College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.
College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China.
Environ Res. 2024 Mar 15;245:118090. doi: 10.1016/j.envres.2023.118090. Epub 2023 Dec 30.
The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.
大熊猫是一种以竹子为食的严格草食动物，但仍保留着典型的肉食性消化系统。微生物基因和基因组的参考目录缺乏，在很大程度上限制了大熊猫肠道微生物组的抗生素抗性组和功能探索。在这里，我们整合了 177 份圈养和野生大熊猫的粪便宏基因组，构建了一个包含约 450 万个非冗余基因的大熊猫综合基因目录（GPIGC），并重建了 393 个宏基因组组装基因组（MAGs）。基因的分类和功能特征表明，大熊猫的圈养状态显著改变了核心微生物组成和微生物基因的分布。在圈养大熊猫的肠道中检测到更高丰度和更高普遍性的抗生素抗性基因（ARGs），并且 ARG 的分布受到地理因素的影响，无论是圈养还是野生个体。Escherichia 作为圈养大熊猫肠道中普遍存在的属，是 ARGs 的主要载体，这意味着 Escherichia 存在 ARG 传播的高风险。我们还发现，多种赋予质粒介导的多粘菌素抗性的 mcr 基因变体在圈养和野生大熊猫的肠道中广泛存在。与几种杂食性和草食性哺乳动物相比，GPIGC 和 MAGs 中的碳水化合物活性酶（CAZyme）基因比例较低。许多 Clostridium MAGs 的成员在成年、老年和野生大熊猫的肠道中显著富集。Clostridiaceae 分离株和 MAGs 的基因组中含有完整木质纤维素降解和产生短链脂肪酸（SCFA）途径的关键基因或酶，表明这些细菌有潜力利用低营养的竹子饮食。总的来说，我们的数据提供了大熊猫肠道中详尽的参考基因目录和 MAGs，全面了解了抗生素抗性组和微生物对高木质纤维素饮食的适应性。
