4 | DISCUSSION
In this study, we constructed a gene catalogue of the gut microbiome of
wild SNMs for the first time by processing 143 fecal individual samples,
which contained 18,169,322 non-redundant genes. The RGC also represents
the first gene-set of the gut microbiome from wild NHP populations and
provides a comprehensive resource for further investigations of the NHP
gut microbiome. Compared with previous studies of the SNMs gut
microbiome (V. L. Hale et al., 2018; Trevelline & Moeller, 2022; Xu et
al., 2015), the RGC comprehensively characterizes the gut microbiome of
SNMs and probably contains most of the gut microbial genes prevalent in
wild SNM populations. Metagenomic data from 10 wild Sichuan SNMs
researched in a previous study showed a mapping rate of more than 75%
in the RGC, but there was relatively poor representation in captive
SNMs, with an average mapping rate was 49.83% (Table S8). Previous
studies have suggested that the captivity environment has a significant
effect on the gut microbiome of SNMs (Hui Zhu, 2018; Mingpu Qi, 2017).
Similar results have also been reported in other NHPs (Clayton et al.,
2016; Emmanouil Angelakis, 2016; V. L. Hale et al., 2018; Tayte P
Campbell, 2020). This proves that the RGC is reliable in describing the
gut microbiome of SNMs. Therefore, a comprehensive analysis of the gut
microbiome based on the RGC is of practical significance for studying
their dietary adaptation, which could further guide the development of
better conservation strategies for these endangered species.
We used this catalogue to study the characteristics of the SNMs gut
microbiome.
In our study, both taxonomic and functional results suggested that the
gut microbiome of SNMs was related to structural carbohydrate
degradation. Notably, our results were identical to those of previous
studies at the phylum level, while the differences were large at the
genus level (Wang et al., 2021; Yao et al., 2021). At the phylum level,
Firmicutes and Bacteroides were the main groups in the RGC (Figure 2b).
This is consistent with the results of previous studies on Sichuan SNMs
(Wang et al., 2021; Yao et al., 2021), Yunnan SNMs (Xia et al., 2022)
and Guizhou SNMs (V. L. Hale, Tan, C.L., Niu, K., Yang, Y., Zhang, Q.,
Knight, R., 2019). At the genus level, Clostridium ,Prevotella , Ruminococcus and Bacteroides were the
groups with the highest relative abundance in the RGC (Figure 2c), which
was different from the results of previous single-species studies (V. L.
Hale, Tan, C.L., Niu, K., Yang, Y., Zhang, Q., Knight, R., 2019; Wang et
al., 2021). This was likely because previous studies on the gut
microbiome of SNMs were mainly based on 16S rRNA analysis and small
sample sizes (Xia et al., 2022; Yao et al., 2021), preventing the
results from describing the general characteristics of the SNMs gut
microbiome. The consistency of the main phyla reflected that the gut
microbiome of SNMs was related to their dietary adaptation. Many
Firmicutes bacteria, including Clostridium , are able to utilize
xylose, xylan and xyloglucan, which are the major hemicellulose
components of plant cell walls (Canfora, Meex, Venema, & Blaak, 2019).
These results once again verified the reliability and comprehensiveness
of the RGC and preliminarily demonstrated that the gut microbiome
composition of SNMs plays an important role in their dietary adaptation.
Alpha and beta diversity analyses also revealed the important role of
the gut microbiome in the dietary adaptation of SNMs (Figure 3b, 3c and
3d). The comparative analysis of 12 mammals including SNMs, ruminants
and monogastric animals, indicated that the gut microbiome of SNMs was
clustered more closely to that of ruminants (Figure 3d), which was
similar to previous findings (Zhou et al., 2014). As the morphology of
mammalian GIT underwent convergent evolution to adapt to herbivory,
their microbiome might have developed similar compositional
configurations in unrelated hosts with similar gut structures (R. E. Ley
et al., 2008). We further found evidence of coevolution between SNMs and
ruminants during dietary adaptation. In SNMs, Ruminococcus ,Treponema and Clostridium were significantly enriched at
the genus level, and GH78, GH13 and GH109 were significantly enriched in
carbohydrate enzymes (GHs). The genera that were significantly enriched
in ruminants were Fibrobacter , Butyrivibrio andPrevotella , and the GHs that were significantly enriched were
GH25 and GH5 (Figure 4a and 4b; Figure S5). Although the genera and GHs
that were significantly enriched in SNMs and ruminants were different,
these genera and GHs were mainly associated with the digestion of
structural carbohydrates. For example, Ruminococcus ,Clostridium and Butyrivibrio belong to Firmicutes and are
related to the degradation of cellulose (Canfora et al., 2019), and GH5
and GH78 both have cellulase activity (Christiane Liers, 2021). However,
the genera and GHs that were significantly enriched in monogastric
animals were related to the degradation of fat and protein and
oligosaccharides, such as Bacteroides (Naofumi Yoshida, 2021)
(Figure 4a and 4b). This indicated that the gut microbes of SNMs and
ruminants evolved similar digestive strategies in the process of
adapting to the plant diet and further suggested that the gut microbiome
is an important part of host dietary adaptation.
SNMs and ruminants also display similar physiological adaptation
strategies to plant-based diets, and they are both foregut fermentative
animals (Liu et al., 2022). The rumen of ruminants and the enlarged
saccular stomach of SNMs provide a large space for the bacteria to
ferment cellulose and other substances (D., 1998; Karasov & Douglas,
2013; P., 1988), but the fermentation efficiency of SNMs may be lower
than that of ruminants, because the sacculated stomach of SNMs does not
show as strong functional division as ruminants, and the differentiation
is intermediate between those of monogastric animals and ruminants (D.
J. Chivers, Hladik, C.M, 1980). Previous studies have reported that the
morphology of the GIT has an important impact on the composition and
function of bacterial communities (R. E. Ley et al., 2008). In our
study, we found that the relative abundance of 1859 genera (over 50%)
and 37 GHs in SNMs was higher than that in monogastric animals but lower
than that in ruminants (Table S14). Most of these GHs were associated
with degradation of structural polysaccharides, such as GH10, GH12, GH9,
GH14 and so on (Table S15). We also found that as the host GIT structure
adapted to herbivory, the diversity and abundance of GHs related to the
fermentation of structural carbohydrates also increased (Table S14),
suggesting that the dual effects of GIT morphology and the gut
microbiome promoted the dietary adaptive evolution in foregut
fermentative animals, which provides a new perspective for exploring the
evolutionary path of the gut microbiome in these animals.
In addition, we defined a set of core gut bacterial genera, includingClostridium , Ruminococcus , Prevotella ,Bacteroides , Eubacterium , Parabacteroides ,Roseburia , Alistipes and Oscillibacter , based on
the gut microbiome generated by shotgun sequencing of 12 mammalian
species (Figure S4). However, the relative abundance of these genera
varied profoundly between each species (Figure S3), which might result
from the influence of genetic, dietary and physiological characteristics
of the host (R. E. Ley et al., 2008). Our core genera reflected, to some
extent, the basic composition of the mammalian gut microbiome. Previous
studies reported that most of these genera were important keystone
bacteria of the gut microbiome, which are closely related to host food
degradation, nutrient absorption, health, and intestinal homeostasis
(Ruth E Ley, 2016; Petia Kovatcheva-Datchary, 2015). Therefore, it is
highly necessary to focus on these core genera in future analyses of the
mammalian gut microbiome.