Taxonomy - the science of defining and naming groups of biological organisms based on shared characteristics - faced a significant crisis in the last decades and nowadays a rejuvenation of this discipline is required. For this reason, we recently proposed the integration in taxonomy of the most advanced genomics and bioinformatics techniques, taking into account also the holobiont concept (Serra et al., 2019): we named this approach Next Generation Taxonomy. NGTax will explore and expand this rationale establishing an international and inter-sectoral network of organisations across the EU, Africa, China and Russia. The consortium will work on a joint research programme in Next Generation Taxonomy of ciliates and their symbionts, constituting a holobiontic unit. The proposed approach is strongly multidisciplinary including classical morphological analyses, ultrastructure, molecular tools, genomics and bioinformatics. NGTax will pursue six central objectives: i) validate the NGTax approach on many holobiont systems from different ciliate Classes; ii) contribute rejuvenating taxonomic discipline to ensure traditional expertise is not lost but complemented with state of the art sequencing technologies; iii) consolidate and disseminate the NGTax approach to perform the characterization of eukaryotic organisms to let it become a “new reference standard”; iv) train staff members in NGTax, in order to outline novel scientific positions, boost their careers and import/export useful know-how across sectors, disciplines and countries; v) provide advanced training to male and female researches, including researchers from cultural and religious minorities, from developing countries in order to contribute to boost their academic careers and their integration in international collaborative research networks; vi) support European companies in performing know-how exchange with academic sector, developing new services, and creating new interaction with developing countries.