Caves as a reservoir for novel and reoccurring zoonoses — ecological monitoring and metagenomic analysis in real time

The problems

Zoonotic infectious diseases, or zoonoses, are bacterial, viral, or fungal diseases that can be transmitted between animals and humans. More than half of all known infectious diseases are zoonotic, including the bubonic plague, the Spanish flu, HIV/AIDS, and, more recently, COVID-19. Over 30% of the deaths worldwide are due to infectious diseases and 75% of the emerging infectious diseases are zoonoses. We are contemporaries of an unprecedented increase in the discovery of new infectious diseases. Observations from recent years show that an average of one new agent appears each year and originate from animals. Emerging risks increase due to anthropogenic activity and abrupt ecosystems changes. Leading to a disturbance of the balance between the pathogen and the usual host species.

Bats are the second largest order of mammals, their long evolution, small body size, high population densities, close social interaction, spatial mobility, and the ability to colonise anthropogenic environments predispose them to act as reservoirs of viral, bacterial and fungal pathogens. Their life history traits have been hypothesised to create an evolutionarily distinct immunological environment that selects for viral traits that favour human infection. The specific bat physiology and their environmental preferences modulate a microbial flora with unpredictable potential.

Caves are underground habitats with specific environmental conditions, where bats form numerous colonies. Up to date, no detailed studies have characterised the metagenomic diversity of cave dwellings (as bats and blood-sucking insects) and their environment (water and soil). Caves are ecological niches, where various stress factors, such as high humidity, constant low temperature, and darkness can shape the emergence of new pathogens among bats and other hosts.

Funding for this study is provided by the Bulgarian National Science Fund — project CP-06-N51/9 “Caves as a reservoir for novel and reoccurring zoonoses – ecological monitoring and metagenomic analysis in realtime”.