Microbial Ecology

, Volume 74, Issue 1, pp 239–249 | Cite as

Composition of Gut Microbiota in the Gibel Carp (Carassius auratus gibelio) Varies with Host Development

  • Xinghao Li
  • Li Zhou
  • Yuhe Yu
  • Jiajia Ni
  • Wenjie Xu
  • Qingyun Yan
Host Microbe Interactions


To understand how a bacteria-free fish gut ecosystem develops microbiota as the fish ages, we performed a 1-year study on the gut microbiota of hatchling gibel carp (Carassius auratus gibelio). Our results indicate that the gut microbial diversity increases significantly as the fish develop. The gut microbial community composition showed significant shifts corresponding to host age and appeared to shift at two time points despite consistent diet and environmental conditions, suggesting that some features of the gut microbial community may be determined by the host’s development. Dietary and environmental changes also seem to cause significant shifts in the fish gut microbial community. This study revealed that the gut microbiota of gibel carp assemble into distinct communities at different times during the host’s development and that this process is less affected by the surrounding environment than by the host diet and development. Community phylogenetic analyses based on the net relatedness index further showed that environmental filtering (host selection) deterministically governs the gut microbial community composition. More importantly, the influence of host-associated deterministic filtering tends to weaken significantly over the course of the host’s development. However, further studies are needed to assess whether this host development-dependent shift in gut microbiota will still exist under different rearing strategies.


Gut microbiota High-throughput sequencing 16S rRNA gene Gibel carp Phylogenetic diversity Net relatedness index 



The authors gratefully acknowledge Ellie Lin for help with English. This work was supported by the National Natural Science Foundation of China (Nos. 31400109, 31372202, and 31500417) and the Guangdong Natural Science Foundation (No. 2014A030310281).

Supplementary material

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Xinghao Li
    • 1
    • 2
  • Li Zhou
    • 1
  • Yuhe Yu
    • 1
  • Jiajia Ni
    • 3
    • 4
  • Wenjie Xu
    • 1
    • 2
  • Qingyun Yan
    • 1
    • 5
  1. 1.Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Institute of MicrobiologyGuangzhouChina
  4. 4.State Key Laboratory of Applied Microbiology Southern ChinaGuangzhouChina
  5. 5.Environmental Microbiome Research Center, School of Environmental Science and EngineeringSun Yat-sen UniversityGuangzhouChina

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