Faecal microbiota differences between an autochthonous pig breed and a commercial line

The gut microbiota is recognized as one of the most complex microbial ecosystems in mammals. In pigs, the structure of this microbial community significantly influences their overall physiological functions, with breed also contributing to its diversity. This study explores the potential differences in the bacterial composition of the faecal microbiota between two pig breeds: the autochthonous Nero Siciliano (NS) and a commercial crossbreed (CB) (Landrace × Large White). To determine if differences in faecal microbiota composition occur, five NS pigs and seven CB pigs, all managed under identical breeding conditions, were compared at three different time points. The analysis of alpha and beta diversity metrics suggested that time influenced the bacterial profile's shape. The two pig breeds differed taxonomically in their faecal microbiota composition, showing dynamic changes over time. The prediction of Enzyme Commission numbers was similar between the breeds and time points, but the overall predicted functional profile of the microbial communities differed according to breed and time points. The relative abundances of biosynthesis pathways and macromolecule modification pathways were higher in NS, whereas metabolite precursor and energy generation pathways were higher in CB. Findings of this study can contribute to a better understanding of the faecal microbiota in autochthonous and commercial pigs, providing further insights for breeding management.