Certain bacterial colonists induce a highly specific T cell response. A hallmark of this encounter is that adaptive immunity develops preemptively, in the absence of an infection. However, the functional properties of colonist-induced T cells are not well defined, limiting our ability to understand anticommensal immunity and harness it therapeutically. We addressed both challenges by engineering the skin bacterium Staphylococcus epidermidis to express tumor antigens anchored to secreted or cell-surface proteins. Upon colonization, engineered S. epidermidis elicits tumor-specific T cells that circulate, infiltrate local and metastatic lesions, and exert cytotoxic activity. Thus, the immune response to a skin colonist can promote cellular immunity at a distal site and can be redirected against a target of therapeutic interest by expressing a target-derived antigen in a commensal.

Certain bacterial strains from the microbiome induce a potent, antigen-specific T cell response. However, the specificity of microbiome-induced T cells has not been explored at the strain level across the gut community. Here, we colonize germ-free mice with a complex defined community (97 or 112 bacterial strains) and profile T cell responses to each strain individually. Unexpectedly, the pattern of T cell responses suggests that many T cells in the gut repertoire recognize multiple bacterial strains from the community. We constructed T cell hybridomas from 92 T cell receptor (TCR) clonotypes; by screening every strain in the community against each hybridoma, we find that nearly all of the bacteria-specific TCRs exhibit a one-to-many TCR-to-strain relationship, including 13 abundant TCR clonotypes that are polyspecific for 18 Firmicutes in the community. By screening three pooled bacterial genomic libraries against 13 pooled hybridomas, we discover that they share a single target: a conserved substrate-binding protein (SBP) from an ABC transport system. Treg and Th17 cells specific for an epitope from this protein are abundant in community-colonized and specific-pathogen-free mice. Our work reveals that T cell recognition of Firmicutes is focused on a widely conserved cell-surface antigen, opening the door to new therapeutic strategies in which colonist-specific immune responses are rationally altered or redirected.

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Immune modulation has become central to treating cancer. However, global immune stimulation is only effective in a subset of patients and can lead to serious complications, including colitis and type I diabetes. Newer modalities like engineered T cells and tumor vaccines are more specific, but they have shown limited efficacy in solid tumors and are difficult to scale. Bacterial strains from the human microbiome can induce antigen-specific T cells to help maintain barrier function. Here, we redirect CD8+ and CD4+ T cells elicited by the skin commensal Staphylococcus epidermidis to recognize tumor cells by expressing tumor-derived antigens in the bacterial cell. S. epidermidis expressing the model antigen ovalbumin (S. epidermidis-OVA) stimulates antigen-specific CD8+ and CD4+ T cells in vitro. The subcellular localization of the antigen skews the response: cell wall-attached OVA preferentially stimulates CD8+ T cells whereas secreted OVA predominantly induces CD4+ T cells. In a syngeneic tumor model (OVA-expressing B16 melanoma), mice colonized topically with S. epidermidis-OVA exhibit a marked reduction in subcutaneous tumor volume compared to mice colonized with S. epidermidis expressing mCherry; this effect is dependent on live bacteria and a combination of CD8+ and CD4+ T cells. S. epidermidis-OVA also reduces tumor burden when tumor cells are injected intravenously (a model of metastasis), demonstrating that the antitumor effect operates in tissues distant from the site of bacterial colonization. S. epidermidis strains expressing neoantigen peptides from the B16 tumor cell line exhibit potent antitumor efficacy without inducing an autoimmune response against melanocytes in healthy tissue. Antigen-expressing colonists are a simple but powerful strategy to elicit a targeted T cell response in the context of cancer and other diseases.