Exploring endogenous lactic acid bacteria potential: Isolation to genetic insights on aromatic compounds

This study aimed to explore the technological potential of endogenous lactic acid bacteria (LAB) isolated from milk and cheese produced in São Paulo, Brazil, for use in the preparation of fermented dairy products. A total of 562 microorganisms were isolated, with Lacticaseibacillus rhamnosus and Enterococcus faecalis being the predominant species. Among these, 169 isolates were characterized for their technological properties, and Principal Component Analysis (PCA) was applied to rank the most promising strains. Based on this analysis, 43 isolates were selected and evaluated for acidification potential, autolysis, antimicrobial activity, antibiotic susceptibility, and aromatic compound production. Lactobacillus delbrueckii CTR1 exhibited the highest acidification potential (ΔpH 1.00). Lacticaseibacillus rhamnosus JLR3 displayed strong antimicrobial activity, particularly against Salmonella Enteritidis and Staphylococcus aureus, while Enterococcus faecium ITR5 was effective against Escherichia coli. The aromatic compound profile of fermented milks led to the selection of Lacticaseibacillus rhamnosus AQTR10 and Enterococcus xinjiangensis AQLM2 for sequencing and functional characterization. These strains were shown to produce diacetyl (butane-2,3-dione), acetoin (3-hydroxy-butan-2-one), acetic acid (ethanoic acid), and acetaldehyde (ethanal). Functional annotation revealed that L. rhamnosus possesses the genetic machinery for diacetyl and acetoin biosynthesis via the citrate pathway, as well as for acetaldehyde and acetic acid production through an aldehyde dehydrogenase-encoding gene. In E. xinjiangensis, genetic evidence for acetaldehyde biosynthesis was identified. These findings suggest that the two LAB strains isolated from dairy samples in southeastern Brazil hold promise as adjunct cultures for fermented dairy product development.