Yang Jingru, Qiang Zhuang, Zhang Dandan, Hao Huimin, Wei Jie, Maira Hamid Syeda, Wang Weimin, Nie Zhulan
College of Life Science and Technology, Tarim University, Alar, China.
State Key Laboratory Breeding Base of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Crops and Ministry of Science and Technology, Alar, China.
Front Microbiol. 2025 Jun 24;16:1617701. doi: 10.3389/fmicb.2025.1617701. eCollection 2025.
This study investigates the gut microbiota composition and functional adaptations in three indigenous fish species from the Kizil River, Xinjiang: (SB), (DM), and (TY), recognizing their ecological significance and the need for conservation insights. Shotgun metagenomics was employed to profile the gut microbiota and functional potential. Taxonomic and functional annotations were analyzed, including identification of dominant taxa, biomarkers (LEfSe), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for metabolic functions, and Carbohydrate-Active enZymes (CAZy) database annotations. Environmental parameters (crude oil pollution, nitrogen levels, pathogen presence) were assessed, and dietary shifts during overwintering were characterized. Distinct gut microbiota profiles were identified: Proteobacteria, , and Pseudomonas were dominant overall. Species-specific biomarkers were Micromonospora (DM); Proteobacteria, Firmicutes, Aeromonas, and Bacillus (SB); and Mucoromycota, Vibrio, and Alcanivorax (TY). DM and SB exhibited significantly higher Firmicutes/Bacteroidetes ratios and enhanced nutrient utilization capabilities compared to TY. Key functional pathways included enriched fructose/mannose metabolism (SB) and oxidative phosphorylation (DM). CAZy analysis revealed high CE3 abundance across species, with GT6/GT10 (SB) and PL22 (TY) serving as unique enzymatic biomarkers. Dietary shifts during overwintering occurred: DM and TY transitioned towards herbivory, while SB retained carnivorous tendencies despite increased plant consumption. All species showed reduced immunity, with DM and SB particularly vulnerable to -related infections. Environmental analysis revealed crude oil pollution, elevated nitrogen levels, and contamination with . TY demonstrated notable salinity adaptability but heightened sensitivity to pollution. Host phylogeny exerted a strong influence on microbiota composition and metabolic functions. The results demonstrate host-specific microbial adaptation driven by phylogeny. The distinct functional profiles (nutrient utilization, key metabolic pathways like fructose/mannose metabolism and oxidative phosphorylation, CAZy enzymes) reflect ecological niche specialization. The observed dietary shifts and reduced winter immunity, compounded by environmental stressors (crude oil, nitrogen, ), highlight critical vulnerabilities, especially for DM and SB. TY's salinity adaptation is counterbalanced by pollution sensitivity. This study provides essential insights for developing targeted conservation strategies and sustainable aquaculture practices for these indigenous species within their natural habitat, emphasizing the need for pollution mitigation.
（SB）、（DM）和（TY）的肠道微生物群组成及功能适应性，认识到它们的生态意义以及获取保护见解的必要性。采用鸟枪法宏基因组学来描绘肠道微生物群及其功能潜力。分析了分类学和功能注释，包括优势类群的鉴定、生物标志物（线性判别分析效应大小）、代谢功能的京都基因与基因组百科全书（KEGG）通路以及碳水化合物活性酶（CAZy）数据库注释。评估了环境参数（原油污染、氮含量、病原体存在情况），并对越冬期间的饮食变化进行了特征描述。确定了不同的肠道微生物群概况：变形菌门、和假单胞菌属总体上占主导地位。物种特异性生物标志物分别为小单孢菌属（DM）；变形菌门、厚壁菌门、气单胞菌属和芽孢杆菌属（SB）；以及毛霉亚门、弧菌属和食烷菌属（TY）。与TY相比，DM和SB的厚壁菌门/拟杆菌门比率显著更高，营养利用能力更强。关键功能通路包括富集的果糖/甘露糖代谢（SB）和氧化磷酸化（DM）。CAZy分析显示各物种中CE3丰度较高，GT6/GT10（SB）和PL22（TY）作为独特的酶生物标志物。越冬期间出现了饮食变化：DM和TY转向食草，而SB尽管植物性食物消耗增加，但仍保持食肉倾向。所有物种的免疫力均下降，DM和SB尤其易受相关感染。环境分析显示存在原油污染、氮含量升高以及污染。TY表现出显著的盐度适应性，但对污染的敏感性增强。宿主系统发育对微生物群组成和代谢功能有很大影响。结果表明系统发育驱动宿主特异性微生物适应。不同的功能概况（营养利用、果糖/甘露糖代谢和氧化磷酸化等关键代谢通路、CAZy酶）反映了生态位特化。观察到的饮食变化和冬季免疫力下降，再加上环境压力源（原油、氮、），突出了关键脆弱性，尤其是DM和SB。TY的盐度适应性被污染敏感性所抵消。本研究为在这些本土物种的自然栖息地制定有针对性的保护策略和可持续水产养殖实践提供了重要见解，强调了减轻污染的必要性。
