The intestinal bacterial community of healthy and diseased animals and its association with the aquaculture environment

  • Fulin SunEmail author
  • Chunzhong WangEmail author
  • Lijuan Chen
  • Guozhu Weng
  • Zhipeng Zheng
Applied microbial and cell physiology


Although increasing levels of attention have been targeted towards aquaculture-associated bacteria, the bacterial community of animal intestines and its relationship with the aquaculture environment need to be further investigated. In this study, we used high-throughput sequencing to analyze the bacterial community of pond water, sediment, and the intestines of diseased and healthy animals. Our data showed that Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes were the dominant taxa of bacteria across all samples and accounted for more than 90% of the total sequence. Difference analysis and Venn diagrams showed that most of the intestinal bacterial OTUs (operational taxonomic units) of diseased and healthy animals were the same as those of sediment and water, indicating that the aquaculture environment was the main source of intestinal bacteria. Compared with healthy animals, a considerable reduction of OTUs was evident in diseased animals. Welch’s t test showed that the dominant bacterial taxa in sediment, water, and animal intestine were significantly different (p < 0.05) and each had its own unique dominant microorganisms. In addition, differences between the intestinal bacteria of healthy and diseased animals were represented by potential probiotics and pathogens, such as Bacillus, Vibrio, Oceanobacillus, and Lactococcus. Principal component analysis (PcoA) showed that a similar environment shaped a similar microbial structure. There was a large difference in the spectrum of intestinal bacteria in diseased animals; furthermore, the spectrum of intestinal bacteria in diseased animals was very different from the environment than in healthy animals. This study provides a theoretical basis for a relationship between the intestinal bacteria of healthy and diseased animals and the environment and provides guidance for environmental regulation and disease prevention in aquaculture areas.


Intestinal bacterial community Diseased animals Healthy animals Aquaculture environment 



This research was supported by the Project of Guangdong Science and Technology Department (2017A020216008), the Project of Fujian Science and Technology Department (2016I1002 and 2017T3010), the National Natural Science Foundation of China (41506127).

Compliance with ethical standards

Ethics approval and consent to participate

This paper does not contain any studies with human participants or vertebrate animals performed by any of the authors.

Competing interests

The authors declare that they have no competing interests.

Supplementary material

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ESM 1 (DOCX 13.6 kb)
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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Tropical Oceanography, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
  2. 2.Daya Bay Marine Biology Research Station, South China Sea Institute of OceanologyChinese Academy of SciencesShenzhenChina
  3. 3.Putian Institute of Aquaculture Science of Fujian ProvincePutianChina
  4. 4.Putian Tian Ran Xing Agriculture Development Co. Ltd.PutianChina
  5. 5.Putian Customs Comprehensive Technical Service CenterPutianChina

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