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Background  Safety issues of probiotic products have been reported frequently in recent years. Ten bacterial strains isolated from seven commercial probiotic products on market were evaluated for their safety, by whole-genome analysis.    Results  We found that the bacterial species of three probiotic products were incorrectly labeled. Furthermore, six probiotic product isolates (PPS) contained genes for the production of toxic metabolites, while another three strains contained virulence genes, which might pose a potential health risk. In addition, three of them have drug-resistance genes, among which two strains potentially displayed multidrug resistance. One isolate has in silico predicted transferable genes responsible for toxic metabolite production, and they could potentially transfer to human gut microflora or environmental bacteria. Isolates of  Lactobacillus rhamnosus  and  Bifidobacterium animalis  subsp.  lactis  are associated with low risk for human consumption. Based on a comparative genome analysis, we found that the isolated  Enterococcus faecium  TK-P5D clustered with a well-defined probiotic strain, while  E. faecalis  TK-P4B clustered with a pathogenic strain.    Conclusions  Our work clearly illustrates that whole-genome analysis is a useful method to evaluate the quality and safety of probiotic products. Regulatory quality control and stringent regulations on probiotic products are needed to ensure safe consumption and protect human health.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07539-9.

bmc genomics

Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks