The Key Role of Pseudomonas-Associated Bacteria in Obtaining Nutrition from Bamboo for the Giant Panda (Ailuropoda melanoleuca)

Abstract

Abstract Background The gut microbiota of giant pandas plays a vital role in obtaining nutrition from bamboo. However, despite the importance of cellulose and lignin in bamboo digestion, low cellulase activity has been observed in the panda’s gut, and no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. As a result, the mechanism by which pandas obtain nutrients is still controversial, and it is necessary to determine whether the gut microbiome of giant pandas has the potential to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. The degradation potential of lignin by the most dominant bacteria genus (Pseudomonas) were also explore, including identifying lignin degradation pathway in its genome, detecting lignin enzyme activity, and assessing the efficiency and products of lignin metabolism.Results The central pathways of lignin degradation, including beta-ketoadipate and homogentisate pathway, were found to be enriched in the gut microbiota of wild pandas. Additionally, the gut microbiome of wild bamboo-eating specialists was also enriched with genes from pathways implicated in degrading ferulate and p-coumarate (lignin derivative) into Acetyl-CoA and Succinyl-CoA via protocatechuate branch of beta-ketoadipate pathway, potentially providing the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in the central pathways of lignin degradation and metabolic pathway of lignin derivatives (ferulate and p-coumarate). Herein, three Pseudomonas-associated species isolated from the feces of wild pandas exhibited the laccase, lignin peroxidase, manganese peroxidase activity, as well as extracellular lignin degradation ability in vitro. Based on these results, we propose a potential mechanism for pandas to obtain nutrition from bamboo.Conclusions Notably, our findings indicate that the gut microbiome of pandas, particularly the Pseudomonas bacteria, play a crucial role in obtaining nutrition from lignin. This study provides novel insights into the adaptive evolution of pandas with respect to lignin metabolism.