Yi Yunhai, Liang Lifeng, Wang Zhilin, Ai Peng, You Xinxin, Bian Chao, Shi Qiong, Dong Bo
Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510006, China.
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
Animals (Basel). 2019 Sep 6;9(9):660. doi: 10.3390/ani9090660.
Gut microbiomes in various fish species were widely investigated with the rapid development of next-generation sequencing technologies. However, little is known about gastrointestinal (GI) microbial communities in mudskippers, a representative group of marine amphibious fishes, and their comparisons with other vertebrate animals from different habitats. Here, we performed a comprehensive analysis on microbial composition in five representative vertebrate groups (including amphibious mudskippers, marine and freshwater aquatic fishes, amphibians, and terrestrial animals) via operational taxonomic unit (OTU) survey and obtained a microbial gene catalog of five common fish species by metagenome sequencing. We observed that Cyanobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria were the most substantial bacteria in mudskippers. Differential variances in composition patterns of GI microbiota among the vertebrate groups were determined, although Proteobacteria and Firmicutes were the shared phyla with high abundance. In addition, and were the most abundant genera in core OTUs of these examined omnivores, carnivores, and herbivores. Our metagenomic analysis also showed significant differences between the representative blue-spotted mudskipper and grass carp (both are herbivorous fishes) in microbes at the phylum and class levels and functional gene terms. Moreover, several bacteriocin-related genes were identified in the five common fishes, suggesting their potential contributions to pathogen resistance. In summary, our present work not only sheds new light on the correlation of GI microbiota composition with living habitats and feeding habits of the hosts, but also provides valuable bacterial genetic resources for healthy growth of aquaculture fishes.
随着下一代测序技术的快速发展，人们对各种鱼类的肠道微生物群进行了广泛研究。然而，对于弹涂鱼（一种典型的海洋两栖鱼类）的胃肠道微生物群落，以及它们与来自不同栖息地的其他脊椎动物的比较，我们却知之甚少。在这里，我们通过操作分类单元（OTU）调查，对五个代表性脊椎动物群体（包括两栖弹涂鱼、海洋和淡水水生鱼类、两栖动物和陆地动物）的微生物组成进行了全面分析，并通过宏基因组测序获得了五种常见鱼类的微生物基因目录。我们观察到，蓝藻菌、变形菌、厚壁菌、拟杆菌和梭杆菌是弹涂鱼中最主要的细菌。尽管变形菌和厚壁菌是丰度较高的共有门类，但我们确定了脊椎动物群体之间胃肠道微生物群组成模式的差异。此外，在这些被检查的杂食动物、肉食动物和草食动物的核心OTU中，[此处原文缺失两个属名]是最丰富的属。我们的宏基因组分析还表明，代表性的蓝点弹涂鱼和草鱼（两者都是草食性鱼类）在门和纲水平的微生物以及功能基因术语方面存在显著差异。此外，在这五种常见鱼类中鉴定出了几个与细菌素相关的基因，表明它们对抵抗病原体具有潜在作用。总之，我们目前的工作不仅揭示了胃肠道微生物群组成与宿主的生活栖息地和饮食习惯之间的相关性，还为水产养殖鱼类的健康生长提供了宝贵的细菌遗传资源。
