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The Gut Microbiome in the NOD Mouse

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Type-1 Diabetes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1433))

Abstract

The microbiome (or microbiota) are an ecological community of commensal, symbiotic, and pathogenic microorganisms that outnumber the cells of the human body tenfold. These microorganisms are most abundant in the gut where they play an important role in health and disease. Alteration of the homeostasis of the gut microbiota can have beneficial or harmful consequences to health. There has recently been a major increase in studies on the association of the gut microbiome composition with disease phenotypes.

The nonobese diabetic (NOD) mouse is an excellent mouse model to study spontaneous type 1 diabetes development. We, and others, have reported that gut bacteria are critical modulators for type 1 diabetes development in genetically susceptible NOD mice.

Here we present our standard protocol for gut microbiome analysis in NOD mice that has been routinely implemented in our research laboratory. This incorporates the following steps: (1) Isolation of total DNA from gut bacteria from mouse fecal samples or intestinal contents; (2) bacterial DNA sequencing, and (3) basic data analysis.

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References

  1. Makino S et al (1980) Breeding of a non-obese, diabetic strain of mice. Jikken dobutsu. Exp Anim 29(1):1–13

    CAS  Google Scholar 

  2. Bluestone JA, Herold K, Eisenbarth G (2010) Genetics, pathogenesis and clinical interventions in type 1 diabetes. Nature 464(7293):1293–1300

    Article  CAS  PubMed  Google Scholar 

  3. Schulte BM et al (2012) Cytokine and chemokine production by human pancreatic islets upon enterovirus infection. Diabetes 61(8):2030–2036

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Wen L et al (2008) Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455(7216):1109–1113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Wikipedia. Accessed from https://en.wikipedia.org/wiki/Microbiota .

  6. Macpherson AJ, Uhr T (2004) Compartmentalization of the mucosal immune responses to commensal intestinal bacteria. Ann N Y Acad Sci 1029:36–43

    Article  CAS  PubMed  Google Scholar 

  7. Stecher B, Hardt WD (2011) Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14(1):82–91

    Article  CAS  PubMed  Google Scholar 

  8. Natividad JM et al (2012) Commensal and probiotic bacteria influence intestinal barrier function and susceptibility to colitis in Nod1-/-; Nod2-/- mice. Inflamm Bowel Dis 18(8):1434–1446

    Article  PubMed  Google Scholar 

  9. Kim YS, Ho SB (2010) Intestinal goblet cells and mucins in health and disease: recent insights and progress. Curr Gastroenterol Rep 12(5):319–330

    Article  PubMed  PubMed Central  Google Scholar 

  10. Dave M et al (2012) The human gut microbiome: current knowledge, challenges, and future directions. Transl Res 160(4):246–257

    Article  CAS  PubMed  Google Scholar 

  11. Dominguez-Bello MG et al (2011) Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 140(6):1713–1719

    Article  CAS  PubMed  Google Scholar 

  12. Allin KH, Nielsen T, Pedersen O (2015) Mechanisms in endocrinology: Gut microbiota in patients with type 2 diabetes mellitus. Eur J Endocrinol 172(4):R167–R177

    Article  CAS  PubMed  Google Scholar 

  13. Tai N, Wong FS, Wen L (2015) The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity. Rev Endocr Metab Disord 16(1):55–65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Llorente C, Schnabl B (2015) The gut microbiota and liver disease. Cell Mol Gastroenterol Hepatol 1(3):275–284

    Article  PubMed  PubMed Central  Google Scholar 

  15. Mafra D, Fouque D (2015) Gut microbiota and inflammation in chronic kidney disease patients. Clin Kidney J 8(3):332–334

    Article  PubMed  PubMed Central  Google Scholar 

  16. Goto Y, Kurashima Y, Kiyono H (2015) The gut microbiota and inflammatory bowel disease. Curr Opin Rheumatol 27(4):388–396

    Article  CAS  PubMed  Google Scholar 

  17. Wright EK et al (2015) Recent advances in characterizing the gastrointestinal microbiome in Crohn’s disease: a systematic review. Inflamm Bowel Dis 21(6):1219–1228

