3.2 Metagenomic analysis of gut bacterial metabolic functions in
giant pandas
A total of 22 draft MAGs were obtained from metagenomics analysis, in
which 13 were classified to the genus level (Table 1). We focused on the
KEGG database-mapped metabolic pathways associated withStreptococcus, Pseudomonas, Lactobacillus, Enterococcus,
Lactococcus, and Acinetobacter in the diet conversion experiment
due to their significantly different abundances among groups based on
16S rRNA gene analyses. Catalase-peroxidase (EC 1.11.1.21, katG ),
catechol
2,3-dioxygenase (EC 1.13.11.2, dmpB ), NADPH: quinone reductase
(EC 1.6.5.5, qor ) and triacylglycerol lipase
(EC
3.1.1.3, TGL2 ) that are associated with lignin degradation were
observed in all of these genomes (Figure 2a). Further, several genes
involved in the digestion of hemicellulose including alpha-glucuronidase
(EC 3.2.1.139, aguA ), xylan 1,4-beta-xylosidase (EC 3.2.1.37,XYL4 ) and endo-1,4-beta-xylanase (EC 3.2.1.8, xynA ) were
observed in the genomes. In addition, genes involved in cellulose
digestion including cellulase (EC 3.2.1.4, aguA ),
beta-glucosidase (EC 3.2.1.21, bglB ), 6-phospho-beta-glucosidase
(EC 3.2.1.86, celF ), and
protein-Npi-phosphohistidine—cellobiose phosphotransferase (EC
2.7.1.205, celB ) were also observed. The enzymes involved in
cellulose digestion pathways are shown in a schematic in Figure 2b.
To better evaluate the capacity for lignocellulose
degradation in the communities, specific genes identified in the
metagenomic binning analyses were annotated using the CAZys database
(Figure 2c). The auxiliary activities (AAs) family including AA3, AA4,
AA6, and AA7 representatives that are associated with lignin degradation
were abundant among communities. These AA families were mostly found inStreptococcus (accounting for 30.7% of their total genes), in
addition to Pseudomonas (5.6%), Lactococcus(5.6%), Lactobacillus (4.7%), Enterococcus(2.6%), and Acinetobacter (0.9%). A total of 26 CAZy families
representing the glycoside hydrolases (GHs) and carbohydrate esterases
(CEs) classes that are involved in hemicellulose digestion were
observed, but mostly in the Acinetobacter MAGs (20.4%).
Nevertheless, the genes were also observed in the Pseudomonas ,Streptococcus, Enterococcus, and LactobacillusMAGs, comprising 14.6%, 11.7%, 7.2%, and 7.0% of their total genes,
respectively. Several families involved in cellulose digestion including
GH1, GH2, GH3, GH5, and GH8 were identified that represented
beta-1,4-beta-glucanases (EC 3.2.1.74), 1,4-beta-cellobiosidases (EC
3.2.1.91), and beta-1,4-beta-glucanases (EC 3.2.1.74). GH1, GH3, and GH5
genes were mostly observed in the Acinetobacter MAGs, accounting
for 4.4%, 2.1%, and 0.3% of their total genes, respectively.
Conversely, GH2 was mostly observed in Enterococcus (3.1%) MAGs,
while GH8 were mostly observed in Pseudomonas (0.2%) andAcinetobacter (0.1%) MAGs.