Gut microbiome dynamics associated with lifestyle shifts
Wild giant pandas
exhibited
significantly higher gut bacterial community richness and diversity than
did wild-training I/II pandas, consistent with previous studies of
primates (Clayton et al 2016) and bears
(Borbón-García et al 2017). The increased richness and diversity could
be due to the exposure to more diverse microbial meta-communities via
habitats of wild giant pandas compared to those of wild-training I
pandas (Burns et al 2016,
Schmidt et al 2019,
Wu et al 2017).
Proteobacteria
and Firmicutes dominated the bacterial communities among all hosts with
different lifestyles, which is consistent with previous studies
(Zhang et al 2018,
Zhu et al 2011). However, Proteobacteria
was the most dominant phylum in the gut of wild-training I giant pandas,
while Firmicutes was the most abundant phylum in wild-training II and
reintroduced pandas. Proteobacteria have also been observed as the
dominant phylum in the gut communities of wild-training I giant pandas
(Wei et al 2015), while Firmicutes have
been observed as the dominant phylum in the guts of wild pandas
(Zhu et al 2011). Similarly,
Firmicutes were the dominant phylum
in wild deer mice and musk deer (Li et al
2017, Schmidt et al 2019) that primarily
ingest insoluble fibers that are degraded by cellulose and
hemicellulose-digesting enzymes including cellulase, beta-glucosidase,
and xylan 1,4-b-xylosidase (Costa et al
2012, Zhu et al 2011). Non-captive
giant
pandas require maximal energy from their diets due to environmental
stressors that wild-training I giant pandas do not experience
(Schmidt et al 2019).
Consequently, we also hypothesized
that environmental stressors/threats (including pathogens, intraspecific
competition, and interspecific competition, among others) may be
important factors that drive the composition of panda intestinal
bacterial communities during lifestyle shifts. In addition to the above,
Bacteroidetes, Verrucomicrobia, and Actinobacteria abundances were
higher in the wild giant panda communities compared to those of the
reintroduced pandas (Non-parametric factorial Kruskal-Wallis sum-rank
test, LDA>4). Bacteroidetes have been positively associated
with the digestion of carbohydrates and proteins, and may help
facilitate the development of gut immune systems
(Ley et al 2006,
Li et al 2017). In addition,
Actinobacteria have been positively associated with fat digestion
(Wu et al 2011). Thus, these results
suggest that wild giant pandas had more complex environmental habitats
and food choices that likely affected their GM.
Verrucomicrobia have been notably not previously observed in the guts of
giant pandas although they were relatively abundant in the gut
communities of wild pandas in our study. Verrucomicrobia have been
observed in the gut communities of primates and termites in addition to
various other environments (Dedysh et al 2006,
He et al 2010,
Lee et al 2009,
Manjula et al 2016,
Su et al 2016). The more microbial
species that a host comes into contact with, the more likely it is that
those species will persist in the host’s gut microbiome
(Schmidt et al 2019,
Smits et al 2017,
Chave 2010). These observations support
our suggestion that wild giant pandas were more adapted to natural
environments and interacted with more diverse microbial species than did
wild-training I giant pandas.
At the genus level, Escherichia were significantly enriched in
the wild-training I panda gut bacterial communities (Non-parametric
factorial Kruskal-Wallis sum-rank test, LDA>4).Escherichia have also been observed as the major bacterial taxa
in the guts of captive giant pandas (Xue et al 2015), humans (Lagier et
al 2012) and pigs (Niu et al 2015) gut.
Conversely, Streptococcus andLeuconostoc were more abundant in the wild-training II giant
panda gut communities, while Clostridium, Leuconostoc, andTuricibacter were more enriched in the reintroduced panda
communities (Non-parametric factorial Kruskal-Wallis sum-rank test,
LDA>4). These genera may be involved in the more complete
digestion of bamboo in non-captive giant pandas, which could then help
the pandas gain adequate energy from limited nutritional sources
(Oyeleke and Okusanmi 2008, Zhu et al
2011).
