3 | RESULTS
3.1 | Construction of a reference gene catalogue of the SNM s gut microbiome
We generated a gene catalogue of the gut microbiome in SNMs, comprising 18,169,322 non-redundant genes with an average length of 573 bp and 32.39% of these genes were identified as complete (Figure 1; Table S3). Of these non-redundant genes, only 9,829,597 (54.1%) genes were taxonomically classified. Of these, more than 99.35% could be assigned to bacteria, and the remaining 0.65% being genes from viruses (0.24%) and archaea (0.41%) (Table S5; Figure 2a). At the phylum level, most of the annotated genes belonged to Firmicutes (41.99%), followed by Proteobacteria (3.43%), Bacteroidetes (3.28%) and Actinobacteria (1.17%). Moreover, 6,037,022 (33.2%) and 6,809,541 (37.5%) of the bacterial genes in the RGC could be annotated to the genus and species levels, respectively. At the genus level, most of the annotated genes (5.25%) belonged to Clostridium , followed by Ruminococcus(2.11%), Roseburia (1.38%), Eubacterium (1.17%) andOscillibacter (1.05%) (Figure S1; Table S5).
Functional annotation of the gut bacterial genes contained in RGC revealed a total of 8,061 KOs and 44,671 OGs, which represented 33.54% (6,049,083) and 56.30% (10,221,423) of the RGC, respectively (Table S6). These results illustrated that the gut microbiome of SNMs is a highly complex taxonomic assemblage with many unknown genes. Pathways associated with metabolism linked to the degradation of carbohydrate, amino acid, energy, nucleotide, cofactors and vitamins were enriched (Figure S2; Table S9). Further, genetic information processing pathways (replication and repair, and translation), and environmental information processing pathways (membrane transport and signal transduction) were also enriched (Figure S2; Table S9). Additionally, we mapped the RGC to the CAZy database. The results provided us with a complete picture of the carbohydrate enzymes presented in SNMs gut microbiome. We obtained 371 enzyme families from 390,733 annotated genes. These genes accounted for ~2.15% of the total bacterial genes in the RGC. There is a wide diversity of glycoside hydrolases (GH) catalytic modules in the RGC, including 140 GH families. This indicated that the SNMs have a strong ability to digest structural carbohydrates, which is related to their dietary adaptation. GHs are one of the major enzymes in the gut microbiome and hydrolyse the glycosidic linkage of glycosides (Lee et al., 2014). They play a crucial role in the digestion of complex carbohydrates, such as starch and cellulose.