Science China Life Sciences

, Volume 61, Issue 6, pp 696–705 | Cite as

Comparative study on the gut microbiotas of four economically important Asian carp species

  • Xinghao Li
  • Yuhe Yu
  • Chang Li
  • Qingyun YanEmail author
Research Paper


Gut microbiota of four economically important Asian carp species (silver carp, Hypophthalmichthys molitrix; bighead carp, Hypophthalmichthys nobilis; grass carp, Ctenopharyngodon idella; common carp, Cyprinus carpio) were compared using 16S rRNA gene pyrosequencing. Analysis of more than 590,000 quality-filtered sequences obtained from the foregut, midgut and hindgut of these four carp species revealed high microbial diversity among the samples. The foregut samples of grass carp exhibited more than 1,600 operational taxonomy units (OTUs) and the highest alpha-diversity index, followed by the silver carp foregut and midgut. Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria were the predominant phyla regardless of fish species or gut type. Pairwise (weighted) UniFrac distance-based permutational multivariate analysis of variance with fish species as a factor produced significant association (P<0.01). The gut microbiotas of all four carp species harbored saccharolytic or proteolytic microbes, likely in response to the differences in their feeding habits. In addition, extensive variations were also observed even within the same fish species. Our results indicate that the gut microbiotas of Asian carp depend on the exact species, even when the different species were cohabiting in the same environment. This study provides some new insights into developing commercial fish feeds and improving existing aquaculture strategies.


Asian carp gut microbiota feeding habit pyrosequencing Hypophthalmichthys molitrix Hypophthalmichthys nobilis Ctenopharyngodon idella Cyprinus carpio 


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This work was supported by the National Natural Science Foundation of China (31400109, 31372202) and the Youth Innovation Promotion Association, Chinese Academy of Sciences (Y22Z07).

Supplementary material

11427_2016_9296_MOESM1_ESM.docx (813 kb)
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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Laboratory of Protozoology, Institute of Evolution and Marine BiodiversityOUCQingdaoChina
  2. 2.Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
  3. 3.Environmental Microbiomics Research Center, School of Environmental Science and EngineeringSun Yat-sen UniversityGuangzhouChina

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