Giant pandas consume different structural parts of bamboo (shoots, leaves and culms) during different seasons. Previous research showed different bamboo parts have varying nutritional content and that a long-term diet consisting of a single part of bamboo resulted in remarkable metabolic changes within captive giant pandas. However, the effects on the gut microbiome of giant pandas, as a result of a single bamboo part diet, have not been investigated. Here, we evaluated the changes in gut microbial communities based on single bamboo part diets and their potential implications by using 16S rRNA gene-based amplicon sequencing and metagenome shotgun sequencing. We found that the composition and function of the gut microbiome from captive giant pandas fed exclusively culms were significantly different from that of individuals fed shoots or leaves. During the culm feeding period, the gut microbiome showed strongest digestive capabilities for cellulose, hemicellulose and starch, and had the highest potential abilities for the biosynthesis of bile acids, fatty acids and amino acids. This suggests the microbiome aids in breaking down culm, which is more difficult for giant pandas to digest, as a means to compensate for the nutrient poor content of the culm. Genes related to fatty acid metabolism and tricarboxylic acid cycle enzymes were more abundant during the leaf stage diet than that in the shoot and culm stages. Thus, the microbiome may help giant pandas, which typically have low lipase levels, with fat digestion. These results illustrate that adaptive changes in the gut microbiome community and function may be an important mechanism to aid giant panda digestion when consuming different structural parts of bamboo.

Background: The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains in southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations between metabolite types and bacterial genus were detected. Conclusions: There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.

Climate change-induced food shortages pose major threats to wildlife conservation, and the exclusive reliance of giant pandas on bamboo makes them particularly vulnerable. The aim of this study was to provide insight into the reasons for the foraging strategies of giant pandas to selectively forage for different bamboo parts (bamboo shoot, culm, and leaf) during different seasons. This study used a metabolomic approach to analyze the fecal metabolites of giant pandas and conducted a correlation analysis with their gut microbiota. The results indicate that the fecal metabolites of giant pandas differ significantly depending on the bamboo parts they forage on, with higher sugar content observed when they consume bamboo culm with high fiber content. By functional annotation, culm group metabolites were enriched in the galactose metabolic pathway, while shoot group metabolites were enriched in the phenylalanine, tyrosine and tryptophan biosynthesis pathways. Moreover, Streptococcus showed a significant positive correlation with glucose and acetic acid content. Therefore, the foraging strategy of giant pandas is based on the ability to utilize the nutrient content of different bamboo parts. Captive feeding and habitat construction should enrich bamboo species to allow them to express their natural foraging strategies and improve their welfare and reproductive status.

The impact of dietary microorganisms on host microbiota is recognized, but the underlying mechanisms remain unclear. This study examined the effects of bamboo surface microbiota, including virulence factors, antibiotic resistance genes (ARGs), and mobile genetic elements from different bamboo parts (leaves, shoots, and culms), on giant panda gut microbiota using three pairs of twins. Results showed that bamboo and fecal samples shared 1670 microbial species, with shoot surface microbiota contributing the highest proportion (21%, Bayesian source tracking) of contemporaneous gut microbiota, primarily by increasing abundances of Escherichia coli and ARGs. Klebsiella pneumoniae and Salmonella enterica also showed high co-occurrence in both bamboo and fecal samples, indicating potential colonization. Additionally, Streptococcus suis, Acinetobacter, and Mycobacterium progressively declined in fecal samples as bamboo shoot intake increased, suggesting these microbes are likely transient. The findings emphasize the impact of foodborne microorganisms on the host and the importance of conservation management.

The spread of antibiotic resistance genes (ARGs) in the environment exacerbates the contamination of these genes; therefore, the role plants play in the transmission of resistance genes in the food chain requires further research. Giant pandas consume different bamboo parts at different times, which provides the possibility of investigating how a single food source can affect the variation in the spread of ARGs. In this study, metagenomic analysis and the Comprehensive Antibiotic Resistance Database (CARD) database were used to annotate ARGs and the differences in gut microbiota ARGs during the consumption of bamboo shoots, leaves, and culms by captive giant pandas. These ARGs were then compared to investigate the impact of bamboo part consumption on the spread of ARGs. The results showed that the number of ARGs in the gut microbiota of the subjects was highest during the consumption of bamboo leaves, while the variety of ARGs was highest during the consumption of shoots. Escherichia coli, which poses a higher risk of ARG dissemination, was significantly higher in the leaf group, while Klebsiella, Enterobacter, and Raoultella were significantly higher in the shoot group. The ARG risk brought by bamboo shoots and leaves may originate from soil and environmental pollution. It is recommended to handle the feces of giant pandas properly and regularly monitor the antimicrobial and virulence genes in their gut microbiota to mitigate the threat of antibiotic resistance.

The intestinal microbiota is important for the health of the host and recent studies have shown that some genes of the host regulated the composition of the intestinal microbiota. Group 10 phospholipase A2 (PLA2G10) is a member of the lipolytic enzyme family PLA2, which hydrolyze the ester bond at the sn-2 position of phospholipids to produce free fatty acids and lysophospholipids. PLA2G10 is secreted into the intestinal lumen, but its impact on the gut microbiota remains unclear. In this study, we generated intestine-specific Pla2g10 knock-in mice, and used 16S RNA sequencing to compare their gut microbiota with that of their wild-type (WT) littermates. Results showed that gut-specific Pla2g10 knock-in induced both PLA2G10 mRNA and protein levels in the colon. Moreover, intestinal Pla2g10 overexpression reduced the α-diversity of the gut microbiota relative to that of WT mice. The abundance of Bacteroidetes was lower in the Pla2g10 knock-in mice than that in the control mice, while the ratio of Firmicutes/Bacteroidetes was higher. Furthermore, the abundance of the genus Allobaculum was reduced, whereas the abundance of beneficial bacteria genera, including Enterorhabdus, Dubosiella, and Lactobacillus, was increased by host intestinal Pla2g10 overexpression. In summary, intestinal Pla2g10 overexpression increased the proportions of beneficial bacterial in the colonic chyme of mice, providing a potential therapeutic target for future improvement of the gut microbiota.