Profiling of bacterial and fungal communities of Mexican cheeses by high throughput DNA sequencing

Abstract

Cheese is a live food whose preparation involves procedures and microbial communities playing an important role for the final product. We characterized the bacterial and fungal diversity of seventeen different Mexican cheeses by high-throughput DNA sequencing of 16S/18S rDNA libraries. We propose the existence of bacterial and fungal core communities, where at genera level, bacteria include Streptococcus spp., Lactococcus spp., Lactobacillus spp., Aerococcus spp., and Weisella spp. while at species level, the fungal community includes Galactomyces reessii, Scheffersomyces stipitis, Saccharomyces cerevisiae (baker's yeast), and S. cerevisiae_rm11-1a. In addition to the bacterial and fungal core communities, we found members of the cheese microbiota that could be associated to other factors of the cheese manufacturing process. Co-occurrence analysis made in this work, indicates that bacterial and fungal communities maintain positive and negative interactions which are important to shape the resident microbial communities in cheeses. This work is a contribution to the description of the microbial diversity found in some Mexican cheeses.

Keywords: Cheese bacteria; Cheese fungi; Cheese microbiota; Cheese yeast; Co-occurrence analysis; High throughput sequencing; Mexican cheeses.