The composition of gut bacterial communities in the reintroduced giant
panda were closer to those of the wild pandas, although significant
differences were observed between the reintroduced and wild panda
communities at the phylum and genus levels (Non-parametric factorial
Kruskal-Wallis sum-rank test, LDA>4). These observations
suggest that the reintroduced giant pandas still maintained differences
in their GM relative to wild pandas despite living in the same
environment. For example, Clostridium , Leuconostoc ,Turicibacter, and Acinetobacter were more abundant in
reintroduced panda communities. Conversely, Pseudomonas ,Sphingobacterium, and Flavobacterium were more abundant in
the communities of wild pandas. All of these genera are associated with
cellulose, hemicellulose, and lignin degradation (Dahal and Kim 2016,
Jiménez et al 2015,
Williams et al 2016,
Zhu et al 2011), which is an important
characteristic for the complete convergence of reintroduced giant pandas
to wild pandas. Different habitats can influence the composition of GM
through contact with different habitats, foods, and other materials
(Borbón-García et al 2017, Li et al 2017,
Chave 2010). Thus, these results suggest
that additional time is needed for the complete conversion of
reintroduced giant panda gut communities to those of wild pandas.
As with the bacterial communities, the richness and diversity of
reintroduced and wild giant panda fungal communities were significantly
higher than in those of wild-training I pandas (p <
0.05, ANOVA). Thus, captivity could lead to decreased richness and
diversity of gut fungal communities of giant pandas. The underlying
mechanism behind these differences are likely the same as for the
bacterial communities, wherein food, space, and interactions with human
keepers are limited for captive giant pandas
(Schaller et al 1985), and thereby limit
potential interactions with meta-communities relative to wild pandas.
Ascomycota and Basidiomycota were the dominant phyla in the communities
of wild-training I, wild-training II, and reintroduced pandas, although
their relative abundances varied among groups.
Ascomycota
and Basidiomycota have been observed as dominant in the vaginas of giant
pandas (Chen et al 2017), the guts of
humans (Christian et al 2013), guts of
dogs (Handl et al 2011), bamboo (Zhou et
al 2017), soils (Xu et al 2012), and in
the near-surface atmosphere (Bowers et al
2013). Indeed, Ascomycota and Basidiomycota are ubiquitous and abundant
among most environments. Given that gut microbiome composition is driven
by the frequency of contact with microbial species by hosts
(Schmidt et al 2019,
Smits et al 2017,
Wheeler et al 2012), these results
suggest that environmental microbiota may be one of the most important
lifestyle factors that affect giant panda gut fungal communities.
Considerable variation was observed among the fungal genera associated
with lifestyles.Candidawas the dominant genus in the gut communities of captive pandas, which
may help in the digestion and absorption of carbohydrates
(Christian et al 2013,
Iannotti et al 1973). Captive giant
pandas are ensured a fixed amount of carbohydrates (e.g. shoots and
panda cakes) compared to semi-captive and reintroduced pandas
(Schaller et al 1985).
In
contrast, Cryptococcus was enriched in the gut communities of
wild-training II giant pandas, while Mrakiella was abundant in
those of the reintroduced pandas.Cryptococcusis common in natural environments and can remain in non-infective states
in bodies while later reactivating and spreading to other body areas,
causing serious diseases in hosts with weakened immune systems
(Hagen et al 2017,
Litvintseva and Mitchell 2009).Mrakiella are found in soils and waters, especially in
low-temperature environments within various regions
(Thomas-Hall et al 2010). These results
consequently suggested that diet and the microbial species within
specific environments may be important factors that shape the
composition of intestinal fungal communities during lifestyle shifts.
A total of 31 fungal genera exhibited significantly different abundances
in the gut communities of reintroduced and wild giant pandas
(Non-parametric factorial Kruskal-Wallis sum-rank test,
LDA>4), albeit with low relative abundances exceptCalycina. Calycina was enriched in the communities of the wild
pandas and belongs to the Helotiales order
(Zhang and Zhuang 2004) that is
associated with root endophytes (Tedersoo et al 2010). These results
support that wild giant pandas may have more comprehensive dietary
structures or more contact with microbial meta-communities within
environments compared to reintroduced pandas, which would then enhance
the dietary diversity of reintroduced pandas and contribute to the
recovery of natural gut fungal community compositions as seen in wild
pandas.