Bacto soytone

Berries were processed according to Renouf et al. (2005 (link)) with slight modifications. Basically, berries were placed in a sterile 500 mL flask containing a solution of Bacto Soytone (Sigma-Aldrich, St. Louis, MO, USA; 10 g/L) and Tween 80 (Sigma-Aldrich; 2 mL/L) to wash them and to release the microorganisms from the surface. This step was carried out twice at 20°C for 3 h with slow shaking. The washing solutions were then filtered through 0.45 μm Whatman nitrocellulose membrane filters (Sigma-Aldrich) and stored at 4°C until DNA extraction.
Total genomic DNA was extracted from the two filter membranes independently using the PowerWater® DNA Isolation Kit (MO BIO Laboratories Inc., Carlsbad, CA, USA), according to the manufacturer's instructions. The quantification and quality control of the DNA was determined with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The concentration of the DNA samples was normalized and the sequencing was carried out at the Functional Genomics Centre (University of Verona, Verona, Italy) using an Illumina HiSeq 2000 (Illumina Inc., San Diego, CA, USA) platform which generated 2 × 100-bp pair-end sequencing reads.

B. adolescentis strain E 298 b (Variant c) (DSMZ no. 20086) was purchased from DSMZ. The culture medium was prepared according to the DSMZ website and B. adolescentis was grown in an anaerobic workstation (Gene Science AG300). B. adolescentis was cultured anaerobically in sterilized DSMZ Medium 58 containing casein peptone (tryptic digest, Sigma-Aldrich), yeast extract (Sigma-Aldrich), meat extract (Sigma-Aldrich), bacto soytone (BD), glucose (Sigma-Aldrich), K₂HPO₄, MgSO₄ × 7 H₂O, MnSO₄ × H₂O, Tween 80, NaCl, cysteine-HCl × H₂O (Sigma-Aldrich), salt solution and 0.025% resazurin (Sigma-Aldrich). The purity of cultures was monitored by Gram staining and the c.f.u. was counted by plating serial dilutions on agar plates.