Current Microbiology

, Volume 75, Issue 10, pp 1316–1323 | Cite as

Analysis of the Gut Microbial Diversity of Dairy Cows During Peak Lactation by PacBio Single-Molecule Real-Time (SMRT) Sequencing

  • Weicheng Li
  • Qiangchuan Hou
  • Yanjie Wang
  • Huimin Ma
  • Yahua Liu
  • Feiyan Zhao
  • Jing Li
  • Lai-yu Kwok
  • Jie Yu
  • Zhihong Sun
  • Tiansong SunEmail author



The gut microbes of dairy cows are strongly associated with their health, but the relationship between milk production and the intestinal microbiota has seldom been studied. Thus, we explored the diversity of the intestinal microbiota during peak lactation of dairy cows.


The intestinal microbiota of nine dairy cows at peak lactation was evaluated using the Pacific Biosciences single-molecule real-time (PacBio SMRT) sequencing approach.


A total of 32,670 high-quality 16S rRNA gene sequences were obtained, belonging to 12 phyla, 59 families, 107 genera, and 162 species. Firmicutes (83%) were the dominant phylum, while Bacteroides (6.16%) was the dominant genus. All samples showed a high microbial diversity, with numerous genera of short chain fatty acid (SCFA)-producers. The proportion of SCFA producers was relatively high in relation to the identified core intestinal microbiota. Moreover, the predicted functional metagenome was heavily involved in energy metabolism.


This study provided novel insights into the link between the dairy cow gut microbiota and milk production.



We would like to express our gratitude to Professor Heping Zhang for his support, particularly for providing facilities to perform this work. Never forget why you started, and your mission can be accomplished. Funding was provided by National Natural Science Foundation of China.

Author Contributions

TS and ZS designed the study. WL and JL collected samples. FZ and YL processed. HM and YW sequenced samples. WL and QH analyzed the data. WL, JY, and LK wrote the paper.


This research was supported by the Science and Technology Major Project of Inner Mongolia Autonomous Region.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

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Supplementary material 5 (DOCX 12 KB)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Weicheng Li
    • 1
  • Qiangchuan Hou
    • 1
  • Yanjie Wang
    • 1
  • Huimin Ma
    • 1
  • Yahua Liu
    • 1
  • Feiyan Zhao
    • 1
  • Jing Li
    • 1
  • Lai-yu Kwok
    • 1
  • Jie Yu
    • 1
  • Zhihong Sun
    • 1
  • Tiansong Sun
    • 1
    Email author
  1. 1.Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural AffairsInner Mongolia Agricultural UniversityHohhotChina

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