IDDF2023-ABS-0308 Whole-genome comparative analysis of enterococcus lactis revealed its ability to lactic acid and multiple vitamins biosynthesis as a potential probiotic

Background

Enterococcus lactis was reported to be able to adhere to intestinal epithelial cell lines efficiently and protect against hepatotoxicity. However, most strains of E. lactis were isolated from fermented dairy products, and the characteristics of human-sourced E. lactis are largely unclear. Here, we analyzed probiotic characteristics and evaluated the safety of strains isolated from the faeces of a large cohort of healthy people on the genomic level.

Methods

Faecal samples from 184 healthy donors were collected and cultured in an anaerobic chamber. Based on 16S amplicon sequencing taxonomy identification, DNAs of clones were extracted and deeply sequenced. Then, assembled genomes of strains were performed taxonomic classification and functional annotations by aligning to Genome Taxonomy Database and EggNOG Database respectively. To evaluate the safety of those strains, antibiotic resistance and virulence factor genes were annotated.

Results

Genomes from cultured clones were clustered into 7 strains based on the average nucleotide identity with a cutoff of 99%. We found 1964 core genes and an average of 633 unique genes for each strain from a total of 4986 genes by comparative analysis. The functions of core genes focus on lactic acid production pathways (including galactose and D-galacturonate degradation), vitamin production pathways (riboflavin, biotin, cobalamin, and ascorbate biosynthesis pathways), and antibiotic resistance pathways (beta-lactam and vancomycin resistance). Interestingly, the distribution of unique genes was strain specificity. We found that besides the common D-galactonate degradation pathway, two strains encoded a novel D-galactonate degradation pathway (De Ley-Doudoroff pathway), which suggested these two strains may degrade D-galacturonate more effectively and may have better hepatotoxicity protection ability. Moreover, some antibiotic resistance genes and virulence factor genes also showed strain specificity, especially for genes ErmB, earAv, acm, and sgrA. Of all the 14 plasmids found in these strains, the plasmid-5 that carried a mobilization gene mobC was the most widespread.

Conclusions

Our results reveal that two human-sourced E. lactis strains have the potential superiority of becoming probiotics for their lactic acid production and multiple vitamin biosynthesis ability. Further assessments are also needed for drug resistance and virulence factor affection caused by these strains.