The Microbiome and Resistome of Red Deer in Mecklenburg-Western Pomerania differs between seasons

The microbiome of wild animals influences their health and can harbour zoonotic pathogens as well as act as a reservoir for antimicrobial resistances (AMR). For this reason, the study of these microbiomes is important for the One Health approach and wildlife conservation matters. As red deer are widespread in Germany and the knowledge about the gut microbiome and resistome of these animals in Europe is limited, this study utilised shotgun metagenomic sequencing on faecal samples of 76 hunt-harvested red deer which were taken in a single region over the course of one year. The influence of biological factors like sex and age of the animals but also season on the microbial and AMR composition was investigated through shotgun metagenomics. The use of this method for the investigation of AMR in red deer has been reported infrequently and might be a suitable option for future projects. The description of the archaeome provides a basis for future research on this topic, which has received little attention to date. While sex and age dependencies were not detectable, seasonality of the bacterial composition was proposed to be influenced by rare taxa. A stable core microbiome resulted in a largely consistent abundance and composition of resistance gene reads. The bacterial composition was similar to the one described in earlier studies and aligns with the physiological needs of the species. Abundance of AMR was low and comparable to similar studies, still, resistance genes were found consistently across samples.