3.3 | Comparison of the RGC with the gene catalogues of cynomolgus macaque, human, mouse, pig and ruminants
The RGC was compared to the catalogues of monogastric animals (human (IGC) (J. Li et al., 2014), cynomolgus macaque (X. Li et al., 2018), mouse (Xiao et al., 2015) and pig (Xiao et al., 2016)) and ruminants (dairy cattle, water buffalo, yak, goat, sheep, roe deer and water deer) (Xie et al., 2021). Our results showed that the RGC comprised more genes than the human catalogue (9.9 M, 1267 samples), cynomolgus macaque catalogue (1.99 M, 20 samples), mouse catalogue (2.6 M, 184 samples), pig catalogue (7.7 M, 287 samples), roe deer catalogue 13.7 M, 50 samples) and water deer catalogue (7.7 M, 50 samples), but fewer genes than that of the yak (32.9 M, 50 samples), water buffalo (34.4 M, 50 samples), dairy cattle (35.5 M, 60 samples), goat (20.97 M, 60 samples) and sheep catalogues (24.2 M, 50 samples) (Table S6; Figure 3a). Alpha diversity analysis of the 12 species showed that the alpha diversity (Shannon Index) of the RGC was not significantly different from that of most ruminants (goat, sheep, yak and water buffalo) at the genus level (Figure 3b). Since ruminants and SNMs have high levels of structural carbohydrates in their diet, they need to ferment these substances (such as cellulose) for nutrients. At the KO functional level, the alpha diversity results showed that the RGC had no significant difference with water deer (Figure 3c), and monogastric animals generally had higher functional diversity than ruminants and ruminant-like animals (SNMs) (Figure 3c). In conclusion, the gut microbes of SNMs and ruminants are more similar.
We also constructed phylogenetic and hierarchical trees of the 12 species of hosts and their gut microbes at the genus level to further characterize the relationship between SNMs and ruminant gut microbes. The SNMs gut microbes clustered with ruminant gut microbes (Figure 3d). PCoA showed a similar trend at both the functional and taxonomic levels, showing that SNMs gut microbes was more closely related to ruminant gut microbes than to monogastric animal gut microbes (Figure 3e and Figure 3f). SNMs and ruminants have similar dietary characteristics and GIT structures adapted to foregut fermentation (Liu et al., 2022). As the mammalian gut evolved morphologically toward herbivory adaptation, their microbiome reached a compositional configuration similar to that in unrelated hosts that have similar GIT structures and diets (R. E. Ley et al., 2008; Liu et al., 2022).