Cultural and metagenomic insights of halophilic and halotolerant bacteria in cheese rinds

Halophilic and halotolerant bacteria are usually reported as living in natural environments, although they may also be isolated from food, such as cheese. In cheese, these salt-loving were characterized hitherto occasionally and, consequently, studies about their technological functions are scarce. Therefore, we selected thirteen cheese rinds to characterize systematically these microorganisms by cultural methods, using different salt-based media. Indeed, we identified 35 strains with unique 16S rRNA and rpoB sequences, whose whole-genome was sequenced. Among these isolates, we obtained six B. aurantiacum and three S. equorum strains and we demonstrated their genetic diversity through pan-genome analysis with their respective genomes available in the database. Additionally, based on Average Nucleotide Identity analysis, we obtained ten potential new halophilic species, of which the majority (8) belonged to the Gram-negative group. The availability of these genomic sequences opens the possibility to detect and quantify their presence in metagenomic data, which allowed investigate the representativeness of 66 halophilic and halotolerant bacteria species (26 isolated herein and 40 supplementary genomes) in 74 cheese rind metagenomes. Interestingly, genera such as Halomonas, Psychrobacter and Pseudoalteromonas have proven abundant in cheese produced in different countries and, in particular, in washed cheese rinds. Finally, correlation analysis reveals that several halophilic species are often co-occurring, suggesting their interactions form a complex ecosystem allowing their mutual development.