High-throughput assessment of bacterial ecology in hog, cow and ovine casings used in sausages production

• Hog, cow and ovine casings have distinct bacterial community structures.
• Bifidobacterium strains were isolated for the first time from casings.
• Technological preparation of casings has strong effects on casing bacterial ecology.

Natural casings derived from different intestine portions have been used for centuries in the production of fresh and dry-fermented sausages. Here we analysed 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. Several strains of Staphylococcus, Lactobacillus, Bifidobacterium, Vagococcus and Clostridium were counted, isolated and characterised at phylogenetic level. High-throughput sequencing analyses revealed a high 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.Natural casings were demonstrated to be complex ecological environments, whose role as microbiological inoculants in the production of sausages should not be underestimated.