From gut to food and back to gut: bacterial diversity in animal casings used in the production of dry fermented sausages

Introduction Typical dry fermented sausages have been produced for centuries using natural casings, which are portions of animal intestines derived from slaughtering. Natural casings are very important components of many traditional meat fermented products, and they represent a peculiar case study of gut-derived environments that are used for the production of edible fermented foods. Materials & Methods In the present study we investigated by means of culture-dependent methods and Illumina high-throughput sequencing of 16S rRNA amplicons the bacterial ecology of hog, cow and ovine casings at different stages of their preparation for sausages production. Results Several strains of Staphylococcus, Lactobacillus, Bifidobacterium, Vagococcus and Clostridium were counted in significant amounts, isolated and characterized at phylogenetic level. High-throughput sequencing analyses revealed a highly diverse bacterial diversity, which differed strongly between casings of different animal species. The technological processes involved in the preparation for casing had also a strong impact on the casings bacterial ecology, with a significant reduction of undesired microorganisms, and an increase in the proportion of lactobacilli and staphylococci. Conclusions Overall results indicate that natural casings are an important source of several bacterial species whose role both in the fermentation and in the microbiological properties of the final products has been underestimated.