A metagenome-wide association study of gut microbiota in type 2 diabetes (original) (raw)

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Sequence Read Archive

Data deposits

The raw Illumina read data of all 368 samples has been deposited in the NCBI Sequence Read Archive under accession numbers SRA045646 and SRA050230. The assembly data, updated metagenome gene catalogue, annotation information, and MGLs are published in the GigaScience database, _Giga_DB[35](/articles/nature11450#ref-CR35 "Li, S. et. al. Type 2 diabetes gut metagenome (microbiome) data from 368 Chinese samples. GigaScience http://dx.doi.org/10.5524/100036

             (2012)").

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Acknowledgements

We thank L. Goodman for editing the manuscript and providing comments. This research was supported by the Ministry of Science and Technology of China, 863 program (2012AA02A201), the National Natural Science Foundation of China (30890032, 30725008, 30811130531, 31161130357), the Shenzhen Municipal Government of China (ZYC200903240080A, BGI20100001, CXB201108250096A, CXB201108250098A), the Danish Strategic Research Council grant (2106-07-0021), the Ole Rømer grant from Danish Natural Science Research Council, the Solexa project (272-07-0196), and the European Commission FP7 grant HEALTH-F4-2007-201052. The Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention and Care (LuCamp, http://www.lucamp.org). The Novo Nordisk Foundation Center for Basic Metabolic Research is an independent Research Center at the University of Copenhagen partially funded by an unrestricted donation from the Novo Nordisk Foundation (http://www.metabol.ku.dk). We are also indebted to many additional faculty and staff of BGI-Shenzhen who contributed to this work.

Author information

Author notes

  1. Junjie Qin, Yingrui Li, Zhiming Cai, Shenghui Li, Jianfeng Zhu and Fan Zhang: These authors contributed equally to this work.

Authors and Affiliations

  1. BGI-Shenzhen, Shenzhen 518083, China
    Junjie Qin, Yingrui Li, Shenghui Li, Jianfeng Zhu, Suisha Liang, Wenwei Zhang, Yuanlin Guan, Dongqian Shen, Yangqing Peng, Dongya Zhang, Zhuye Jie, Wenxian Wu, Youwen Qin, Wenbin Xue, Junhua Li, Xiaoping Li, Weineng Chen, Ran Xu, Mingbang Wang, Qiang Feng, Meihua Gong, Jing Yu, Yanyan Zhang, Ming Zhang, Zhaoxi Zhang, Hua Chen, Ruifu Yang, Weimou Zheng, Songgang Li, Huanming Yang, Jian Wang, Karsten Kristiansen & Jun Wang
  2. Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
    Zhiming Cai, Xiaojuan Sun, Zesong Li & Aifa Tang
  3. Peking University Shenzhen Hospital, Shenzhen, 518036, China
    Fan Zhang, Lingchuan Han, Donghui Lu, Peixian Wu & Yali Dai
  4. Medical Research Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China,
    Shilong Zhong
  5. The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark,
    Torben Hansen, Oluf Pedersen & Jun Wang
  6. Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, 94820, CA, USA
    Gaston Sanchez & Rasmus Nielsen
  7. Department of Structural Biology, VIB, 1050 Brussels, Belgium,
    Jeroen Raes, Gwen Falony & Shujiro Okuda
  8. Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, 1050 Brussels, Belgium,
    Jeroen Raes, Gwen Falony & Shujiro Okuda
  9. Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France,
    Mathieu Almeida, Emmanuelle LeChatelier, Pierre Renault, Nicolas Pons, Jean-Michel Batto & S. Dusko Ehrlich
  10. State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
    Ruifu Yang
  11. Institute of Biomedical Sciences, University of Copenhagen & Faculty of Health Science, University of Aarhus, DK-8000 Aarhus, Denmark,
    Oluf Pedersen
  12. Hagedorn Research Institute, DK-2820 Gentofte, Denmark,
    Oluf Pedersen
  13. Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark,
    Karsten Kristiansen & Jun Wang

Authors

  1. Junjie Qin
  2. Yingrui Li
  3. Zhiming Cai
  4. Shenghui Li
  5. Jianfeng Zhu
  6. Fan Zhang
  7. Suisha Liang
  8. Wenwei Zhang
  9. Yuanlin Guan
  10. Dongqian Shen
  11. Yangqing Peng
  12. Dongya Zhang
  13. Zhuye Jie
  14. Wenxian Wu
  15. Youwen Qin
  16. Wenbin Xue
  17. Junhua Li
  18. Lingchuan Han
  19. Donghui Lu
  20. Peixian Wu
  21. Yali Dai
  22. Xiaojuan Sun
  23. Zesong Li
  24. Aifa Tang
  25. Shilong Zhong
  26. Xiaoping Li
  27. Weineng Chen
  28. Ran Xu
  29. Mingbang Wang
  30. Qiang Feng
  31. Meihua Gong
  32. Jing Yu
  33. Yanyan Zhang
  34. Ming Zhang
  35. Torben Hansen
  36. Gaston Sanchez
  37. Jeroen Raes
  38. Gwen Falony
  39. Shujiro Okuda
  40. Mathieu Almeida
  41. Emmanuelle LeChatelier
  42. Pierre Renault
  43. Nicolas Pons
  44. Jean-Michel Batto
  45. Zhaoxi Zhang
  46. Hua Chen
  47. Ruifu Yang
  48. Weimou Zheng
  49. Songgang Li
  50. Huanming Yang
  51. Jian Wang
  52. S. Dusko Ehrlich
  53. Rasmus Nielsen
  54. Oluf Pedersen
  55. Karsten Kristiansen
  56. Jun Wang

Contributions

The project idea was conceived and the project was designed by Ju.W., K.K., O.P., R.N. and S.D.E.; J.Q., Y.L., Sh.L. and Ju.W. managed the project. F.Z., Z.C., R.X., Su.L., L.H., D.L., P.W., Y.D., X.S., Z.L., A.T., S.Z., M.W., Q.F. and T.H. performed sample collection and clinical study. Wen.Z., M.G., J.Y., Y.Z. and W.X. performed DNA experiments. Ju.W., K.K., O.P., R.N., S.D.E., J.Q., Y.L., Sh.L. and J.Z. designed the analysis. J.Q., Y.L., Sh.L., J.Z., Su.L., Y.G., Y.P., D.S., X.L., W.C., D.Z., Y.Q., M.Z., Z.Z., Z.J., G.S., J.L., J.R., S.O., H.C. and W.W. performed the data analysis. J.Q., Sh.L., J.Z., Y.G., Y.P., M.A., E.L., P.R., N.P. and J.-M.B. worked on metagenomic linkage group method. J.Q., D.S., Su.L., Y.Q., J.R., G.F. and S.O. did the functional annotation analyses. J.Q., Sh.L., D.S., J.Z., Y.P. and Y.L. wrote the paper. Ju.W., O.P., K.K., R.N., S.D.E., Ji.W., H.Y., So.L., Wei.Z. and R.Y. revised the paper.

Corresponding author

Correspondence toJun Wang.

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The authors declare no competing financial interests.

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Qin, J., Li, Y., Cai, Z. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes.Nature 490, 55–60 (2012). https://doi.org/10.1038/nature11450

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