Climate change and tuberculosis drive non-adaptive shifts in the faecal microbiota of wild meerkats

<title>Abstract</title> Climate change and climate-driven increases in infectious disease threaten wildlife populations globally. Yet, their combined long-term effects on gut microbial communities remain unknown. Over the past two decades, wild meerkats inhabiting the Kalahari have experienced rapid climate change paired with increasing tuberculosis (TB) disease prevalence. Here we show that over this period the meerkat faecal microbiota has become inflated in Bacteroides and Fusobacterium, and depleted in members of Bacilli. Changes were underpinned by both rainfall patterns and TB status, with increasing taxa primarily linked to TB infection, and decreasing taxa primarily associated with drought. A decline in co-occurring clusters of Bacilli was associated with decreased survival, suggesting that shifts may not be adaptive but rather reflect a breakdown in microbial homeostasis. Our findings demonstrate that the impact of climate change and infectious diseases extends beyond hosts to gut microbial communities, potentially accelerating threats to wildlife health and survival.