Immunoglobulin A (IgA) is the most abundant mammalian antibody isotype, constituting more than 80% of all antibody-secreting plasma cells at steady state. IgA is particularly prevalent at barrier surfaces such as the intestinal mucosa, where it forms a first line of defense in conjunction with innate mediators, including mucus and antimicrobial peptides. IgA is thought to coat and contain the resident commensal microbiota and provide protection against enteric pathogens. IgA responses occur under normal homeostatic conditions and involve both T cell–dependent and T cell–independent pathways of differentiation in mucosa-associated lymphoid tissues such as Peyer’s patches. However, despite its abundance, the specificity of homeostatic IgA has long remained elusive.

To elucidate the specificity and origins of homeostatic IgA, we performed unbiased, large-scale cloning and characterization of monoclonal antibodies (mAbs) from single murine IgA plasma cells and other B cell populations of different origins. All antibodies were expressed recombinantly with an IgG1 isotype to compare their reactivity independent of their monomeric or multimeric nature.

Panels of single cell–derived mAbs were cloned from various B cell and IgA plasma cell populations, and their microbiota-reactivity was characterized by using a combination of bacterial flow cytometry and 16S ribosomal RNA (rRNA) sequencing. Additionally, mAbs were assayed by enzyme-linked immunosorbent assay (ELISA) for polyreactivity—a peculiar property of certain antibodies that facilitates binding to a variety of structurally diverse antigens. Several insights emerged from this characterization: (i) Microbiota-reactive and polyreactive antibodies arose naturally in all naïve B cell populations but were significantly enriched among IgA-secreting plasma cells. (ii) Microbiota-reactive and polyreactive antibodies from naïve B cells and IgA plasma cells showed similar patterns of binding to a broad, but defined, subset of microbiota. This binding included many members of Proteobacteria but largely excluded those of Bacteroidetes and Firmicutes, the predominant phyla in the colon. Interestingly, broadly neutralizing antibodies against influenza virus, which had previously been shown to be frequently polyreactive, were also commonly microbiota-reactive and displayed binding patterns that resembled IgAs. These patterns of microbiota-reactivity thus appear to be a general property of polyreactive antibodies. (iii) The microbiota-reactive and polyreactive IgA repertoire emerged via a mechanism that was largely independent of T cell help or somatic hypermutation. Instead, naturally microbiota-reactive and polyreactive recirculating naïve B cells were selected to become IgA plasma cells in Peyer’s patches. Although some antibodies subsequently acquired somatic mutations, these did not substantially alter their reactivity. (iv) Differentiation of microbiota-reactive and polyreactive IgAs occurred independent of microbiota or exogenous dietary antigen. Analysis of germ-free mice and germ-free mice fed an antigen-free diet demonstrated that microbiota-reactive and polyreactive IgA plasma cells arose naturally, even in the absence of exogenous antigens.

We conclude that homeostatic intestinal IgAs are natural polyreactive antibodies with innate specificity to microbiota. These data suggest that IgA antibodies, though derived from the adaptive immune system, possess innate-like recognition properties that may facilitate adaptation to the vast and dynamic array of exogenous microbiota and dietary antigens encountered at mucosal surfaces.