Feasibility of genome-wide screening for biosafety assessment of probiotics: A case study of Lactobacillus helveticus MTCC 5463
Abstract
Recent years have witnessed an explosion in genome sequencing of probiotic strains for accurate identification and characterization. Regulatory bodies are emphasizing on the need for performing phase I safety studies for probiotics. The main hypothesis of this study was to explore the feasibility of using genome databases for safety screening of strains. In this study, we attempted to develop a framework for the safety assessment of a potential probiotic strain, Lactobacillus helveticus MTCC 5463 based on genome mining for genes associated with antibiotic resistance, production of harmful metabolites, and virulence. The sequencing of MTCC 5463 was performed using GS-FLX Titanium reagents. Genes coding for antibiotic resistance and virulence were identified using Antibiotic Resistance Genes Database and Virulence Factors Database. Results indicated that MTCC 5463 carried antibiotic resistance genes associated with beta-lactam and fluoroquinolone. There is no threat of transfer of these genes to host gut commensals because the genes are not plasmid encoded. The presence of genes for adhesion, biofilm, surface proteins, and stress-related proteins provides robustness to the strain. The presence of hemolysin gene in the genome revealed a theoretical risk of virulence. The results of in silico analysis complemented the in vitro studies and human clinical trials, confirming the safety of the probiotic strain. We propose that the safety assessment of probiotic strains administered live at high doses using a genome-wide screening could be an effective and time-saving tool for identifying prognostic biomarkers of biosafety.
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Senan et al. in 2015 showed that genomic screening using specialized databases can identify antibiotic resistance genes and virulence factors, saving time and covering safety aspects costly to cover using traditional clinical trial methods.
“For example, Senan et al., in 2015, showed that genomic screening using specialized databases can identify antibiotic resistance genes and virulence factors, saving time and covering safety aspects that are costly to cover using traditional clinical trial methods [16,154].”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [154]
High variability of biological datasets on different sequence determination platforms causes problems with reliability of source data, underestimating the accuracy of AI models.
“For example, the high variability of biological datasets on different platforms for sequence determination causes problems with the reliability of the source data, which undoubtedly underestimates the accuracy of the AI model [154,172].”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [154]
Although LAB are generally regarded as safe, there are rare cases of the emergence of infections and antibiotic resistance by certain probiotics.
“Although LAB are GRAS, there are rare cases of the emergence of some infections and antibiotic resistance [18].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [18]
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- Authors
- Senan, S., Prajapati, J. B., & Joshi, C. G.
- Affiliations
- South Dakota State University (US)
- Anand Agricultural University (IN)
- Corresponding author
- Senan, S.
- Venue
- Probiotics and Antimicrobial Proteins
- Published
- 2015-07-30
- Volume
- 7
- Issue
- 4
- Pages
- 249-258
- ISSN
- 1867-1306 (ISSN-L)
- 1867-1314
- OpenAlex
- W2181984099
- Cited by
- 46
- References
- 43
- Citations by year
- 2025: 5 · 2024: 5 · 2023: 6 · 2022: 8 · 2021: 4 · 2020: 5 · 2019: 3 · 2018: 2 · 2017: 6 · 2016: 2
- FWCI
- 4.45
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Probiotics and Antimicrobial Proteins (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Indian Council of Agricultural Research
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- antibiotic resistance genes, beta-lactam resistance, fluoroquinolone resistance, virulence factors, hemolysin gene, adhesion genes, biofilm genes, probiotic regulation
- MeSH terms
- Consumer Product Safety, Feasibility Studies, Hemolysin Proteins, Virulence, Genome, Bacterial, Probiotics, Drug Resistance, Bacterial, Databases, Genetic, Lactobacillus helveticus
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