RNA-Seq of dairy biofilm: biofilm 3
The biofilms formed on stainless steel slides at 4C for 96 hours under stirring at 60 rpm in a CDC biofilm reactor with raw milk samples were collected by alternating sonication and vortexing. The biofilm suspensions were then filtered, and DNA was extracted using the eGENE-UP PCR system. The quality and quantity of the extracted DNA were assessed using the ND 1000 spectrophotometer NanoDrop and the Qubit dsDNA HS assay, respectively. Amplification of the 16S rRNA gene (V3-V4 region) was performed using a two-step dual-indexed PCR protocol, and sequencing was conducted on Illumina platforms. Purification and quality checks were carried out using agarose gels, a Bioanalyzer, and spectrophotometric assays.