Safety and efficacy concerns in Indian probiotics: Insights from whole-genome sequencing and in vitro assessment

Acute diarrhea remains a major public health challenge in India, particularly among children, where probiotics are commonly used as adjunctive therapy. However, concerns regarding the quality, safety, and regulatory oversight of commercial probiotic formulations persist. This study evaluated 13 probiotic products marketed in India for antibiotic susceptibility, gastrointestinal survivability, and safety. A combined in vitro and genomic approach was employed, including microbial enumeration, MALDI-TOF identification, MIC testing, time-kill assays, simulated gastrointestinal survival, and whole-genome sequencing to assess strain identity, antimicrobial susceptibility, antimicrobial resistance genes (ARGs), and virulence-associated determinants. Five of the 13 products showed discrepancies between labeled and laboratory-enumerated CFU counts, and some contained contaminants such as Enterococcus faecium. Several bacterial probiotics used outdated nomenclature (e.g., “LAB” or Lactobacillus sporogenes), inconsistent with current taxonomy. Bacterial probiotics were found to be susceptible to co-prescribed antibiotics, which may compromise their therapeutic persistence. Whole-genome sequencing identified multiple antimicrobial resistance determinants, including tet(L), erm(34), blaBCL-1, catA10, and ant(4′)-Ib. Among these, tet(L), catA10, and ant(4′)-Ib showed higher predicted potential for mobilization, supported by literature and the presence of insertion sequence elements in this study. In contrast, erm(34) and blaBCL-1 are generally considered chromosomally encoded intrinsic resistance determinants. In contrast, the yeast probiotic Saccharomyces boulardii is intrinsically resistant to antibacterial agents and shows superior gastrointestinal survivability. Overall, inconsistencies in labeling, composition, and genomic safety underscore the need for strain-level labeling, genomic validation, and stronger regulatory oversight to ensure probiotic quality and safety.