1 | INTRODUCTION
Accumulating evidence indicates that the gut microbiome plays an
essential role in modulating the host’s whole-body metabolism (Qin et
al., 2012; Turnbaugh et al., 2006), immune system (Sylwia Smolinska,
2016; X. Zhang, Chen, Zhao, & Li, 2020) and adaptation to specific
diets and extreme environments (Baniel et al., 2021; H. Li et al., 2018;
X. Li et al., 2022; Z. Zhang et al., 2016). Therefore, a deeper
understanding of host-microbiome interactions is important for
understanding host adaptive evolution and health. In recent years, a
reference catalogue of gut microbiome genes has been constructed to
reduce data redundancy in large-scale gut metagenomic studies to improve
the estimation of the diversity and genetic potential of gut microbiome
and serve as a basis for metagenome-wide association studies (Xiao et
al., 2016; Xiao et al., 2015; Xie et al., 2021). The catalogue of
reference genes is a powerful tool to help us gain a comprehensive
understanding of the gut microbiome and is also essential for in-depth
functional metagenomic analyses such as species/gene profiling,
microbial biomarker discovery, and functional annotation (J. Li et al.,
2020; Thingholm et al., 2019). To date, many catalogues of reference
genes for the gut microbiome have been established in a variety of
mammals, including humans (J. Li et al., 2014; Qin et al., 2010),
rodents (Degnan et al., 2012) and ruminants (J. Li et al., 2020; Xie et
al., 2021). This has greatly promoted knowledge of the interactions
between host physiology and their gut microbiome, and is also of great
significance for understanding host dietary adaptation and health status
monitoring (R. E. Ley et al., 2008; Thingholm et al., 2019).
Nonhuman primates (NHPs) are our closest living relatives and among the
most widespread and successful mammals that underwent adaptive
radiation. Therefore, studies of the NHP gut microbiome are fundamental
in investigations of the ecological and evolutionary adaptation
mechanisms of NHPs and even mammals (Amato et al., 2016; Clayton et al.,
2018; Goldberg, 2008). Mimicking human dietary patterns in NHP animal
models has improved our understanding of the complex interplay between
diet, obesity, and the gut microbiome in humans (Newman et al., 2021).
Therefore, studies of the NHP gut microbiome may provide important clues
for understanding the characteristics of these bacterial communities in
the human gut and provide useful guidance and reference for studying the
interaction between humans and their gut microbiome (Jianan Sang 2022).
In addition, the impact of gut microbiome homeostasis on the
conservation of endangered NHPs is of particular concern (Basabose,
2002). Except phylogenetic relationships, the NHP gut microbiome is
influenced by multiple other factors, such as diet (Baniel et al.,
2021), physiology (Bennett et al., 2016), habitat quality (Barelli et
al., 2015), and social interactions (Bennett et al., 2016). For example,
the gut microbial structure of geladas (Theropithecus gelada )
adapted to seasonal dietary changes through rapidly change (Baniel et
al., 2021). The richness and diversity of gut microbes in the Udzungwa
red colobus (Procolobus gordonorum ) were reduced due to dietary
changes caused by human disturbance and habitat degradation (Barelli et
al., 2015). Therefore, it is very important to study the gut microbiome
of NHPs to understand the mechanisms of dietary adaptation and to
develop better conservation strategies for these endangered species.
However, considering that NHPs occupy a variety of habitats and niches,
most previous studies considered a single species or a small number of
captive individuals, which is far from being able to completely and
accurately represent the general characteristics of intestinal
microbiome in NHPs (Degnan et al., 2012; X. Li et al., 2018). The key to
detailed analysis of the gut microbiome in NHPs is the availability of
comprehensive gene catalogues of wild individuals (Zhu et al., 2020).
Therefore, the establishment of a comprehensive reference gene catalogue
of the gut microbiome in wild NHPs is of practical significance for
further developing the potential resource pool of the gut microbiome in
wild NHPs and exploring the relationships of the gut microbiome with
ecological adaptation and conservation in NHPs.
Among NHPs, snub-nosed monkeys (Rhinopithecus spp) (SNMs) are a
group of endangered colobines including five living species of Sichuan
SNM (R. roxellana ), Yunnan SNM (R. bieti ), Guizhou SNM
(R. brelichi ), Tonkin SNM (R. avunculus ) and Myanmar SNM
(R. strykeri ), of which Yunnan SNMs, endemic to the Tibetan
Plateau, are the NHPs with the highest altitudinal distribution (Quan
Gouqiang, 2002). Additionally, the living conditions of SNMs are more
severe than those of other primates, with features such as low
temperatures and limited oxygen (Li BG, 2002; Long YC, 1994), indicating
that SNMs should be suitable for studying the mechanisms adaptation to
extreme environments. SNMs have sacculated stomachs and are folivores
with foregut fermentation. In recent years, the genomic study of SNMs
revealed its genetic mechanism underlying dietary adaptations and found
evidence for functional evolution in the colobine RNASE1 gene that
enables digestion of the high concentrations of bacterial RNA derived
from symbiotic microflora (Zhou et al., 2014). Moreover, the digestion
of cellulose by the gut microbiome is also an important part of the
dietary adaptation of SNMs (Wang et al., 2021). Studies have shown that
the gut microbial structure of SNMs is similar to that of ruminants, but
the fermentation efficiency is lower than ruminants (D. J. Chivers,
Hladik, C.M, 1980). The sacculated stomachs of SNMs do not exhibit the
same strong functional division as the rumens of ruminants (D. Chivers,
1994). It is still not fully understood how the gut microbiome and
gastrointestinal tract (GIT) help SNMs extract sufficient energy and
nutrients from a high-fibre diet (Ganzhorn, 1992; Wang et al., 2021).
Previous studies of single SNM species have limited the description of
the overall genetic diversity of their gut microbiome (V. L. Hale et
al., 2018; V. L. Hale, Tan, C.L., Niu, K., Yang, Y., Zhang, Q., Knight,
R., 2019; Yao et al., 2021). Therefore, a comprehensive exploration of
the gut microbiome in a large number of wild SNMs is needed to further
elucidate their dietary adaptation mechanism, and the establishment of a
reference gene catalogue of the gut microbiome in wild SNMs is a
reasonable next step. Such a catalogue will provide an important
database and framework for analysing the relationships of the gut
microbiome with dietary adaptation and for making conservation plans. It
will also provide a data basis and reliable criteria for studies of the
gut microbiome as well as health, immunity, and adaptation to extreme
environments in SNMs.
Here, we constructed an integrated
reference gene catalogue of Rhinopithecus gut microbiome (RGC) by
processing 143 fecal individual samples from wild populations of SNMs
(Yunnan SNM, Sichuan SNM, and Myanmar SNM). The aim of this study was to
comprehensively characterize the gut microbiome of SNMs and lay a solid
foundation for revealing the relationship between the gut microbiome and
host evolutionary adaptation and health. We envisage that the present
gut bacterial gene catalogue and functional characterization will serve
as a valuable reference and resource for studying the evolution of the
gut microbiome in foregut fermenters, also for the study of mammalian
evolution and functional adaptation models provides a wide range of
perspectives.