2.5 | Estimation of the relative abundances of genes, taxa and function terms
To calculate the gene relative abundance, high-quality reads from each sample were aligned against the RGC by Bowtie2 (v2.3.5) (Langmead & Salzberg, 2012). Sequenced-based abundance profiling was determined as described in previous studies (Qin et al., 2012). The relative abundances of taxa, KOs, OGs and CAZymes were calculated by summing the abundance of the respective genes belonging to each category per sample, based on the taxonomic assignments and KO, OG and CAZymes annotations, respectively (J. Li et al., 2014).
Published gene relative abundance profiles and gene catalogues of 11 species were downloaded and analysed by the same taxonomic and functional annotation pipeline in our study. These catalogues of 11 species included human (Homo sapiens ) gut microbiome (ICG) (J. Li et al., 2014), pig (Sus scrofa ) gut microbiome (Xiao et al., 2016), mouse (Mus musculus ) gut microbiome (Xiao et al., 2015), cynomolgus macaque (Macaca fascicularis ) gut microbiome (X. Li et al., 2018), and gut microbiome of various ruminants (Bos taurus ,B. grunniens , Bubalus bubalis , Capra aegagrus ,Ovis aries , Capreolus pygargus and Hydropotes inermis ) (Xie et al., 2021) (Table S4).