Trends in Microbiome and Digital One Health

Microbial and viral diversity remains largely unexplored in laboratory settings. This underscores the continued importance of cultivation-independent methods for studying the genetic make-up of microbial and viral dark matter across diverse ecosystems. Metagenomics and single-cell sequencing are indispensable tools in microbiome research, offering insights into both the microbial identities present and the potential functions. In this presentation, I will discuss several studies conducted in my lab that use these approaches. While we apply shotgun metagenomics, our focus also extends beyond traditional bulk techniques, as we try to find the needles in the haystack. To achieve this, we employ sorting and genome sequencing of individual environmental cells, using labeled probes or substrates as bait for targeted capture and investigations. Additionally, we explore microeukaryotes at the single-cell genomic level, treating them as micro-consortia that may host bacterial endosymbionts or viral entities like giant viruses or virophages. This holistic approach not only enriches our understanding of microbial communities and specifically inter-organismal interactions, but also brings us full circle to the realm of metagenomic exploration.