Abstract
Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.
Highlights
Among the lactic acid bacteria, Lactobacillus is the prominent genus, which presently embraces more than 200 species [1]
The Average Nucleotide Identity (ANI) values are found to be around 98% and Amino Acid Identity (AAI) values varied from 97% to 99% with L. paracasei (n = 74) strains (Supplementary Figure S1 and Supplementary Table S1)
We reassembled and analyzed gut isolated Lbs2 strains earlier identified as L. casei species and placed it under the L. paracasei species, after careful genomic analysis
Summary
Among the lactic acid bacteria, Lactobacillus is the prominent genus, which presently embraces more than 200 species [1]. These species are commonly found in a wide variety of niches (e.g., the gastrointestinal tract, fruit, vegetables, wine, milk, and meat), including the complex microbial community. These bacteria are widely used in many biotechnological applications, e.g., as a vaccine carrier, in bioplastic production, as probiotics, or as starter cultures, indicating their high commercial value [1]. In this study, we did extensive analysis to place the species in their respective corrected taxa
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