3.1 Variation of gut bacterial composition due to giant panda
diet conversion
After quality filtering, a total of 13,650,999 bacterial 16S rRNA gene
sequences were obtained from 168 fecal samples from the diet conversion
experiment. The sequences were clustered into 3,027 OTUs at the 97%
sequence identity threshold.
Both
community richness (Chao1 index) and diversity (Shannon index) varied
with host diet and significant differences in these values were observed
between the three experimental groups
(p < 0.05, ANOVA
test) (Figure 1a, b). Specifically,
gut bacterial diversity increased when transitioning from OMD to MBD and
OBD
diets, while richness conversely declined. PCoA analysis also indicated
that samples from the same diet group clustered together and separately
from those of different groups (Figure 1c). Indeed, significant
differences in community structure were identified among the three
groups based on BC distances (p < 0.05, AMOVA).
Proteobacteria
and Firmicutes were the dominant phyla among communities sampled
during
diet conversion, comprising more than 90.0% of the total sequences
(Figure 1d). However, Proteobacteria was the most dominant phylum in OMD
(comprising 85.5% of the total sequences) and MBD (57.7%) communities,
while Firmicutes was the most dominant phylum in OBD (58.3%)
communities. Further, the abundance of Proteobacteria was significantly
highest in OMD (85.5%) communities than in other groups and was
considerably lower in the OBD (35.1%) communities (non-parametric
factorial Kruskal-Wallis sum-rank test, LDA > 4) (Figure
1e). Conversely, Firmicutes abundances increased markedly from the OMD
(13.5%) to the OBD (58.3%) communities (Non-parametric factorial
Kruskal-Wallis sum-rank test, LDA>4), and were
significantly higher in the OBD samples (Figure 1d, e).
The distribution of the 10 most abundant genera in each group
(comprising > 80.0% of the total sequences in each group)
were further investigated (Figure 1f). The three most abundant genera in
the OMD samples were Escherichia-Shigella (80.1%),
Streptococcus (7.9%), and Lactobacillus (1.9%). The abundances
of Escherichia-Shigella sharply decreased in the OBD communities
relative to the OMD communities (Non-parametric factorial Kruskal-Wallis
sum-rank test, LDA>4) (Figure 1e, f). The three most
abundant genera in the MBD communities were Escherichia-Shigella(43.8%), Streptococcus (16.8%), and Lactobacillus(10.1%). Streptococcus abundances were significantly higher in
the MBD group than in other groups (7.9% and 11.4% in OMD and OBD)
(Non-parametric factorial Kruskal-Wallis sum-rank test,
LDA>4) (Figure 1e, f). Lastly, Pseudomonas(13.4%), Lactobacillus (12.7%), and Clostridium (12.2%)
were the three most abundant genera in the OBD communities. In addition,Pseudomonas, Lactobacillus , Clostridium, Enterococcus,
Lactococcus, Turicibacter, Acinetobacter , Cetobacterium, andHafnia-Obesumbacteriumabundances also significantly increased when transitioning from the OMD
(0.2%, 1.9%, 0.1%, 0.4%, 1.0%, 0.0%, 0.2%, 0.0%, and 0.0%,
respectively) to the OBD (13.4%, 12.7%, 12.2%, 7.0%, 4.8%, 3.9%,
3.9%, 3.6% and 2.4%, respectively) communities (Non-parametric
factorial Kruskal-Wallis sum-rank test, LDA>4) (Figure 1e,
f).