Data mining analysis of terminal restriction fragment length polymorphism shows geographical differences in the human gut microbiota

Andoh,Akira; Kobayashi,Toshio; Kuzuoka,Hiroyuki; Suzuki,Yasuo; Matsui,Toshiyuki; Nakamura,Shiro; Matsumoto,Takayuki; Fujiyama,Yoshihide; Bamba,Tadao

doi:10.3892/br.2013.127

July-August 2013 Volume 1 Issue 4

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July-August 2013 Volume 1 Issue 4

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Article

Data mining analysis of terminal restriction fragment length polymorphism shows geographical differences in the human gut microbiota

Authors:
- Akira Andoh
- Toshio Kobayashi
- Hiroyuki Kuzuoka
- Yasuo Suzuki
- Toshiyuki Matsui
- Shiro Nakamura
- Takayuki Matsumoto
- Yoshihide Fujiyama
- Tadao Bamba
View Affiliations / Copyright

Affiliations: Division of Mucosal Immunology, Graduate School, Shiga University of Medical Science, Otsu 520‑2192, Japan, Miyagi University, Sendai 982‑0215, Japan, Research and Development Laboratories, EN Otsuka Pharmaceutical Co., Ltd., Hanamaki, Iwate 025‑0312, Japan, Department of Internal Medicine, Toho University Sakura Medical Center, Sakura 285‑8741, Japan, Department of Gastroenterology, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka 818‑8502, Japan, Division of Lower Gastroenterology, Hyogo College of Medicine, Nishinomiya, Hyogo 663‑850, Japan, Department of Medicine, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
Pages: 559-562
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Published online on: May 30, 2013

https://doi.org/10.3892/br.2013.127
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Abstract

Environmental factors are important for shaping the gut microbiota. In this study, terminal‑restriction fragment length polymorphism (T‑RFLP) analysis was performed, and data mining analysis was applied to investigate the geographical differences in the gut microbiota in Japan. A total of 121 healthy individuals living in four different districts (Shiga, Hyogo, Fukuoka and Chiba prefectures) in Japan were enrolled. Their gut microbiota profiles were evaluated by T‑RFLP analysis, and data mining analysis using the Classification and Regression Tree (C&RT) approach was performed. Data mining analysis provided a decision tree that clearly identified the various groups of subjects (nodes). Some nodes characterized the subjects from the four geographically distinct regions. Overall, 21 of the 35 subjects from the Hyogo Prefecture were mainly included in Node 21, 11 of the 16 subjects from the Shiga Prefecture were mainly included in Node 19, 37 of 40 subjects from the Chiba Prefecture were mainly included in Node 6 and 28 of 30 subjects from the Fukuoka Prefecture were included in Node 3. Only eight operational taxonomic units (OTUs) of the total 100 OTUs contributed to the characterization of the gut microbiota of the four geographically distinct districts in Japan. Geographical differences in the human gut microbiota were identified in Japan. Data mining analysis appears to be one of the optimal tools for characterization of the human gut microbiota.

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Journals

International Journal of Molecular Medicine

International Journal of Oncology

Molecular Medicine Reports

Oncology Reports

Experimental and Therapeutic Medicine

Oncology Letters

Biomedical Reports

Molecular and Clinical Oncology

World Academy of Sciences Journal

International Journal of Functional Nutrition

International Journal of Epigenetics

Medicine International

Data mining analysis of terminal restriction fragment length polymorphism shows geographical differences in the human gut microbiota

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