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Numerous factors have been shown to influence microbiome composition, including host genetics, diet and environmental variables. Recent studies have explored how host genetics influence human gut microbial communities, and those of pre-clinical models e.g. mice. However to date no studies have determined the influence of host genetics and extreme environments on wild animal microbiomes. Furthermore, when ‘wild’ species have been utilised this has typically involved working on captive individuals, restricted to a single species or limited to single sampling without replicates. Here we present work which takes advantage of a unique opportunity to directly investigate host organism genetic influences and environment on the resident microbiome. Our dataset comprised samples from individuals of two closely related sympatric, independently adapted arid mouse species, subject to the same stresses and diet; Acomys cahirinus and Acomys russatus. These desert dwellers are very highly adapted to the extreme environment they live in, and therefore represent an exciting opportunity to probe key microbiome-environment-host genetic questions. Samples are replicates from wild individuals, separated by a period of four months. Wild individuals were captured on two occasions and faecal samples collected. DNA extracted and subjected to shotgun metagenomic sequencing, generating NGS data. Preliminary analysis allowed us to probe community composition and relative abundance within individuals, and between members of the same species. Utilising Kraken, Centrifuge and Metaphlan we have found that abundant taxa include Lactobacillus and Roseburia. Ongoing analysis will enable us to establish the relative influence of host genetics on the metagenome composition of the two species.