The aim of the projet was to identify microbial antagonists of Plasmopara viticola, the causal agent of downy mildew in European cultivated grapevine (Vitis vinifera L.), by reconstucting microbial interaction networks from metabarcoding data and absolute abundance data of bacterial and fungal communities in symptomatic and asymptomatic leaf samples. The total fungal and bacterial abundances in grapevine leaf samples were estimated using digital droplet PCR (ddPCR). They are available in the present file, along with the molecular biology protocol. The number of copies of the target DNA sequences (16S for bacteria and ITS for fungi) per uL of DNA extract is indicated in the 'Conc. init' column. The 'Library_Name' column allows the absolute abundance data to be linked with the metabarcoding data that are available in the NCBI (PRJNA797948, PRJNA797225). Absolute quantification by ddPCR was performed for all leaf samples collected in the BCMicrobiome project and for the negative extraction controls (coded TN in the ‘Sample_ID2’ column). Negative PCR controls and positive PCR controls for ddPCR analysis are coded NTC and Tpos in ‘Sample_ID1’ column, respectively. Metabarcoding analysis also included controls (negative extraction controls, negative PCR controls and positive PCR controls) that were not deposited in the NCBI but are available from the present file.