School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650500, China.
Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical School, Kunming, Yunnan 650031, China.
Zool Res. 2023 Jul 18;44(4):793-807. doi: 10.24272/j.issn.2095-8137.2022.195.
Intestinal microbes are closely related to vital host functions such as digestion and nutrient absorption, which play important roles in enhancing host adaptability. As a natural "laboratory", caves provide an outstanding model for understanding the significance of gut microbes and feeding habits in the habitat adaptability of hosts. However, research on the relationship between gut microbes, feeding habits, and the adaptability of troglobites remains insufficient. In this study, we compared the characteristics of the intestinal microbes of cavefish and surface fish and further established the relationship between intestinal and habitat microbes. Furthermore, we conducted environmental DNA (eDNA) (metabarcoding) analysis of environmental samples to clarify the composition of potential food resources in the habitats of the cavefish and surface fish. Results showed that the structure of the gut microbes was more related to ecological type (habitat type) than phylogenetic relationships. While horizontal transfer of habitat microbes was a source of gut microbes, hosts also showed strong selection for inherent microbes as dominant microorganisms. Differences in the composition and structure of gut microbes, especially dominant microbes, may enhance the adaptability of the two fish types from the perspectives of food intake, nutrient utilization, and harmful substance metabolism, suggesting that food resources, predation patterns, intestinal flora, digestive and absorptive capacity, and feeding habits and preferences are linked to habitat adaptability. These results should facilitate our understanding of the significance of fish gut microbes to habitat adaptation and provide a new perspective for studying the adaptive mechanisms of cavefish.
肠道微生物与宿主的重要功能密切相关，如消化和营养吸收，这些功能在增强宿主适应性方面发挥着重要作用。洞穴作为一种天然的“实验室”，为理解肠道微生物和摄食习性在宿主栖息地适应性中的意义提供了杰出的模型。然而，关于肠道微生物、摄食习性和洞穴生物的适应性之间的关系的研究仍然不足。在本研究中，我们比较了洞穴鱼和洄游性鱼类肠道微生物的特征，并进一步建立了肠道和栖息地微生物之间的关系。此外，我们还对环境样本进行了环境 DNA(eDNA)(宏条形码)分析，以阐明洞穴鱼和洄游性鱼类栖息地中潜在食物资源的组成。结果表明，肠道微生物的结构与生态类型（栖息地类型）的关系比与系统发育关系更密切。虽然栖息地微生物的水平转移是肠道微生物的一个来源，但宿主对固有微生物也表现出强烈的选择，使其成为优势微生物。肠道微生物组成和结构的差异，特别是优势微生物的差异，可能从食物摄入、营养利用和有害物质代谢等方面增强了两种鱼类的适应性，这表明食物资源、捕食模式、肠道菌群、消化吸收能力以及摄食习性和偏好与栖息地适应性有关。这些结果有助于我们理解鱼类肠道微生物对栖息地适应的重要性，并为研究洞穴鱼类的适应机制提供了新的视角。
