Applied Microbiology and Biotechnology

, Volume 100, Issue 8, pp 3577–3586 | Cite as

Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene

  • Xiaoyang Wu
  • Honghai ZhangEmail author
  • Jun Chen
  • Shuai Shang
  • Qinguo Wei
  • Jiakuo Yan
  • Xiangyu Tu
Applied genetics and molecular biotechnology


Intestinal microbes are part of a complex ecosystem. They have a mutual relationship with the host and play an essential role in maintaining the host’s health. To optimize the feeding strategies and improve the health status of the dhole, which is an endangered species, we analyzed the structure of fecal microbes in four captive dholes using high-throughput Illumina sequencing targeting the V3–V4 region of the 16S rRNA gene. The diversity indexes and rarefaction curves indicated high microbial diversity in the intestines of the four dholes. The average number of operational taxonomical units (OTUs) in the four samples was 1196, but the number of OTUs common to all libraries was 126, suggesting only a few dominant species. Phylogenetic analysis identified 19 prokaryotic phyla from the 16S rRNA gene sequences, of which only 5 phyla were core microbiota: Bacteroidetes (21.63–38.97 %), Firmicutes (20.97–44.01 %), Proteobacteria (9.33–17.60 %), Fusobacteria (9.11–17.90 %), and Actinobacteria (1.22–2.87 %). These five phyla accounted for 97 % of the bacteria in all the dholes apart from one, in which 78 % of the bacteria were from these phyla. The results of our study provide an effective theoretical basis from which to reach an understanding of the biological mechanisms relevant to the protection of this endangered species.


Dhole (Cuon alpinusFecal microbes 16S rRNA Illumina MiSeq sequencing 



This research was supported by the Special Fund for Forest Scientific Research in the Public Welfare (201404420), the National Natural Science Fund of China (31372220, 31172119), the Natural Science Fund of Shandong Province of China (ZR2011CM009), and the Ph.D. Programs Foundation of Ministry of Education of China (20113705110001). The authors thank all the supports.

Compliance with ethical standards


This study was funded by the Special Fund for Forest Scientific Research in the Public Welfare (201404420), the National Natural Science Fund of China (31372220, 31172119), the Natural Science Fund of Shandong Province of China (ZR2011CM009), and the Ph.D. Programs Foundation of Ministry of Education of China (20113705110001).

Conflict of interest

All of the authors declare that they have no conflict of interest.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Xiaoyang Wu
    • 1
  • Honghai Zhang
    • 1
    Email author
  • Jun Chen
    • 1
  • Shuai Shang
    • 1
  • Qinguo Wei
    • 1
  • Jiakuo Yan
    • 1
  • Xiangyu Tu
    • 1
  1. 1.College of Life ScienceQufu Normal UniversityQufuChina

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