Gut microbiome dynamics associated with dietary shifts
Gut bacterial community diversity increased when transitioning from the
OMD to OBD diets of pandas, while richness exhibited an opposite trend.
Gut bacterial community richness has been observed as higher in pandas
with lower fiber diets compared to those with higher fiber diets
(Guo et al 2018,
Wu et al 2017). These results may be
explained by the variable structural complexity of fiber and the
relatively low richness of bacteria that can use fiber as a growth
substrate (Lynd et al 2002). However,
high fiber diets can increase the
diversity of GM in humans, while high fat diets are associated with
lower diversity (Carlotta et al 2010,
Tap et al 2016,
Zhernakova et al 2016). Competitive
interactions among bacteria are ubiquitous in natural systems, although
many studies have shown that lignocellulose is a complex substrate that
promotes positive interactions and synergistic growth of bacterial
populations compared to labile substrates like glucose and fat (Haruta
et al 2002, Sarunyou et al 2012, Deng et
al2016). Indeed, lignocellulose is a cross-linked structure that is
difficult to degrade. Thus, bacteria may need to form consortia to
synergistically achieve lignocellulose degradation
(Deng et al 2016, Perez et al 2002). Thus,
fiber content could be an important factor underlying variation in
richness and diversity of gut microbial populations among the pandas in
the OMD, MBD, and OBD groups. Consequently, our results support that
high fiber diets could increase the diversity, but decrease the richness
of gut bacterial communities in giant pandas.
Among all sampled gut communities, the Proteobacteria and Firmicutes
dominated, which is consistent with previous studies of giant panda GMs
(Yang et al 2018,
Zhang et al 2018). Proteobacteria may be
more dominant in the guts of herbivores with low metabolic rates
(Dill-McFarland et al 2016), which is
consistent with the low expenditure and physical activity of giant
pandas (Yonggang et al 2015). Firmicutes are typically dominant in the
guts of mammalian herbivores and play critical roles in fiber digestion
(Dill-McFarland et al 2016,
Nelson et al 2010). Interestingly,
Firmicutes abundances exhibited a gradient in the transition from OMD to
OBD group communities. Firmicutes abundances have also been positively
associated with fiber content in human guts
(Carlotta et al 2010), in addition to
significantly associated with supplemented dietary fiber in dogs
(Costa et al 2012). The positive
association of Firmicutes abundances with lignocellulose ingestion in
giant pandas could suggest that they are important for digesting high
fiber bamboo foods into more labile nutritional components.
At the genus level, Streptococcus (Firmicutes phylum) abundances
have been shown to significantly increase upon introduction of a bamboo
diet (Ouwehand et al 2010). Moreover,Streptococcus are associated with giant panda gut
mucus
(Williams et al 2016) that is critical
for dietary conversions of giant pandas from low diet to high fiber
diets. Mucus helps protect guts from injuries due to high fiber contents
and aids the movement of high fiber components through the gut
(Montagne et al 2003).
