <i>bifidum</i> IATA13, and <i>B</i>. <i>longum</i> IATA05) isolated from maternal-infant fecal samples were assessed in vitro following the FAO/WHO guidelines. Their probiotic potential was evaluated through simulated gastrointestinal digestion in the CF context, their adhesion to mucin, and their carbohydrate fermentation capacity. Additionally, their impact on colonic microbiota modulation was analyzed using static in vitro colonic fermentation with fecal inocula from four pediatric patients with CF to assess the presence of different bacterial groups associated with dysbiosis via qPCR and short-chain fatty acid production by GC-MS. Three strains (IATA01, IATA35, and IATA05) demonstrated survival after gastrointestinal digestion, with IATA01 exhibiting the highest adhesion to mucin but limited carbohydrate fermentation capacity. All strains increased the <i>Bifidobacterium</i> levels after colonic fermentation, while their effects on reducing pathogenic groups and promoting beneficial bacteria such as <i>Akkermansia</i> and <i>Faecalibacterium</i> varied depending on the strain and the individual inoculum. These findings highlight the strain-specific effects of <i>Bifidobacterium</i> and evidence a specific impact on colonic microbiota, depending on the composition of the basal inoculum, highlighting individual-specific responses.