Faecal microbiome varies with social group, age and bovine tuberculosis infection in the European Badger (Meles meles)

Host-associated microbes are key components of animal health and physiology, with particular importance for determining responses to pathogen infection. The gut microbiota is highly variable at the individual level, being shaped by a multitude of factors including diet, social behaviour, and age. Yet the relative influence of these traits on microbiota composition, and the consequences of this variation for host responses to pathogens remain unresolved. Here we investigate factors that shape the faecal microbiome in European badgers (Meles meles). Badgers act as a wildlife reservoir of Mycobacterium bovis, a zoonotic pathogen and the causative agent of bovine TB (bTB) in cattle, but the potential role of the microbiome in shaping patterns of infection and severity of disease are not known. Analysing 165 samples from 72 badgers over 3 years, we found that social group and age were key determinants of faecal microbiota composition, and identified several bacterial genera associated with bTB infection. Investigation of microbiome dynamics at the individual level using longitudinally sampled badgers revealed marked heterogeneity in age-dependent microbiome trajectories that were not detectable from population level trends in chronological age. These data provide novel insights into the factors associated with microbial community dynamics in complex wild systems and highlight the need for individual-level and longitudinal approaches to studying host-microbiome associations.