We
observed the presence of the gene encoding
Protein-Npi-phosphohistidine-cellobiose phosphotransferase (EC
2.7.1.205, celB ) in the Streptococcus MAG, which is
important for cellulose digestion (Lai et
al 1997), thus indicating the potential for cellobiose utilization by
the Streptococcus in these panda gut communities. In addition,
genes encoding beta-glucosidase (EC 3.2.1.21, bglB ) and
6-phospho-beta-glucosidase (EC 3.2.1.86 celF ) were identified in
the Streptococcus MAG, as inferred from comparison to the KEGG
databases. Beta-glucosidase (EC 3.2.1.21) and 6-phospho-beta-glucosidase
(EC 3.2.1.86) are both involved in cellulose digestion
(Ghorai et al ,
Rytioja et al 2014). In particular, GHs
are often associated with digestion of cellulose and hemicellulose
(Stewart et al 2018), and were
accordingly identified in the Streptococcus MAG via comparison to
the CAZy databases. It should be noted that cellulose and hemicellulose
are cross-linked with lignin, and the removal of lignin is the first
step in digesting cellulose and hemicellulose
(Rytioja et al 2014). Accordingly, several
enzyme-encoding genes involved in hemicellulose and lignin degradation
were present in the Streptococcus MAG including CE1, CE3, CE4,
CE5, AA3, AA4, AA6, and AA7 group genes
(Zhang et al 2018,
Zhen and Jr 2016). Moreover, several
other cellulose, hemicellulose, and lignin degradation associated genes
were also observed in the Pseudomonas , Enterococcus,
Lactococcus, and Acinetobacter MAGs including cellulase (EC
3.2.1.4) and 1,4-beta-cellobiosidase (EC 3.2.1.91). The combined
activities of cellulase and 1,4-beta-cellobiosidase can convert
cellulose into
cellobiose,
and cellobiose is a key intermediate in the conversion of cellulose to
D-glucose (Lifeng et al 2011). Consistent
with these genomic predictions, Pseudomonas, Clostridium,Lactobacillus, Enterococcus, Lactococcus and Acinetobacterabundances exhibited a gradient of increase when transitioning from the
OMD to OBD group pandas. Clostridium and Enterococcus have
been positively correlated with crude fiber digestibility, whileLactobacillus , Enterococcus, andPseudomonas have been
positively associated with acid detergent fiber digestibility (Niu et al
2015). Moreover, the involvement of Pseudomonas andAcinetobacter in the degradation of lignin has been previously
demonstrated (Jiménez et al 2015). Thus,
our results indicate that Streptococcus , Pseudomonas ,Enterococcus, Lactococcus, Acinetobacter, andClostridium may contribute to the utilization of cellulose and
hemicellulose from bamboo, thereby providing energy and nutrients for
their giant panda hosts.
Interestingly, gut
bacterial
communities of giant pandas were more similar to those of carnivores
than herbivores in a previous comparison of human GM and 59 other
mammalian species (Ley et al 2008). Likewise, Xue et al. observed
that the composition of gut bacterial communities in giant pandas were
more similar to those of bears and entirely distinct to those of
herbivores via comparison among 57 mammalian species including giant
pandas, its close relatives, typical carnivores, and distantly related
herbivores (Xue et al 2015). We therefore hypothesize that the gut
bacterial communities of bears and even carnivores have the potential to
metabolize fiber or otherwise that these bacterial communities have
evolved in concert with giant panda evolution. Nevertheless, additional
research is needed to evaluate the above hypothesis.
No
significant differences were observed in the richness and diversity of
fungal communities among the three dietary groups. Interestingly,
Basidiomycota
abundances significantly increased in the transition from the OMD to OBD
diets, suggested that they may play a role in the utilization of bamboo
by giant pandas.
Ascomycota
and
Basidiomycota have been previously shown to dominate the fungal gut
communities of giant pandas (Tun et al
2014, Zhang et al 2018b), which
coincides with their dominance in soil (Xu
et al 2012) and bamboo (Zhou et al 2017)
fungal communities. These observations have led to the hypothesis that
giant panda gut microbiomes may originate from their food sources or
even from soils (Hannula et al 2019,
Nina et al 2013). Candida was the
dominant fungal genus in the OMD communities and significantly declined
in abundance in the transition from the OMD to OBD diets. Candidaabundances in gut fungal communities have been strongly associated with
the consumption of
carbohydrates
(Christian et al 2013,
Iannotti et al 1973). Milk has higher
carbohydrate contents than bamboo (Mainka et al 1989), suggesting thatCandida may be involved in milk metabolism in the guts of newborn
giant pandas.Cystofilobasidium ,Guehomyces,and Gibberella abundances increased markedly in the transition
from the OMD to OBD diets (Non-parametric factorial Kruskal-Wallis
sum-rank test, LDA>4). Therefore, we also hypothesized thatCystofilobasidium , Guehomyces, and Gibberella may
contribute to the ability of giant pandas to digest bamboo.