Variations in the Fecal Microbiota of Red Deer in Relation to the Hunting Area in the Friuli-Venezia Giulia Region, Italy

The gut microbiota of red deer is a topic of growing interest, particularly with regard to its ecological and physiological importance. The diversity and composition of these microbial communities is influenced by environmental variables, diet and interactions with other organisms in their habitat. Fecal samples were collected in 10 hunting reserves in the Friuli-Venezia Giulia region, Italy. In each hunting reserve, five individual samples were taken from the ground for a total of 50 samples. After DNA extraction, the V3–V4 16s rRNA regions were sequenced. The raw data were uploaded to QIIME2 and taxonomic annotation was performed. Significant differences between the deer sampled in the hunting reserves (p < 0.05) were calculated for the phyla Firmicutes and Cyanobacteriota and for the ratio of Firmicutes to Bacteroidota, especially for the mountain reserves in the north and northeast compared to the reserves in the hills in the west. Shannon and Chao1 alpha diversity indices varied between reserves (p < 0.01) and the Bray–Curtis beta diversity index also indicated differences in microbiota between hunting reserves. The different habitats and vegetation of the reserves could explain the differences observed. Understanding the dynamics of the microbiota of red deer provides important information about their health and feeding behavior and also has far-reaching implications for species conservation.