**Abstract**

The implementation of sustainable control strategies aimed at disrupting the transmission of vector-borne pathogens requires a comprehensive knowledge of the vector ecology in the different eco-epidemiological contexts, as well as the local pathogen transmission cycles and their dynamics. However, even when focusing only on one specific vector-borne disease, achieving this knowledge is highly challenging, as the pathogen may exhibit a high genetic diversity and multiple vector species or subspecies and host species may be involved. In addition, the development of the pathogen and the vectorial capacity of the vectors may be affected by their midgut and/or salivary gland microbiome. The recent advent of Next-Generation Sequencing (NGS) technologies has brought powerful tools that can allow for the simultaneous identification of all these essential components, although their potential is only just starting to be realized. We present a metabarcoding approach that can facilitate the description of comprehensive host-pathogen networks, integrate important microbiome and coinfection data, identify at-risk situations, and disentangle the transmission cycles of vector-borne pathogens.

This powerful approach should be generalized to unravel the transmission cycles of any pathogen and their dynamics, which in turn will help the design and implementation of sustainable, effective, and locally adapted control strategies.

**Keywords:** vector-borne diseases, transmission cycles, vector ecology, behavior, metabarcoding, next-generation sequencing (NGS), blood meals, microbiome, EcoHealth, One Health
