Nanodrop nd 1000 spectrophotometer

Frozen tissue was ground into a fine powder using a ⅛′′ steel ball bearing with 1 min shaking at 25 Hz in a TissueLyser II (Qiagen, Hilden, Germany). Total RNA was extracted from finely ground tissue using TRIzol reagent (#T9424‐200ML; Sigma‐Aldrich, St. Louis, MO, USA) at a ratio of 1 ml solution per 100 mg ground tissue. Residual phenol was removed from the crude extract through two chloroform extractions at a ratio of 1:5 (v/v), followed by precipitation using isopropanol at 1:1 (v/v). The precipitated RNA was washed twice with 70% ethanol and resuspended in 1 mm sodium citrate buffer (pH 5.4). RNA quantification was performed through spectrophotometric analysis at 260 nm using the Nanodrop ND‐1000 Spectrophotometer, and RNA quality was assessed using 1% agarose gel electrophoresis or the LabChip GX Touch (PerkinElmer, Waltham, MA, USA). Five micrograms of purified total RNA was combined with 5 μl of TURBO DNase buffer and 1 μl TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) in a 50 μl reaction and incubated at 37°C for 30 min. DNA nuclease‐treated RNA was then purified using 1.8× Sera‐Mag paramagnetic particles.

Microbial Plaque DNA was extracted from plaque samples using the Zymo Quick-DNA Fungal Bacterial Miniprep KIT (Zymo Research, Irvine, CA, USA), and extraction was performed according to the manufacturer’s protocol. DNA quality and quantity were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The Qubit 4.0 Fluorometer was used to quantify the metagenomic DNA (mgDNA) using the Qubit dsDNA HS assay kit according to the manufacturer’s protocol (MAN0017455 Rev. A.0). The mgDNA purity was established using the NanoDrop ND-1000 spectrophotometer, while the LapChip GXII was used to determine the genomic quality score following use of the DNA Reagent Kit (PerkinElmer, Waltham, MA, USA) and Genomic DNA (gDNA) Quality Control kit according to the manufacturer’s protocol (CLS140166 Rev. C; Supplementary Report). A genomic score between 0 and 5 was used, with 5 indicating high-quality gDNA.