Qubit fluorometer microplate reader

The DNA extractions from the samples were performed using DNeasy Ultraclean microbial kits (Qiagen, Germany) according to the manufacturer’s protocol. The quality of DNA and its concentrations were assessed using a NanoDrop system and a Qubit Fluorometer/microplate reader (Thermo Fisher Scientific, USA).
The RNA extractions from the samples were performed using the RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. Ribosomal RNA was removed from the total RNA using the Illumina Ribo-Zero rRNA kit (Illumina, USA) according to the manufacturer’s protocol.

The DNA extractions from the samples were performed using DNeasy Ultraclean microbial kits (Qiagen, Germany) according to the manufacturer’s protocol. The quality of DNA and its concentrations were assessed using a NanoDrop system and a Qubit Fluorometer/microplate reader (Thermo Fisher Scientific, USA).
The RNA extractions from the samples were performed using the RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. Ribosomal RNA was removed from the total RNA using the Illumina Ribo-Zero rRNA kit (Illumina, USA) according to the manufacturer’s protocol.

Genomic DNA from the bacterial pellets was extracted using a NucleoSpin Soil kit (Macherey-Nagel, Duren, Germany) following the manufacturers’ instructions with a modification in the sample lysis step. For efficient lysis, the bacterial pellets were resuspended in the optional enhancer SX solution and SL1 buffer and homogenized using TissueLyser II (Qiagen, Hilden, Germany) at a speed of 30 oscillations/s for 5 min. The concentrations and quality of DNA were evaluated using a NanoDrop system and Qubit Fluorometer/microplate reader (Thermo Fisher Scientific, USA). 16S rRNA gene amplicon sequencing targeting the V4 variable region was performed using the Illumina HiSeq 2500 system, producing 2 × 250-bp paired-end reads. Altogether, 3,031,524 high-quality paired-end reads (median, 20,760 per sample) from 3 fecal inoculum replicates and 143 in vitro samples in Exp1 and 8,117,537 high-quality paired-end reads (median, 231,733 per sample) from one fecal inoculum sample and 32 in vitro samples in Exp2 were generated.