Magnapure lc je379 platform

Genomic DNA from the solid residues of the fermentation reactions was extracted using the MagNaPure LC JE379 platform (ROCHE) and the DNA Isolation Kit III (Bacteria, Fungi) Ref. 03264785001, following the manufacturer’s instructions, with a previous lysozyme lysis. DNA was quality-checked by agarose gel electrophoresis (0.8% wt/vol agarose in Tris-acetate-EDTA buffer) and quantified using the Qubit 3.0 Fluorometer (Invitrogen) and the Qubit dsDNA HS Assay Kit.
In order to prepare amplicon libraries, DNA at 5 ng/µL in Tris 10 mM (pH 8.5) was used for the Illumina protocol for the small subunit ribosomal RNA gene (16S rRNA) Metagenomic Sequencing Library Preparation (Cod 15044223 Rev. A). PCR primers targeting the V3–V4 hypervariable region of the 16S rRNA gene were designed as described by Klindworth et al.^{53 (link)} (Supplementary Table 6). These primers contain adapter sequences added to the gene-specific sequences to make them compatible with the Illumina Nextera XT Index Kit (FC-131-1096). After 16S rRNA gene amplification and indexing, amplicons were multiplexed and sequenced in an Illumina MiSeq sequencer according to the manufacturer’s instructions in a 2 × 300 cycle paired-end run (MiSeq Reagent Kit v3MS-102-3001).

Genomic DNA was extracted from the solid residues deriving from the fermentation process using the MagNA Pure LC JE379 platform (Roche) and DNA Isolation Kit III (Bacteria, Fungi; REF 03264785001), following the manufacturer’s instructions, with a previous lysis with lysozyme at a final concentration of 0.1 mg/ml. DNA integrity was determined by agarose gel electrophoresis (0.8% w/v agarose in Tris-acetate-EDTA buffer) and DNA samples were quantified using a Qubit 3·0 Fluorometer (Invitrogen). All DNA samples were stored at −80°C until further processing.

The bacterial suspensions obtained from
the solid part deriving from in vitro fermentation
were lysed with lysozyme at a final concentration of 0.1 mg/mL. Then,
the extraction of genomic DNA was performed with the MagNA Pure LC
JE379 platform (Roche) and DNA Isolation Kit III (Bacteria, Fungi)
(REF 03264785001), following the manufacturer’s instructions.
Agarose gel electrophoresis (0.8% w/v agarose in Tris-acetate-EDTA
buffer) was used to determine DNA integrity, while the sample DNA
was quantified with a Qubit 3·0 Fluorometer (Invitrogen). Finally,
the DNA samples were stored at −20 °C until further processing.