Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis)

  • Wenxi Qian
  • Weiping Ao
  • Cunhui Jia
  • Zhipeng LiEmail author
Original Paper


The rumen microbiome contributes greatly to the degradation of plant fibres to volatile fatty acids and microbial products, affecting the health and productivity of ruminants. In this study, we investigated the dynamics of colonisation by bacterial communities attached to reeds and cottonseed hulls in the rumen of Tarim red deer, a native species distributed in the desert of the Tarim Basin. The reed and cottonseed hull samples incubated in nylon bags for 1, 6, 12, and 48 h were collected and used to examine the bacterial communities by next-generation sequencing of the bacterial 16S rRNA gene. Prevotella1 and Rikenellaceae RC9 were the most abundant taxa in both the reed and cottonseed hull groups at various times, indicating a key role of these organisms in rumen fermentation in Tarim red deer. The relative abundances of cellulolytic bacteria, such as members of Fibrobacter, Treponema 2, Ruminococcaceae NK4A214 and Succiniclasticum increased, while that of the genus Prevotella 1 decreased, with increasing incubation time in both reeds and cottonseed hulls. Moreover, the temporal changes in bacterial diversity between reeds and cottonseed hulls were different, as demonstrated by the variations in the taxa Ruminococcaceae UCG 010 and Papillibacter in the reed group and Sphaerochaeta and Erysipelotrichaceae UCG 004 in the cottonseed hull group; the abundances of these bacteria first decreased and then increased. In conclusion, our results reveal the dynamics of bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer.


Tarim red deer Dynamics PrevotellaCellulolytic bacteria 



This study is supported by the Opening Project of Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group (Grant No. HS201702) to ZPL, and National Natural Science Foundation of China (Grant Nos. 31460610 and 31660671) to WXQ.

Compliance with ethical standards

Conflict of interest

We declare no conflict of interest exits among the authors, and manuscript is approved by all authors for submission. All authors declare that the work is original research that has not been published previously, and is not under consideration for publication elsewhere.

Human and animal participants

All animal care procedures were approved and authorised by the animal ethics committee of Tarim University.

Supplementary material

10482_2019_1260_MOESM1_ESM.tif (780 kb)
Figure S1. The dynamic composition at the phylum level of bacteria attached to reeds after 1, 6, 12, and 48 h of incubation in the rumen of Tarim red deer. (TIFF 779 kb)
10482_2019_1260_MOESM2_ESM.tif (731 kb)
Figure S2. The dynamic composition at the phylum level of bacteria attached to cottonseed hulls after 1, 6, 12, and 48 h of incubation in the rumen of Tarim red deer. (TIFF 731 kb)
10482_2019_1260_MOESM3_ESM.tif (1 mb)
Figure S3. Taxonomic representation showing the statistically and biologically difference in reed after 1, 6, 12, and 48 h of incubation in the rumen of Tarim red deer. Differences are represented by the colour of the most abundant class (Green, purple, red and blue indicating the samples after 1, 6, 12 and 48 h). The diameter of each circle’s diameter is proportional to the taxa abundance. (TIFF 1027 kb)
10482_2019_1260_MOESM4_ESM.tif (1.2 mb)
Figure S4. Taxonomic representation showing the statistically and biologically difference in cottonseed hulls over the incubation time. Differences are represented by the colour of the most abundant class (Green, purple, red and blue indicating the samples after 1, 6, 12 and 48 h). The diameter of each circle’s diameter is proportional to the taxa abundance. (TIFF 1225 kb)


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Authors and Affiliations

  1. 1.College of Animal ScienceTarim UniversityAlarChina
  2. 2.Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction GroupAlarChina
  3. 3.Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant SciencesChinese Academy of Agricultural SciencesChangchunChina

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