Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses

  • Mei San Tang
  • Rowann Bowcutt
  • P’ng Loke
Part of the Methods in Molecular Biology book series (MIMB, volume 1799)


The microbial communities that reside within the mammalian host play important roles in the development of a robust host immune system. With the advent of sequencing technology and barcoding strategy of the bacterial 16S ribosomal RNA (rRNA) gene, microbiota studies are becoming more economical but also more important in many immunology studies. Here, we described a representative study protocol to characterize how the microbiota changes during an intestinal helminth infection, with emphasis on subtle aspects of the experimental design that are critical for data interpretation.

Key words

16S rRNA Microbiota Helminth Type 2 immunity 



We thank Laurie M. Cox and the Blaser lab at the New York University School of Medicine for assistance with setting up 16S rRNA sequencing in our laboratory and for providing the reverse barcoded primer constructs. We thank David Artis for seed stock of T. muris.


  1. 1.
    Belkaid Y, Hand Timothy W (2014) Role of the microbiota in immunity and inflammation. Cell 157(1):121–141. Scholar
  2. 2.
    Girgis NM, Gundra UM, Pn L (2013) Immune regulation during helminth infections. PLoS Pathog 9(4):e1003250. Scholar
  3. 3.
    McSorley HJ, Maizels RM (2012) Helminth infections and host immune regulation. Clin Microbiol Rev 25(4):585–608. Scholar
  4. 4.
    Harnett W, Harnett MM (2010) Helminth-derived immunomodulators: can understanding the worm produce the pill? Nature Rev 10(4):278–284. Scholar
  5. 5.
    Brindley PJ, Mitreva M, Ghedin E, Lustigman S (2009) Helminth genomics: the implications for human health. PLoS Negl Trop Dis 3(10):e538. Scholar
  6. 6.
    Mutapi F The gut microbiome in the helminth infected host. Trends Parasitol 31(9):405–406.
  7. 7.
    Lee SC, Tang MS, Lim YAL, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Pn L (2014) Helminth colonization is associated with increased diversity of the gut microbiota. PLoS Negl Trop Dis 8(5):e2880. Scholar
  8. 8.
    Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, Gause WC, Blaser MJ, Bonneau RA, Lim YA, Loke P, Cadwell K (2016) Helminth infection promotes colonization resistance via type 2 immunity. Science 352(6285):608–612. Scholar
  9. 9.
    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108(Suppl 1):4516–4522. Scholar
  10. 10.
    Grencis RK (2015) Immunity to helminths: resistance, regulation, and susceptibility to gastrointestinal nematodes. Annu Rev Immunol 33:201–225. Scholar
  11. 11.
    Morgan XC, Huttenhower C (2012) Chapter 12: human microbiome analysis. PLoS Comput Biol 8(12):e1002808. Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of MicrobiologyNew York University School of MedicineNew YorkUSA
  2. 2.UCB CelltechSloughUK

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