The concept of pathogenesis has evolved considerably over recent years, and the scenario a microbe + virulence factors = disease is probably far from reality in a number of cases. Actual pathogens have extremely broad biological diversity and are found in all major groups of microorganisms (viruses, bacteria, fungi, protozoa ...). Their pathogenicity results from strong and often highly specific interactions they have with either their microbial environment, hosts and/or arthropod vectors. In this review, we explore the contribution of metagenomic approaches towards understanding pathogens within the context of microbial communities. With this broader view, we discussed the concept of pathobiome and the research questions that this raises
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