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Microbial colonization influences early B-lineage development in the gut lamina propria


The RAG1/RAG2 endonuclease (RAG) initiates the V(D)J recombination reaction that assembles immunoglobulin heavy (IgH) and light (IgL) chain variable region exons from germline gene segments to generate primary antibody repertoires1. IgH V(D)J assembly occurs in progenitor (pro-) B cells followed by that of IgL in precursor (pre-) B cells. Expression of IgH μ and IgL (Igκ or Igλ) chains generates IgM, which is expressed on immature B cells as the B-cell antigen-binding receptor (BCR). Rag expression can continue in immature B cells2, allowing continued Igκ V(D)J recombination that replaces the initial VκJκ exon with one that generates a new specificity3,4,5. This ‘receptor editing’ process, which can also lead to Igλ V(D)J recombination and expression3,6,7, provides a mechanism whereby antigen encounter at the Rag-expressing immature B-cell stage helps shape pre-immune BCR repertoires. As the major site of postnatal B-cell development, the bone marrow is the principal location of primary immunoglobulin repertoire diversification in mice. Here we report that early B-cell development also occurs within the mouse intestinal lamina propria (LP), where the associated V(D)J recombination/receptor editing processes modulate primary LP immunoglobulin repertoires. At weanling age in normally housed mice, the LP contains a population of Rag-expressing B-lineage cells that harbour intermediates indicative of ongoing V(D)J recombination and which contain cells with pro-B, pre-B and editing phenotypes. Consistent with LP-specific receptor editing, Rag-expressing LP B-lineage cells have similar VH repertoires, but significantly different repertoires, compared to those of Rag2-expressing bone marrow counterparts. Moreover, colonization of germ-free mice leads to an increased ratio of Igλ-expressing versus Igκ-expressing B cells specifically in the LP. We conclude that B-cell development occurs in the intestinal mucosa, where it is regulated by extracellular signals from commensal microbes that influence gut immunoglobulin repertoires.

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Figure 1: Gut LP RAG2+ B-lineage cells in weanling age mice.
Figure 2: RAG2–GFP+ LP B-lineage developmental subsets.
Figure 3: Distinct segment usage in RAG2+ cells from BM versus LP.
Figure 4: Effects of gut colonization on development of LP B-lineage cells.

Accession codes


Gene Expression Omnibus

Data deposits

Microarray data have been deposited in MIAME format into the Gene Expression Omnibus GEO database under accession number GSE48870, and repertoire sequencing data have been deposited into the GEO database under accession number GSE48805.


  1. Jung, D., Giallourakis, C., Mostoslavsky, R. & Alt, F. W. Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu. Rev. Immunol. 24, 541–570 (2006)

    Article  CAS  Google Scholar 

  2. Yu, W. et al. Continued RAG expression in late stages of B cell development and no apparent re-induction after immunization. Nature 400, 682–687 (1999)

    Article  CAS  ADS  Google Scholar 

  3. Tiegs, S. L., Russell, D. M. & Nemazee, D. Receptor editing in self-reactive bone marrow B cells. J. Exp. Med. 177, 1009–1020 (1993)

    Article  CAS  Google Scholar 

  4. Gay, D., Saunders, T., Camper, S. & Weigert, M. Receptor editing: an approach by autoreactive B cells to escape tolerance. J. Exp. Med. 177, 999–1008 (1993)

    Article  CAS  Google Scholar 

  5. Pelanda, R. et al. Receptor editing in a transgenic mouse model: site, efficiency, and role in B cell tolerance and antibody diversification. Immunity 7, 765–775 (1997)

    Article  CAS  Google Scholar 

  6. Retter, M. W. & Nemazee, D. Receptor editing occurs frequently during normal B cell development. J. Exp. Med. 188, 1231–1238 (1998)

    Article  CAS  Google Scholar 

  7. Hertz, M. & Nemazee, D. BCR ligation induces receptor editing in IgM+IgD bone marrow B cells in vitro. Immunity 6, 429–436 (1997)

    Article  CAS  Google Scholar 

  8. Lanning, D., Zhu, X., Zhai, S. K. & Knight, K. L. Development of the antibody repertoire in rabbit: gut-associated lymphoid tissue, microbes, and selection. Immunol. Rev. 175, 214–228 (2000)

    Article  CAS  Google Scholar 

  9. Jenne, C. N., Kennedy, L. J. & Reynolds, J. D. Antibody repertoire development in the sheep. Dev. Comp. Immunol. 30, 165–174 (2006)

    Article  CAS  Google Scholar 

  10. Ratcliffe, M. J. Antibodies, immunoglobulin genes and the bursa of Fabricius in chicken B cell development. Dev. Comp. Immunol. 30, 101–118 (2006)

    Article  CAS  Google Scholar 

  11. Lanning, D. K., Rhee, K. J. & Knight, K. L. Intestinal bacteria and development of the B-lymphocyte repertoire. Trends Immunol. 26, 419–425 (2005)

    Article  CAS  Google Scholar 

  12. Butler, J. E. et al. Antibody repertoire development in fetal and neonatal piglets. VIII. Colonization is required for newborn piglets to make serum antibodies to T-dependent and type 2 T-independent antigens. J. Immunol. 169, 6822–6830 (2002)

