Zhao Na, Guo Jiamin, Zhang Bo, Liu Kai, Liu Yuting, Shen Yubang, Li Jiale
Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China.
Mar Biotechnol (NY). 2022 Apr;24(2):366-379. doi: 10.1007/s10126-022-10113-3. Epub 2022 Mar 18.
Microbiome plays key roles in the digestion, metabolism, and immunity of the grass carp (Ctenopharyngodon idella). Here, we characterized the normal microbiome of the intestinal contents (IC), skin mucus (SM), oral mucosa (OM), and gill mucosa (GM) of the grass carp, as well as the microbiome of the sidewall (SW) of the raising pool, using full-length 16S rRNA sequencing based on the PacBio platform in this specie for the first time. Twenty phyla, 38 classes, 130 families, 219 genera, and 291 species were classified. One hundred four common classified species might be core microbiota of grass carp. Proteobacteria, Bacteroides, and Cyanobacteria were the dominant phyla in the niche of grass carp. Proteobacteria and Bacteroides dominated the taxonomic composition in the SM, GM, and OM, while Proteobacteria, Planctomycetota, and Cyanobacteria preponderated in the IC and SW groups. Microbiota of IC exhibited higher alpha diversity indices. The microbial communities clustered either in SW or the niche from grass carp, significantly tighter in the SW, based on Bray-Curtis distances (P < 0.05). SM, GM, and OM were similar in microbial composition but were significantly different from IC and SW, while IC had similarity with SW due to their common Cyanobacteria (P < 0.05). Differences were also reflected by niche-specific and differentially abundant microorganisms such as Noviherbaspirillum in the SM and Rhodopseudomonas palustris, Mycobacterium fortuitum, and Acinetobacter schindleri in GM. Significantly raised gene expression was found in IC and SM associated with cell cycle control, cell division, chromosome, coenzyme transport and metabolism, replication, recombination and repair, cell motility, post-translational modification, signal transduction mechanisms, intracellular trafficking, secretion, and vesicles by PICRUSt. This work may be of great value for understanding of fish-microbial co-workshops, especially in different niche of grass carp.
微生物群在草鱼（Ctenopharyngodon idella）的消化、代谢和免疫中发挥着关键作用。在此，我们首次基于PacBio平台，利用全长16S rRNA测序对草鱼的肠内容物（IC）、皮肤黏液（SM）、口腔黏膜（OM）和鳃黏膜（GM）的正常微生物群以及养殖池侧壁（SW）的微生物群进行了表征。共分类出20个门、38个纲、130个科、219个属和291个种。104个常见分类物种可能是草鱼的核心微生物群。变形菌门、拟杆菌门和蓝细菌是草鱼生态位中的优势门。变形菌门和拟杆菌门在SM、GM和OM的分类组成中占主导地位，而变形菌门、浮霉菌门和蓝细菌在IC和SW组中占优势。IC的微生物群表现出更高的α多样性指数。基于Bray-Curtis距离（P < 0.05），微生物群落要么聚集在SW中，要么聚集在草鱼的生态位中，在SW中聚集得更紧密。SM、GM和OM的微生物组成相似，但与IC和SW有显著差异，而IC由于其共同的蓝细菌与SW具有相似性（P < 0.05）。差异还体现在特定生态位和差异丰富的微生物上，如SM中的新草螺菌以及GM中的沼泽红假单胞菌、偶然分枝杆菌和辛氏不动杆菌。通过PICRUSt发现，IC和SM中与细胞周期控制、细胞分裂、染色体、辅酶转运和代谢、复制、重组和修复、细胞运动、翻译后修饰、信号转导机制、细胞内运输、分泌和囊泡相关的基因表达显著升高。这项工作对于理解鱼类-微生物协同作用，特别是草鱼不同生态位中的协同作用可能具有重要价值。
