3.5 | Effects of physiological structure of the host
GIT on the gut microbiome
To investigate the relationship between the physiological structure of
the host GIT and their gut microbiome in host dietary adaptation, we
divided the above 12 species into ruminant animals, SNMs (ruminant-like
animals) and
monogastric
animals according to their GIT physiological structures. First, LEfSe
test was used to detect the taxonomic and functional (carbohydrate
active enzyme families) differences
among the three groups. At the genus
level, Ruminococcus , Treponema and Clostridium were
significantly enriched in SNMs, and Fibrobacter ,Butyrivibrio and Prevotella were significantly enriched in
ruminant animals (LDA>4, p <0.05) (Figure
4a, Figure S5). The functions of these genera are all related to the
fermentation of complex carbohydrates such as cellulose (Palevich et
al., 2019; Ransom-Jones, Jones, McCarthy, & McDonald, 2012; Yang Gu &
Jiang, 2010). However, in the monogastric animals, Bacteroides ,Faecalibacterium , Roseburia and Phocaeicola were
significantly enriched, which were associated with the degradation of
fat and protein (LDA>4, p <0.05) (Figure
4a; Figure S5). Carbohydrate active enzyme analysis showed that GHs,
which significantly enriched in SNMs (GH78, GH13, GH109) and ruminant
animals (GH25, GH5), were related to the degradation of structural
polysaccharides. However, GHs that were significantly enriched in
monogastric animals (GH43, GH2, GH92, GH97, GH105, GH29, GH28, GH32,
GH20) were related to the degradation of oligosaccharides
(LDA>3, p <0.05) (Figure 4b; Table S13).
These results suggested that the composition and function of the gut
microbiome are related to the host’s dietary adaptation, and the
structure of gut microbes is more similar between SNMs and ruminants.
In addition, we found that the relative abundance of more than 50%
(1859) of genera in the SNMs gut microbiome were higher than that in
monogastric animals, but lower than that in ruminant animals (Table
S14). Bacillus (Firmicutes, Bacilli), Butyrivibrio(Firmicutes, Clostridia) and Fibrobacter (Fibrobacteres,
Fibrobacterales) had the highest relative abundance among these genera
in the SNMs gut microbiome. Most of these 1859 genera belonged to
Firmicutes (129 genera, average relative abundance in SNMs gut microbes
was 1.44%), Bacteroidetes (245 genera, average relative abundance in
SNMs gut microbes was 0.62%), Proteobacteria (866 genera, average
relative abundance in SNMs gut microbes was 0.41%%), Fibrobacteres (3
genera, average relative abundance in SNMs gut microbes was 0.24%),
Actinobacteria (264 genera, average relative abundance in SNMs gut
microbes was 0.26%), and Tenericutes (4 genera, average relative
abundance in SNMs gut microbes was 0.10%). Bacteria in these phyla have
the ability to degrade complex carbohydrates, especially in Firmicutes
(Yang Gu & Jiang, 2010) and Fibrobacteres (Ransom-Jones et al., 2012).
We further found that the relative abundance of 37 GHs in SNMs was
higher than that in monogastric animals but lower than that in
ruminants. Most of these GHs are associated with the degradation of
structural carbohydrates such as cellulose and starch (Figure S6; Table
S13). Analysis of the correlations between these genera and these GHs
showed that most bacteria correlated positively with these GHs (Table
S15). We also found that with the adaptive evolution of the host GIT
structure to herbivory, the diversity and abundance of GHs related to
the fermentation of structural carbohydrates also increased, and the
relationship between these genera and GHs are more complex. (Table S15),
because the host needed a stronger fermentation capacity to obtain
nutrients.
In summary, the structure of the SNMs gut microbiome was more similar to
that of ruminants, both in taxonomy and function. Moreover, the relative
abundance of some bacteria and carbohydrate enzymes in SNMs was
intermediate to that those of ruminants and monogastric animals,
suggesting that the physiological structure of the host GIT plays a
regulatory role in the gut microbiome during the adaptation evolution of
diet.