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Microbial Diversity

Dr David Bass

Microbial Diversity Theme Lead

David is a specialist in biology ad systematics of protists, particularly those which reside in aquatic hosts and habitats. He is a global leader in the application of high throughput sequencing approaches to identification of cryptic disease agents and, the broader microbial diversity in which they exist.

The Systematics, Pathology, and Diagnostics teams at Cefas, within the Aquatic Animal Health Theme, are leading a wide range of projects investigating microbial diversity (viruses, bacteria, micro-eukaryotes) and its relevance to animal and macroalgal health in aquatic systems, including aquaculture.

Much of this work involves environmental DNA (eDNA)-informed methods, and is based on the following premises, which have largely evolved from our work in this area to date:

  1. the aquatic environment harbours very high levels of microbial diversity, including endemic pathogens, including opportunists, and others that influence the health of animal and plant hosts;
  2. emerging pathogens are frequently encountered, necessitating an informed horizon scanning procedure for detecting them and assessing risk;
  3. hosts in these systems are intimately associated with a previously unrecognized diversity of microbes (the so-called ‘holobiome’). Many of these microbes are new to science, and their functions are often unknown;
  4. the ‘one-pathogen-one-disease’ paradigm is insufficient to explain many disease scenarios, and the pathobiome concept is more applicable, i.e. understanding the combined effect of more than one microbial agent on host health at a mechanistic level.


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