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Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale

文献类型：期刊论文

作者Zhang, Zhimin1,2; Li, Dapeng2; Xu, Weitong2; Tang, Rong2; Li, Li2
刊名FRONTIERS IN MICROBIOLOGY
出版日期2019-11-08
卷号10页码:11
关键词grass carp (Ctenopharyngodon idella) southern catfish (Silurus meridionalis) microbial community gastrointestinal tract skin gill
ISSN号1664-302X
DOI10.3389/fmicb.2019.02576
通讯作者Li, Dapeng(ldp@mail.hzau.edu.cn)
英文摘要Fish are the most widespread aquaculture species and maintain complex associations with microbial consortiums. However, the ecology of these associations present in multiple microhabitats in fish remains elusive, especially on the microbial assembly in fish external (skin and gill) and internal (stomach and intestine) niches, and the relationship with the rearing environment. To understand host dependence and niche differentiation of organ-specific microbiome signatures using a 16S rRNA gene-based sequencing technique, we systematically provided characterizations of a comparative framework relevant to the microbiome of stomach, regional intestine, skin, and gill in two important farmed fish species, herbivorous grass carp (Ctenopharyngodon idella) and carnivorous southern catfish (Silurus meridionalis), and of the rearing water. The different feeding habits of grass carp and southern catfish showed a significant separation of microbial community structure, with great compositional differences across body sites within each species. Site-driven divergences relied on host species: the same types of microhabitats between grass carp and southern catfish harbored differential microbiome. Additionally, body sites had remarkably distinct communities and displayed lower alpha diversity compared to rearing water. Unexpectedly, the stomach of southern catfish had the highest microbial diversity in the digestive tract of the two co-cultured fish species. For external sites within each species, a higher diversity occurred in gill of grass carp and in skin of southern catfish. Our results unveil different topographical microbiome signatures of the co-cultured species, indicating host selection in individual-level microbial assemblages and niche differentiation at the organ scale. This work represents a foundation for understanding the comprehensive microbial ecology of cohabiting farmed fish, suggesting potential applications associated with fish microbiome that urgently needs to be assessed in polycultured operations in aquaculture.
WOS关键词GUT MICROBIOTA ; ATLANTIC SALMON ; SKIN ; COMMUNITY ; EVOLUTION ; SALAR ; CARP ; LANDSCAPE ; DIVERSITY
资助项目Earmarked Fund for China Agriculture Research System[CARS-45] ; National Natural Science Foundation of China[31502140] ; Fundamental Research Funds for the Central Universities[2662015PY119]
WOS研究方向Microbiology
语种英语
WOS记录号WOS:000501010800001
出版者FRONTIERS MEDIA SA
资助机构Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities
源URL[http://ir.ihb.ac.cn/handle/342005/34803]  
专题水生生物研究所_水环境工程研究中心_期刊论文
通讯作者Li, Dapeng
作者单位1.Chinese Acad Sci, Inst Hydrobiol, Wuhan, Hubei, Peoples R China
2.Huazhong Agr Univ, Coll Fisheries, Hubei Prov Engn Lab Pond Aquaculture, Wuhan, Hubei, Peoples R China
推荐引用方式
GB/T 7714		 Zhang, Zhimin,Li, Dapeng,Xu, Weitong,et al. Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale[J]. FRONTIERS IN MICROBIOLOGY,2019,10:11.
APA Zhang, Zhimin,Li, Dapeng,Xu, Weitong,Tang, Rong,&Li, Li.(2019).Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale.FRONTIERS IN MICROBIOLOGY,10,11.
MLA Zhang, Zhimin,et al."Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale".FRONTIERS IN MICROBIOLOGY 10(2019):11.

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来源：水生生物研究所

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