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Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus)

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Abstract

The quantification and community of bacteria in the gastrointestinal (GI) tract (stomach, jejunum, ileum, cecum, colon and rectum) of red kangaroos (Macropus rufus) were examined by using real-time PCR and paired-end Illumina sequencing. The quantification of bacteria showed that the number of bacteria in jejunum and rectum was significantly lower than that in colon and cecum (P < 0.05). A total of 1,872,590 sequences was remained after quality-filtering and 50,948 OTUs were identified at the 97 % similarity level. The dominant phyla in the GI tract of red kangaroos were identified as Actinobacteria, Bacteroidetes and Firmicutes. At the level of genus, the samples from different parts of GI tract clustered into three groups: stomach, small intestine (jejunum and ileum) and large intestine (cecum and rectum). Prevotella (29.81 %) was the most dominant genus in the stomach and significantly (P < 0.05) higher than that in other parts of GI tract. In the small intestine, Bifidobacterium (33.04, 12.14 %) and Streptococcus (22.90, 19.16 %) were dominant genera. Unclassified Ruminococcaceae was the most dominant family in large intestine and the total relative abundance of unclassified bacteria was above 50 %. In identified genera, Dorea was the most important variable to discriminate large intestine and it was significantly higher in cecum than in stomach, small intestine and colon (P < 0.05). Bifidobacterium (21.89 %) was the only dominant genus in colon. Future work on culture in vitro and genome sequencing of those unidentified bacteria might give us insight into the function of these microorganisms in the GI tract. In addition, the comparison of the bacterial community in the foregut of kangaroos and other herbivores and the rumen might give us insight into the mechanism of fiber degradation and help us exploit approaches to improve the feed efficiency and subsequently, reduce the methane emission from herbivores.

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Acknowledgments

This work was financially supported by Nanjing Hongshan Forest Zoo, China. The authors thank Dr. Thomas J. Sharpton and his lab members at Oregon State University for their help in the analysis of Illumina data.

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    Authors and Affiliations

    1. Nanjing Hongshan Forest Zoo, Nanjing, 210028, China

      Meirong Li & Lingling Zhao

    2. Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Nanjing, 210095, China

      Wei Jin, Yuanfei Li, Yanfen Cheng & Weiyun Zhu

    3. Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China

      Wei Jin, Yuanfei Li, Yanfen Cheng & Weiyun Zhu

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    1. Meirong Li
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    2. Wei Jin
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    3. Yuanfei Li
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    Correspondence to Yanfen Cheng.

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    The experimental design and procedures were approved by the Animal Care and Use Committee of Nanjing Agricultural University in compliance with the Regulations for the Administration of Affairs Concerning Experimental Animals (The State Science and Technology Commission of People’s Republic of China, 1988). And our manuscript also complied with the Ethical Rules applicable for World Journal of Microbiology and Biotechnology.

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    Meirong Li and Wei Jin have contributed equally to this article.

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    Li, M., Jin, W., Li, Y. et al. Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus). World J Microbiol Biotechnol 32, 98 (2016). https://doi.org/10.1007/s11274-016-2054-z

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