Whole genome sequencing for the risk assessment of probiotic lactic acid bacteria

Abstract

Probiotic bacteria exhibit beneficial effects on human and/or animal health, and have been widely used in foods and fermented products for decades. Most probiotics consist of lactic acid bacteria (LAB), which are used in the production of various food products but have also been shown to have the ability to prevent certain diseases. With the expansion of applications for probiotic LAB, there is an increasing concern with regard to safety, as cases with adverse effects, i.e., severe infections, transfer of antimicrobial resistance genes, etc., can occur. Currently, in vitro assays remain the primary way to assess the properties of LAB. However, such methodologies are not meeting the needs of strain risk assessment on a high-throughput scale, in the context of the evolving concept of food safety. Analyzing the complete genetic information, including potential virulence genes and other determinants with a negative impact on health, allows for assessing the safe use of the product, for which whole-genome sequencing (WGS) of individual LAB strains can be employed. Genomic data can also be used to understand subtle differences in the strain level important for beneficial effects, or protect patents. Here, we propose that WGS-based bioinformatics analyses are an ideal and cost-effective approach for the initial in silico microbial risk evaluation, while the technique may also increase our understanding of LAB strains for food safety and probiotic property evaluation.

Keywords:

• Lactic acid bacteria
• probiotics
• safety
• risk assessment
• whole-genome sequencing
• high-throughput sequencing

Acknowledgements

We thank Baikui Wang for his help in the preparation of the manuscript. All the authors also would appreciate the critical reading and language editing by Dr. Reshma B Nambiar and Prof. Sebastian Leptihn from Zhejiang University-University of Edinburgh Institute.

Authors’ contributions

Conceptualization, M.Y.; writing—original draft preparation, X.P.; writing—review and editing, X.P., A.E-D.; supervision, M.Y.; funding acquisition, M.Y. All authors have read and agreed to the published version of the manuscript.

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

This research was funded by National Program on Key Research Project of China (2019YFE0103900) as well as European Union’s Horizon 2020 Research and Innovation Programme (861917–SAFFI).