Bacterial diversity of traditional Fossa (pit) cheese and its ripening environment

Bacterial diversity of Fossa (pit) cheese during ripening and its related environment was investigated by culture-dependent and -independent methods. The dominant clones during cheese ripening, among 244 16S rRNA genes (rDNA), belonged to Firmicutes (99%) mainly affiliated with Lactococcus lactis and Streptococcus thermophilus starter species. Sequencing of 16S rDNA from 171 isolates cultured in M17 and MRS media showed an increasing occurrence of non-starter lactic acid bacteria (NSLAB) during ripening such as Lactobacillus plantarum, Lactobacillus casei, Lactobacillus paracasei, Lactobacillus fermentum, Lactobacillus rhamnosus. A greater diversity of NSLAB was found in the isolates than in the clone library. L. plantarum was the dominant species in Fossa cheese (42.9%). Bacterial species identified from pit air and surface samplings (271 clones, 63 strains) revealed 40 different operational taxonomic units belonging to seven taxonomic affiliations: Actinobacteria, Firmicutes, Bactereoidetes, α-, β-, γ-, δ-Proteobacteria; however, no evidence for environmental strains within the Fossa cheese was found.