Phylogenetic analysis of lactic acid bacteria species from cheese: a comparison between taxonomy and physicochemical characteristics

Lactic acid bacteria (LAB) have a wide genetic potential and are applied in areas such as food production, intestinal health, and genetic engineering. Bioinformatics holds fundamental tools for the interpretation of genomic data, allowing for the understanding of DNA and its sequences. Thus, themilk cheese, using the genetic sequences of the 16S ribosomal gene and physicochemical characteristics (i.e., pH, [lactic acid] and antimicrobial activity against selected foodborne pathogens). Sequences of LAB identified as Loigolactobacillus coryniformis (2.5%), Leuconostoc mesenteroides (25%), Lactococcus lactis (25%), Lactococcus cremoris (10%), Lactiplantibacillus plantarum (2.5%), Lacticaseibacillus paracasei (20%), and Enterococcus faecalis (15%), were analysed in the R software, where a multiple sequence alignment was performed with the MSA package. Then, an identity matrix containing the squared root of the pairwise distances was calculated with the Seqinr package, which allowed for the identification of 3 main clusters, formed by the species Leuconostoc mesenteroides (s=12%), Lactococcus lactis (s=28%), and Lacticaseibacillus paracasei (s=26%). Moreover, a phylogenetic tree was built with the Neighbor-Joining method (R2 =0.98), which revealed moderate variability among sequences of the same species from the positions assumed in the cladogram. Additional descriptive statistics allowed the comparison between phylogenetic and taxonomic data. Results showed that LAB species Lactiplantibacillus plantarumpresented greater lactic acid production power (54.8 mg/100gDM) and inhibitory capacity against Listeria monocytogenes (mean inhibition halo at 10°C, 16.76mm and at 37°C, 9.33mm), Staphylococcus aureus (mean inhibition halo at 10°C, 14.46mm and at 37°C, 7.88mm), and Salmonella spp. (mean inhibition halo at 10°C, 10.63mm and at 37°C, 12.14mm). Finally, L. plantarum has been shown to present a diverse functional genome, which may account for its greater potential compared to all species analysed. Further research will yield more understanding of LAB's diverse metabolic and physiological characteristics.