    Article  CAS  Google Scholar 

  13. Wang, J. H. et al. Mechanisms promoting translocations in editing and switching peripheral B cells. Nature 460, 231–236 (2009)

    Article  CAS  ADS  Google Scholar 

  14. Wang, J. H. et al. Oncogenic transformation in the absence of Xrcc4 targets peripheral B cells that have undergone editing and switching. J. Exp. Med. 205, 3079–3090 (2008)

    Article  CAS  Google Scholar 

  15. Monroe, R. J. et al. RAG2:GFP knockin mice reveal novel aspects of RAG2 expression in primary and peripheral lymphoid tissues. Immunity 11, 201–212 (1999)

    Article  CAS  Google Scholar 

  16. Nagaoka, H., Yu, W. & Nussenzweig, M. C. Regulation of RAG expression in developing lymphocytes. Curr. Opin. Immunol. 12, 187–190 (2000)

    Article  CAS  Google Scholar 

  17. Nagaoka, H., Gonzalez-Aseguinolaza, G., Tsuji, M. & Nussenzweig, M. C. Immunization and infection change the number of recombination activating gene (RAG)-expressing B cells in the periphery by altering immature lymphocyte production. J. Exp. Med. 191, 2113–2120 (2000)

    Article  CAS  Google Scholar 

  18. Gärtner, F., Alt, F. W., Monroe, R. J. & Seidl, K. J. Antigen-independent appearance of recombination activating gene (Rag)-positive bone marrow B cells in the spleens of immunized mice. J. Exp. Med. 192, 1745–1754 (2000)

    Article  Google Scholar 

  19. Ueda, Y., Yang, K., Foster, S. J., Kondo, M. & Kelsoe, G. Inflammation controls B lymphopoiesis by regulating chemokine CXCL12 expression. J. Exp. Med. 199, 47–58 (2004)

    Article  CAS  Google Scholar 

  20. Jankovic, M., Casellas, R., Yannoutsos, N., Wardemann, H. & Nussenzweig, M. C. RAGs and regulation of autoantibodies. Annu. Rev. Immunol. 22, 485–501 (2004)

    Article  CAS  Google Scholar 

  21. Raff, M. C., Megson, M., Owen, J. J. & Cooper, M. D. Early production of intracellular IgM by B-lymphocyte precursors in mouse. Nature 259, 224–226 (1976)

    Article  CAS  ADS  Google Scholar 

  22. Desiderio, S. V. et al. Insertion of N regions into heavy-chain genes is correlated with expression of terminal deoxytransferase in B cells. Nature 311, 752–755 (1984)

    Article  CAS  ADS  Google Scholar 

  23. Golby, S. et al. B cell development and proliferation of mature B cells in human fetal intestine. J. Leukoc. Biol. 72, 279–284 (2002)

    CAS  PubMed  Google Scholar 

  24. Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012)

    Article  CAS  ADS  Google Scholar 

  25. Mackie, R. I., Sghir, A. & Gaskins, H. R. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69, 1035S–1045S (1999)

    Article  CAS  Google Scholar 

  26. Ueda, Y., Liao, D., Yang, K., Patel, A. & Kelsoe, G. T-independent activation-induced cytidine deaminase expression, class-switch recombination, and antibody production by immature/transitional 1 B cells. J. Immunol. 178, 3593–3601 (2007)

    Article  CAS  Google Scholar 

  27. Lefrancois, L. & Lycke, N. Isolation of mouse small intestinal intraepithelial lymphocytes, Peyer’s patch, and lamina propria cells. Curr. Protoc. Immunol. Ch. 3, Unit 3.19. (2001)

  28. Reich, M. et al. GenePattern 2.0. Nature Genet. 38, 500–501 (2006)

    Article  CAS  Google Scholar 

  29. Warren, R. L. et al. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res. 21, 790–797 (2011)

    Article  CAS  Google Scholar 

  30. Kepler, T. B. Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors [v1; ref status: indexed,] F1000 Res. 2, 103 (2013)

    Article  Google Scholar 

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This work was supported by National Institutes of Health grants AI020047 (to F.W.A.) and AI89972 (to D.R.W.), Lymphoma and Leukemia SCOR 7009-12 (to F.W.A.), and National Institutes of Health research contract HHSN272201000053C (to T.B.K.). D.R.W. was also supported by an award from the American Academy of Allergy Asthma and Immunology and CSL-Behring and holds a Career Award for Medical Scientists from the Burroughs Wellcome Fund. F.W.A. is an Investigator of the Howard Hughes Medical Institute.

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D.R.W. and F.W.A. designed the study; D.R.W., A.J.P., M.P.G., K.C.-J., J.M.M. and R.A.P. performed experiments; R.M.M. and T.B.K. performed computational analysis of sequencing data; S.J.R. performed immunohistochemistry experiments; D.R.W. and F.W.A. wrote the paper.

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Correspondence to Duane R. Wesemann or Frederick W. Alt.

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Wesemann, D., Portuguese, A., Meyers, R. et al. Microbial colonization influences early B-lineage development in the gut lamina propria. Nature 501, 112–115 (2013).

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