Effects of land-use changes and diet on the viral and bacterial load of black-backed jackals and bat-eared foxes in Namibia - a metagenomics approach to understand the ecological and molecular attributes affecting population health in important pathogen r

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Anthropogenic land-use modification is supposed to stress wildlife with negative effects on health conditions. It also facilitates the contact between wildlife and human associated livestock potentially affecting the transmission rate of pathogens which might be one reason for the increasing number of novel infectious diseases threatening our biodiversity. In the farmlands of central Namibia, we want to investigate how two prevalent modes of land-use (livestock versus game farming) and associated animal communities affect the health status of two prominent canids of southern Africa, the omnivorous black-backed jackal (Canis mesomelas) and the insectivorous-frugivorous bat-eared fox (Otocyon megalotis). Both have been blamed as important pathogen reservoirs and vectors and are abundant also in modified habitats. We will use a metagenomics approach applying next-generation sequencing technologies to qualify, quantify and compare the whole virus (virome) and bacteria community (microbiome). The contact rates with other wildlife and livestock will be investigated by radio-collared individuals. Furthermore, we aim to genotype the immune gene variability (MHC) of both species and to analyse their impact on the pathogen load also using high-throughput methods and multivariate statistics. Our study will increase our understanding of the ecological and molecular attributes affecting population health of host and potential vector species as well as species barriers in viral and bacterial diseases. This will contribute to avoid eradication programs as a management tool during disease outbreaks.