Project objectives and hypotheses

The environment and climate are changing dynamically and will increasingly influence the emergence and spread of new and emerging infections in new geographic and ecological areas. Our project aims to develop a research framework for monitoring the risk of transmission of viral, bacterial, fungal, and protozoan pathogens by insects and animals that inhabit caves and interact with the external environment and humans. We aim to identify the sources and routes of known and novel pathogens for humans and animals. We will focus on caves, which are specific ecological niches with extreme living conditions. We will study caves with high human impact and close contact between microbial species and their permanent or intermediate hosts (arthropods and bats), which can act as reservoirs and vectors of pathogens. The unusual interaction of humans with cave dwellers, such as large bat colonies, can create a chain of epidemic risks. Our goal is to develop and test an approach for monitoring and predicting epidemic outbreaks of new and emerging pathogens in the environment in real time by applying whole genome sequencing and bioinformatics analysis.

To achieve the set goal, we will perform several tasks:

1. Sampling in caves, examining blood and carcass material from bats, mosquitoes, water and soil.

2. Extracting DNA from the samples and performing random (shotgun) whole genome sequencing, aiming to identify all genomes present in the samples. Sequencing 100—140 million nucleotides per sample, which is > 40 Gb of information.

3. Development of bioinformatics approaches for analysis, identification of biodiversity (anatomy of genomes) of viruses, bacteria, fungi and protozoa, interpretation and visualisation of results.

4. Develop a model for predicting the occurrence of new and recurrent infections by assessing the pathogenic potential of the identified species in the samples in relation to the known information in the literature or databases for viral, microbial and protozoan pathogens in animals and humans.

The project is based on the hypotheses that:

(i) The microbiome of bats, bedbug, mosquitoes and subterranean insect fauna can be a reliable indicator of the emergence and spread of new and emerging pathogens in real time.

The results we will obtain will allow us to describe the biodiversity in the caves more accurately and to assess the potential of this biodiversity for the formation and emergence of future epidemics. We accept (ii) the hypothesis that whole genome (shotgun) sequencing for analysis of animal and environment DNA is a more informative and reliable approach to assess the microbial biodiversity than the widely used target sequencing by 16S rDNA, ITS and 18S rDNA marker genes.