Whole metagenome of rat: Cecal Day 3
DNA was isolated from rat cecal samples and quantified using nanodrop 1000. Samples were proceeded for library preparation. Final libraries were quantified using Qubit 4.0 fluorometer (Thermofisher #Q33238) using DNA HS assay kit (Thermofisher #Q32851) following manufacturers protocol. Quality assessment of the raw fastq reads of the individual samples were performed using FastQC v.0.11.9 (default parameters). Read level taxonomic profiling was done by aligning the processed paired-end reads to the pre KMA-indexed NCBI 2019 Genome Build [10] database using KMA. Taxonomic profiling of the samples was done using Kraken2 v.2.1.2 based on KRAKEN2 microbial database which is comprised of archaea, bacteria, fungi, protozoa, viral, UniVec_Core (https://refdb.s3.climb.ac.uk/kraken2-microbial). Taxonomic Krona charts based were plotted using microeco R packages. Heatmap was plotted based on percentage read abundance using Ampvis2 R packages.