The gut microbiota differs between working shepherd dogs bred in pastoral condition and companion dogs

Italy is characterized by ancient pastoral tradition in which the presence of sheepdog breeds is fundamental. These breeds are reared to work with livestock and to protect the herd from the aggression of predator animals. One of the peculiar feature of these breeds lies in their old and typical pastoral diet based on bread, dairy by-product, food waste and what they find accompanying the animals to the pasture. Moreover, they do not undergo any drug treatment and have an excellent state of health. In this context, the aim of this study is to explore, for the first time, the microbiota of dogs bred in pastoral conditions (Sicilian Mastiff) compared to companion dogs (Labrador Retriever) fed with a commercial diet. Genomic DNA has been extracted from faecal samples of 8 Labrador Retriever and 8 Sicilian Mastiff. The 16S gene has been sequenced with Illumina Miseq and raw reads have been processed using QIIME2. The high-quality reads have been classified at phyla, family and genera level with an identity threshold of 75%, 87% and 95%, respectively. A total of 8 phyla, 52 families and 103 bacterial genera have shown a relative abundance greater than 0.1%. The most abundant phylum has been Firmicutes (54%) followed by Bacteroidota (33%), Fusobacteriota and Proteobacteria (5%). It is interesting to note that Sicilian Mastiff has been a higher prevalence of Firmicutes and almost absence of Fusobacteriota and this reflects the ingestion of vegetable that occurs during the accompaniment of animals to pasture. Fusobacterium, Turicibacter and Bacteroides have been very prevalent in Labrador and this reflects a complete diet. Clostridium_sensu_stricto_1 genus has been most prevalent in Sicilian Mastiff, suggesting the co-evolution between this genera and dogs as reported for wolf, and is able to digest protein. Catenibacterium and Prevotella have been prevalent in Sicilian Mastiff and they are able to digest the carbohydrate producing short chain fatty acid that are associated with beneficial effects for gut. The beta diversity analysis, based on Bray-Curtis distances, has shown how different are the two diets (PERMANOVA p>0.001). In conclusion, further studies will have to be done but we could hypothesize that the composition of Sicilian Mastiff’s microbiome reflects not only the diet but also the conditions in which it has evolved that determine a healthy microbiota and useful for a hypothetical transplantation in selected breeds affected by many metabolic diseases.