This data set accompagnies the paper "Revisiting sour rot of grapevine through disease-associated microbiomes: a tripartite co-infection?" by Matthieu Wilhelm, Sébastien Hévin, Patrik Kehrli, Bart Buyck, Katia Gindro, Jean-Luc Wolfender and Valérie Hofstetter. The data collection was carried out by Sébastien Hévin, under the supervision of Katia Gindro, Patrik Kehrli and Valérie Hofstetter in the years 2019-2020 and analyses and work carried out subsequently. The data set is available on GitHub.