## 2 Materials and Methods
### High-Throughput Sequencing and Statistical Analysis  
Samples were analyzed for bacterial taxonomy using the Ion 16 STM Metagenomics Kit according to the manufacturer's instructions (#A26216, Thermo Fisher Scientific, Inc., Walsham, MA, USA). Briefly, the 16S rDNA metagenomic library consisted of pooled and tagged (Ion Xpress Barcode Adapters, #4471250, #4474009, #4474518, Thermo Fisher Scientific, Inc., Walsham, MA, USA) amplicons targeting \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Classification** & **Cultivar** & **Main Purpose of Use** & **Fruit Color** \\ \hline  & Agiorgitiko & Wine & B \\  & Assyrtiko & Wine & W \\  & Fraoula & Table grapes & R \\  & Kakotrygis & Wine & R \\  & Karabraimis & Wine & B \\  & Korinthiaki & Wine, raisins & B \\  & Kotselena & Wine & B \\  & Liminona & Wine & B \\  & [PERSON] (from Cyprus) & Wine & B \\  & Mavrodafni & Wine & B \\  & Mavrokorakas & Wine & B \\ Greek & Moschofilero & Wine & B \\  & Moschatolefko & Wine & W \\  & [PERSON] & Table grapes & W \\  & Robola & Wine & W \\  & Roditis & Wine & R \\  & Savvatiano & Wine & W \\  & Serifiotiko & Wine & B \\  & Tsaousi & Wine & W \\  & Voidomatis & Wine & B \\  & Vertzami & Wine & B \\  & Vidiano & Wine & W \\  & Xinomavro & Wine & B \\  & Malagouzia & Wine & W \\ \hline  & Cabernet Sauvignon & Wine & B \\  & Cardinal & Table grapes & B \\  & Crimson & Table grapes & R \\  & Grenache & Wine & B \\  & Italia & Table grapes & W \\  & Merlot & Wine & B \\  & Perlette & Table grapes & W \\  & Ralli & Table grapes & R \\  & Riesling & Wine & W \\  & Sauvignon Blanc & Wine & W \\  & Soultanina & Table grapes, raisins & W \\  & Syrah & Wine & B \\  & Victoria & Table grapes & W \\ \hline \hline \end{tabular}
\end{table} 
Table 1: List of cultivars analyzed. Fruit color is presented as B, black; R, red; W, white. V2-4-8 and V3-6, 7-9 sets; the combination of the two primer pools allows for sequence-based identification of broad range of bacteria within a mixed population [27]. Briefly, 3 ng of high-quality DNA was amplified using 2X Environmental Master Mix with the provided 10X 16S Primer Sets (Thermo Fisher Scientific, Inc., Walsham, MA, USA). PCR products were purified with AMPure(r) XP beads solution (#A63881, Beckman Coulter, Breia, CA, USA), quantified, pooled, and end-repaired using Ion Plus Fragment Library Kit (#4471252, Thermo Fisher Scientific, Inc., Walsham, MA, USA). Then, amplicons were adapter-ligated, nick repaired, quantified using an Ion Universal Library Quantitation Kit (#A26217, Thermo Fisher Scientific, Inc., Walsham, MA, USA), and the library was pooled and diluted to the required concentration. The library template was prepared using Ion 520(tm) & Ion 530(tm) Kit-OT2 (#A27751, Thermo Fisher Scientific, Inc., Walsham, MA, USA) and was loaded on a Ion 520(tm) Chip (#A27762, Thermo Fisher Scientific, Inc., Walsham, MA, USA). Sequencing was done at the Plant Genetics and Breeding Lab of AUTH on a GeneStudio S5 platform using Ion Torrent(tm) sequencing technology (Thermo Fisher Scientific, Inc., Walsham, MA, USA). Sequencing progress and raw sequences were processed through the Ion Torrent Suite (ver. 5.12.2, Thermo Fisher Scientific, Inc., Walsham, MA, USA), then BAM files were uploaded to the Ion Reporter Platform to obtain Ion 16S Metagenomics report through Ion 16S Metagenomics Workflow (Thermo Fisher Scientific, Inc., Walsham, MA, USA). Ion 16S Metagenomics Workflow uses a premium curated Applied Biosystems(tm) MicroSEQ(tm) ID 16S rRNA database and a curated Greengenes database, that are not user customizable (i.e., thresholds and cut-off values). Therefore, Fastq files (QC-, adaptor-, and barcode trimmed) were exported using the FileExporter plugin through Ion Torrent Suite and uploaded on the MG-RAST server [28] under the project number mgp91606.