title: RNA-Seq of Bifidobacterium mongoliense
design: Total RNA of each considered condition (fecal medium, fecal medium plus autoclaved cheese and cheese broth, in triplicate) was extracted as follows. Briefly, bacterial cell pellets were resuspended in 1 mL of QIAzol lysis reagent (Qiagen, Germany) in a sterile tube containing glass beads (Merk, Germany). Cells were lysed by alternating 2 min of stirring the mix on a Precellys 24 homogenizer (Bertin instruments, France) with 2 min of static cooling in ice. These steps were repeated three times. The lysed cells were centrifuged at 12,000 rpm for 15 min, and the upper phase was recovered. The RNA samples were then purified using the RNeasy mini kit (Qiagen, Germany) following the manufacturers instructions. RNA concentration and purity were evaluated using a spectrophotometer (Eppendorf, Germany). For RNA sequencing, total RNA (from 100 ng to 1g) was treated to remove rRNA by using the QIAseq FastSelect following the manufacturers instructions (Qiagen, Germany). The rRNA depletion yield was checked using a 2200 TapeStation (Agilent Technologies, USA). Then, a whole transcriptome library was constructed using the TruSeq Stranded mRNA Sample preparation kit (Illumina, San Diego, USA). Samples were loaded into a NextSeq high-output v2 kit (150 cycles) (Illumina) as the technical support guide indicated.