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.
