When habitats of wild animals and livestock intersect, a possibility for the transmission of microbiota and pathogens is created. This can be the case when cows are kept on pastures close to natural areas for reasons of animal welfare or landscape conservation. Since red deer (Cervus elaphus) originally are inhabitors of a structured open landscape, pastures of cows are occasionally used for grazing. Even if the contact arising from this is indirect, faecal-oral transmission routes can develop, that have so far been passed over by most research.

Faecal samples from sympatric red deer and cattle will be analysed through shotgun metagenomics to investigate the resistome and the microbiome, as well as potential spillover between the species. In addition to the sequencing, swabs of the sampling material will be cultivated on selective media to isolate ESBL E. coli, if present. The samples are taken from the colon of slaughtered cows and hunted red deer. In addition, we will compare the results with those obtained from fresh droppings to assess whether a non-invasive sampling strategy could be used. Since some bacteria are more prone to carry specific resistance genes, the resistome and microbiome of the investigated animals will be tested for correlations.

One of the 70 red deer investigated so far was positive for ESBL E. coli and an isolate of the strain was obtained. Due to the informative character of the microbiome composition, some deductions based on factors like the Firmicutes-to-Bacteroidetes ratio, bacterial diversity and prevalence of pathogens can be made as to the general state of health of the animal. The use of faecal metagenomics is expected to allow for the non-invasive monitoring and investigation of antimicrobial resistances and gastrointestinal microbiome in sympatric animals.