    PubMed  PubMed Central  Google Scholar 

  18. McCoy KD, Koller Y (2015) New developments providing mechanistic insight into the impact of the microbiota on allergic disease. Clin Immunol 159(2):170–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Vital M et al (2015) Alterations of the murine gut microbiome with age and allergic airway disease. J Immunol Res 2015:892568

    Article  PubMed  PubMed Central  Google Scholar 

  20. Dobbs SM et al (2015) Peripheral aetiopathogenic drivers and mediators of Parkinson’s disease and co-morbidities: role of gastrointestinal microbiota. J Neurovirol 22(1):22–32

    Article  PubMed  PubMed Central  Google Scholar 

  21. Zhao Y, Lukiw WJ (2015) Microbiome-generated amyloid and potential impact on amyloidogenesis in Alzheimer’s disease (AD). J Nat Sci 1(7):e138

    Google Scholar 

  22. Lerner A, Matthias T (2015) Rheumatoid arthritis-celiac disease relationship: Joints get that gut feeling. Autoimmun Rev 14(11):1038–1047

    Article  PubMed  Google Scholar 

  23. Johnson BM et al (2015) Impact of dietary deviation on disease progression and gut microbiome composition in lupus-prone SNF1 mice. Clin Exp Immunol 181(2):323–337

    Article  CAS  PubMed  Google Scholar 

  24. Alkanani AK et al (2015) Alterations in intestinal microbiota correlate with susceptibility to type 1 diabetes. Diabetes 64(10):3510–3520

    Article  CAS  PubMed  Google Scholar 

  25. Burrows MP et al (2015) Microbiota regulates type 1 diabetes through Toll-like receptors. Proc Natl Acad Sci U S A 112(32):9973–9977

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Gulden E, Wong FS, Wen L (2015) The gut microbiota and Type 1 diabetes. Clin Immunol 159(2):143–153

    Article  CAS  PubMed  Google Scholar 

  27. Hu C, Wong FS, Wen L (2015) Type 1 diabetes and gut microbiota: friend or foe? Pharmacol Res 98:9–15

    Article  CAS  PubMed  Google Scholar 

  28. Peng J et al (2014) Long term effect of gut microbiota transfer on diabetes development. J Autoimmun 53:85–94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kostic AD et al (2015) The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 17(2):260–273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Clarridge JE 3rd (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17(4):840–862

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Yarza P et al (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev 12(9):635–645

    CAS  Google Scholar 

  32. Soergel DA et al (2012) Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J 6(7):1440–1444

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Chakravorty S et al (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69(2):330–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Wang Y, Qian PY (2009) Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PloS One 4(10):e7401

    Article  PubMed  PubMed Central  Google Scholar 

  35. Guo F et al (2013) Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PloS One 8(10):e76185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Deusch O et al (2014) Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens. PloS One 9(7):e101021

    Article  PubMed  PubMed Central  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Endocrinology and Metabolism, School of Medicine, Yale University, 208020, New Haven, CT, 06520-8020, USA

    Jian Peng, Youjia Hu & Li Wen

  2. Institute of Molecular and Experimental Medicine, Cardiff School of Medicine, Cardiff University, Tenovus Building, Heath Park, CF14 4XN, UK

    F. Susan Wong

Authors
  1. Jian Peng
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  2. Youjia Hu
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  3. F. Susan Wong
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  4. Li Wen
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Corresponding author

Correspondence to Li Wen .

Editor information

Editors and Affiliations

  1. Diabetes and Metabolism Unit, School of Clinical Sciences, Southmead Hospital, University of Bristol, Bristol, United Kingdom

    Kathleen M. Gillespie

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© 2016 Springer Science+Business Media New York

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Peng, J., Hu, Y., Wong, F.S., Wen, L. (2016). The Gut Microbiome in the NOD Mouse. In: Gillespie, K. (eds) Type-1 Diabetes. Methods in Molecular Biology, vol 1433. Humana Press, New York, NY. https://doi.org/10.1007/7651_2016_331

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  • DOI: https://doi.org/10.1007/7651_2016_331

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3641-0

  • Online ISBN: 978-1-4939-3643-4

  • eBook Packages: Springer Protocols

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