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).