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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.


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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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The authors declare no competing financial interests.

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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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