Applied Microbiology and Biotechnology

, Volume 102, Issue 19, pp 8585–8598 | Cite as

Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health

  • Fei Huang
  • Luqing PanEmail author
  • Mengsi Song
  • Changcheng Tian
  • Shuo Gao
Environmental biotechnology


Microorganisms play crucial roles in nutrient cycling, water quality maintenance, and farmed animal health. Increasing evidences have revealed a close association between unstable microbial environments and disease occurrences in aquaculture. Thereupon, we used high-throughput sequencing technology to comprehensively compare the bacterial communities of water, sediment, and intestine in mariculture ponds at the middle and late stages of Litopenaeus vannamei farming and analyzed whether changes of their microbiota assemblages were associated with environmental factors and shrimp physiological health. Results showed that bacterial community structures were significantly distinct among water, sediment, and intestine; meanwhile, the relative abundances of intestinal dominant taxa were significantly changed between different rearing stages. Compared with intestine and water, shrimp intestine and sediment had a similar profile of the dominant bacterial genera by cluster analysis, and the observed species, diversity indexes, and shared OTUs of bacterial communities in intestine and sediment were simultaneously increased after shrimp were farmed for 90 days. These results reflected a closer relationship between microbiotas in sediment and intestine, which was further proved by nonmetric multidimensional scaling analysis. However, bacterial communities in water, sediment, and intestine responded differently to environmental variables by redundancy and correlation analysis. More importantly, shrimp physiological parameters were closely associated with bacterial variations in the gut and/or ambient, especially the gut microbiota owning significantly high levels of predicted functional pathways involved in disease emergence. These findings may greatly add to our understanding of the microbiota characteristics of the shrimp pond ecosystem and the complex interactions among shrimp, ambient microflora, and environmental variables.


Microbial communities Rearing water Sediment Intestine Shrimp health Environmental factor 



This study was supported by the Key Laboratory of Mariculture (KLM2017005), Ministry Education, Ocean University of China (OUC) and Bio-Form Ecological Environment Corporation of Shandong (20160359). The funders had no role in the study design, data collection, and interpretation and the decision to submit the work for publication.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

The experiment was permitted by the Institutional Animal Care and Use Committee of the Ocean University of China.

Supplementary material

253_2018_9229_MOESM1_ESM.pdf (853 kb)
ESM 1 (PDF 852 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Fei Huang
    • 1
  • Luqing Pan
    • 1
    • 2
    Email author
  • Mengsi Song
    • 1
  • Changcheng Tian
    • 1
  • Shuo Gao
    • 1
  1. 1.The Key Laboratory of Mariculture (Ocean University of China)Ministry of EducationQingdaoChina
  2. 2.Fisheries CollegeOcean University of ChinaQingdaoChina

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