Cultivation-independent analysis of microbial communities on Austrian raw milk hard cheese rinds

• Cultivation-independent analysis of microbial cheese rind populations was done.
• Changes in community composition between cheese producing plants were shown.
• We reveal ripening time-dependent changes in the cheese rind microbiota.
• Pairwise correlation analyses revealed putative co-occurring taxa.
• Halomonas was most abundant in cheese rinds.

“Vorarlberger Bergkäse” (VB) is an Austrian artisanal hard cheese produced from raw cow's milk. The composition of its rind microbiota and the changes in the microbial communities during ripening have not previously been investigated. This study used 16S and 18S rRNA gene cloning and sequencing to characterize the bacterial and fungal communities of seven pooled cheese rind samples taken in seven different ripening cellars of three Austrian dairy facilities. A total of 408 clones for 16S and 322 clones for 18S rRNA gene libraries were used for taxonomic classification, revealing 39 bacterial and seven fungal operational taxonomic units (OTUs). Bacterial OTUs belonged to four different phyla. Most OTUs were affiliated to genera often found in cheese, including high numbers of coryneforms. The most abundant OTU from 16S rRNA gene libraries showed highest similarity to Halomonas. Young cheese rinds were dominated by Actinobacteria or Proteobacteria, particularly by Halomonas and Brevibacterium aurantiacum, while Staphyloccocus equorum was most abundant in old cheeses. The most abundant 18S rRNA OTU had highest similarity to the filamentous fungus Scopulariopsis brevicaulis. Pairwise correlation analyses revealed putative co-occurrences between a number of OTUs. It was possible to discriminate the different cheese rind microbiota at the community-level by facility affiliation and ripening time. This work provides insights into the microbial composition of VB cheese rinds and might allow the processing- and ripening conditions to be improved to enhance the quality of the product.