Abstract
Metabolomics is now a mature phenotyping tool that provides substantial results within various scientific communities. Its application at large-scale, i.e. on large populations and/or samples, has shown its power for research activities from plant science to human epidemiology and medicine, but it still needs key methodological developments for its routine application. Here, we review the current state of large-scale metabolomics applications, providing recent examples of large cohort studies in human and plant/environment research, and present the remaining scientific challenges of both fields. Then, we address the key common methodological issues, from analytics to data science, to fulfil these objectives and go towards a more comprehensive and interoperable large-scale metabolomics, making it a new key actor in the frame of the One-Health future research.