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
Open accessAbstract
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.
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Commercial probiotic products may contain ARGs or transferable resistance determinants, although the level of risk varies substantially among product types, bacterial taxa and analytical pipelines.
“Previous studies have shown that commercial probiotic products may contain ARGs or transferable resistance determinants, although the level of risk varies substantially among product types, bacterial taxa and analytical pipelines [15,16,17,18,19,20].”
From Integrated Phenotypic and Sequencing-Based Resistome Assessment of Antimicrobial Resistance Determinants in a Sample of Commercial Farm-Animal Probiotic Products (2026) · cites this paper as [18]
The Abstract (Results) reports drug-resistance genes in three commercial probiotic-product isolates and differing risk assessments for the taxa studied. But the Results (Genome instability) found no AMR genes on mobile genetic elements and characterized the resistance as intrinsic, not transferable. The paper also does not establish that risk varies by analytical pipeline or systematically compare product types. (LLM, conf=0.88)
Experimental — accuracy not yet measuredProbiotic products and probiotic-associated taxa may carry detectable ARGs, but public-health relevance depends on taxon identity, gene function, genomic context and mobility potential rather than on ARG counts alone.
“previous studies have shown that probiotic products and probiotic-associated taxa may carry detectable ARGs, but that public-health relevance depends on taxon identity, gene function, genomic context and mobility potential rather than on ARG counts alone [15,16,17,18,22,23].”
Commercial probiotic products may require independent identity verification and strain-level confirmation in addition to ARG screening.
“they agree with previous reports that commercial probiotic products may require independent identity verification and strain-level confirmation in addition to ARG screening [18,26]”
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- Authors
- Wang, Y., Liang, Q., Lu, B., Shen, H., Liu, S., Shi, Y., Leptihn, S., Li, H., Wei, J., Liu, C., Xiao, H., Zheng, X., Liu, C., & Chen, H.
- Affiliations
- National Medical Products Administration (CN)
- Sir Run Run Shaw Hospital (CN)
- ZheJiang Institute For Food and Drug Control (CN)
- Corresponding author
- Liu, Chengzhi
- Liu, Chao
- Chen, Huan
- Venue
- BMC Genomics
- Published
- 2021-03-24
- Volume
- 22
- Issue
- 1
- Pages
- 210-210
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC7988973
- OpenAlex
- W3137748009
- Cited by
- 88
- References
- 59
- Citations by year
- 2026: 21 · 2025: 18 · 2024: 18 · 2023: 17 · 2022: 13 · 2021: 1
- FWCI
- 7.31
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Natural Science Foundation of Liaoning Province
- Science and Technology Department of Zhejiang Province (LGN20C050001, 2020C03123)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- probiotic safety, antimicrobial resistance genes, virulence genes, multidrug resistance, Lactobacillus rhamnosus, Bifidobacterium animalis subsp. lactis, Enterococcus faecium, Enterococcus faecalis, comparative genomics, probiotic quality control, health risks
- MeSH terms
- Anti-Bacterial Agents, Humans, Enterococcus faecium, Probiotics, Drug Resistance, Bacterial, Virulence Factors
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