Effects of Corona and Astrovirus infections on the gut microbiomes of bats: the Hipposideros species complex as a model for virus-induced increase of pathogenic bacteria in highly gregarious mammals

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The gut microbiome of a vertebrate has not only metabolic functions, it is also an important driver of immune defence mechanisms. To fulfil these roles, some stability and consistency within the gut microbial community is required. Enteric viruses can disturb the balance of the microbial communities, which can lead to secondary infections and to shifts towards higher number of pathogenic microbe species. If this happens in known pathogen reservoir species, a higher zoonotic risk may arise. Bats constitute the evolutionary origin and reservoirs of a high number of zoonotic pathogens. Among them are astroviruses (AstV), the worldwide leading cause of infectious diarrhoea in children, and different gastrointestinal coronavirus (CoV) species that constitute the ancestors of the viruses that recently caused highly pathogenic SARS and MERS epidemics in humans. Bats are also hosts of zoonotic bacteria although these are understudied. We here propose employing a bat model of four ecologically similar species that – like humans – live in large groups and densities to investigate the microbiome changes induced by CoVs and AstV infections in the gut. Our aim is to identity virus-microbiome interactions and their consequences on the bacterial species community and gene function level in order to understand which pathogenetic and potentially zoonotic virus-induced population-wide microbiome changes may arise in highly gregarious mammals. More than 6500 virus-screened samples from four Hipposideros species from five independent locations in central Ghana are already available from the previous DFG-funded program ‘German-African Cooperation Projects in Infectology’. In contrast to previous studies investigating microbiome changes in wild reservoir species, our study design provides the rare opportunity to control for phylogenetic and environmental variation which will enable us to discriminate between environmental, virus-induced and intrinsic factors.