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.