Abstract
Lacticaseibacillus paracasei has beneficial effects on human health and holds promising potential as a probiotic for use in the development of functional foods, especially dairy products. This species can adapt to a variety of ecological niches and presents fundamental carbohydrate metabolism and tolerance to environmental stresses. However, the population structure, ecology, and antibiotic resistance of Lc. paracasei in diverse ecological niches are poorly understood. Reclassification of Lc. paracasei as a separate species of Lacticaseibacillus has stimulated renewed interest in its research, and a deeper interpretation of it will be important for screening strains beneficial to human health. Here, we collected 121 self-isolated and 268 publicly available Lc. paracasei genomes discussed how genomic approaches have advanced our understanding of its taxonomy, ecology, evolution, diversity, integrated prophage-related element distribution, antibiotic resistance, and carbohydrate utilization. Moreover, for the Lc. paracasei strains isolated in this study, we assessed the inducibility of integrated prophages in their genomes and determined the phenotypes that presented tolerance to multiple antibiotics to provide evidence for safety evaluations of Lc. paracasei during the fermentation processes.
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Data availability
In this study, the sequencing data generated for the 121 Lc. paracasei isolates were deposited in the NCBI Sequence Read Archive (SRA) under project no. PRJNA658852. The additional reference genomes used in this study were downloaded from the NCBI GenBank database. The accession numbers and related information for all individuals are listed in Supplementary Table S1.
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This work was supported by the National Key R&D Program of China (2021YFD2100700), the National Natural Science Foundation of China (Grant Nos. 31972086, 32172173), and the Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province.
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ZP performed bioinformatic analysis, prepared figures, and wrote the original main manuscript text; XL carried out experiments; SC, BY, and WL reviewed the manuscript. JZ, BM, and WC funded this research. All authors have read and agreed to the published version of the manuscript.
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Pei, Z., Li, X., Cui, S. et al. Population genomics of Lacticaseibacillus paracasei: pan-genome, integrated prophage, antibiotic resistance, and carbohydrate utilization. World J Microbiol Biotechnol 39, 280 (2023). https://doi.org/10.1007/s11274-023-03722-0
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DOI: https://doi.org/10.1007/s11274-023-03722-0