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The pathogenicity of disease-associated microbes varies widely between individuals. In this issue of Cell HostMicrobe, Rice et al. demonstrate that interactions between intestinal commensals reciprocally modulate the host immune response to each microbe, ameliorating the inflammation caused by one and dampening antibody responses to the other.

Atypical T cells take a different path Conventional T cells recognize peptides that are presented by polymorphic major histocompatibility complexes (MHCs). By contrast, many tissue-resident T cells, such as mucosal-associated invariant T cells, invariant natural killer T cells, and γδ T cells, respond to modified peptides and small molecules presented by conserved MHC-like molecules. Unconventional T cells are important for host defense and tissue repair and seed tissues during critical early-life windows of development. Constantinides and Belkaid review recent advances describing how unconventional T cell subsets compete for early-life signals, including those from the microbiota, which instruct their development and have enduring consequences for the health of the host. —STS

The microbiota, which consists of commensal bacteria, fungi, and viruses, limits the colonization of pathogens at barrier tissues and promotes immune homeostasis. The latter is accomplished through the induction and regulation of both innate and adaptive immune responses. Innate lymphocytes, which include the type-1 innate lymphoid cell (ILC1), NK cell, type-2 innate lymphoid cell (ILC2), type-3 innate lymphoid cell (ILC3), and lymphoid tissue inducer (LTi) cell populations, and innate-like lymphocytes, such as NKT cells, mucosal-associated invariant T (MAIT) cells, and γδ T cells, are uniquely capable of responding to the microbiota due to their tissue localization and rapid primary responses. In turn, through their effector functions, these lymphocyte populations modulate the composition of the microbiota and maintain the segregation of commensals. This review will focus on how innate and innate-like lymphocytes mediate the crosstalk with the microbiome.

Summary The microbiota plays a fundamental role in regulating host immunity. However, the processes involved in the initiation and regulation of immunity to the microbiota remain largely unknown. Here, we show that the skin microbiota promotes the discrete expression of defined endogenous retroviruses (ERVs). Keratinocyte-intrinsic responses to ERVs depended on cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes protein (STING) signaling and promoted the induction of commensal-specific T cells. Inhibition of ERV reverse transcription significantly impacted these responses, resulting in impaired immunity to the microbiota and its associated tissue repair function. Conversely, a lipid-enriched diet primed the skin for heightened ERV- expression in response to commensal colonization, leading to increased immune responses and tissue inflammation. Together, our results support the idea that the host may have co-opted its endogenous virome as a means to communicate with the exogenous microbiota, resulting in a multi-kingdom dialog that controls both tissue homeostasis and inflammation., Graphical abstract, Highlights • Endogenous retrovirus sensing is required for commensal-specific immunity • Reverse transcription inhibition impairs commensal-induced immunity in the skin • cGAS/STING signaling in keratinocytes is required for skin immunity to the microbiota • Enhanced endogenous retrovirus expression promotes microbiota-induced inflammation, The host immune system uses the endogenous virome to communicate with the exogenous microbiota in a multi-kingdom interaction that modulates tissue repair or inflammation.

Commensals rule the MAITrix Mucosal-associated invariant T (MAIT) cells play an important role in mucosal homeostasis. MAIT cells recognize microbial small molecules presented by the major histocompatibility complex class Ib molecule MR1. MAIT cells are absent in germ-free mice, and the mechanisms by which microbiota control MAIT cell development are unknown (see the Perspective by Oh and Unutmaz). Legoux et al. show that, in mice, development of MAIT cells within the thymus is governed by the bacterial product 5-(2-oxopropylideneamino)-6- d -ribitylaminouracil, which rapidly traffics from the mucosa to the thymus, where it is captured by MR1 and presented to developing MAIT cells. Constantinides et al. report that MAIT cell induction only occurs during a limited, early-life window and requires exposure to defined microbes that produce riboflavin derivatives. Continual interactions between MAIT cells and commensals in the skin modulates tissue repair functions. Together, these papers highlight how the microbiota can direct immune cell development and subsequent function at mucosal sites by secreting compounds that act like self-antigens. Science , this issue p. 494 , p. eaax6624 ; see also p. 419

Bcl6 and E3 ligase cullin 3 complexes mediate negative feedback regulation during thymocyte development and T cell activation to restrain exaggerated Tfh responses., Induction of Bcl6 (B cell lymphoma 6) is essential for T follicular helper (Tfh) cell differentiation of antigen-stimulated CD4+ T cells. Intriguingly, we found that Bcl6 was also highly and transiently expressed during the CD4+CD8+ (double positive [DP]) stage of T cell development, in association with the E3 ligase cullin 3 (Cul3), a novel binding partner of Bcl6 which ubiquitinates histone proteins. DP stage–specific deletion of the E3 ligase Cul3, or of Bcl6, induced the derepression of the Bcl6 target genes Batf (basic leucine zipper transcription factor, ATF-like) and Bcl6, in part through epigenetic modifications of CD4+ single-positive thymocytes. Although they maintained an apparently normal phenotype after emigration, they expressed increased amounts of Batf and Bcl6 at basal state and produced explosive and prolonged Tfh responses upon subsequent antigen encounter. Ablation of Cul3 in mature CD4+ splenocytes also resulted in dramatically exaggerated Tfh responses. Thus, although previous studies have emphasized the essential role of Bcl6 in inducing Tfh responses, our findings reveal that Bcl6–Cul3 complexes also provide essential negative feedback regulation during both thymocyte development and T cell activation to restrain excessive Tfh responses.

The discovery of tissue-resident innate lymphoid cell populations effecting different forms of type 1, 2, and 3 immunity; tissue repair; and immune regulation has transformed our understanding of mucosal immunity and allergy. The emerging complexity of these populations along with compounding issues of redundancy and plasticity raise intriguing questions about their precise lineage relationship. Here we review advances in mapping the emergence of these lineages from early lymphoid precursors. We discuss the identification of a common innate lymphoid cell precursor characterized by transient expression of the transcription factor PLZF, and the lineage relationships of innate lymphoid cells with conventional natural killer cells and lymphoid tissue inducer cells. We also review the rapidly growing understanding of the network of transcription factors that direct the development of these lineages.

How expression of canonical semi-invariant TCRs leads to innate-like effector differentiation is a central enigma of NKT cell development. NKT thymic precursors undergo elevated TCR signals leading to increased Egr2, which directly induces their signature transcription factor, PLZF. PLZF is necessary and sufficient to induce a multipotent, unbiased effector program that precedes terminal differentiation into T-bet(high) NK1.1(+) (NKT1) cells and recently identified NKT2 and NKT17 sublineages. Major variations in polarized NKT sublineages have been uncovered in different mouse strains and in several mutants, with direct impact on NKT cell function but also, unexpectedly, on the development and function of conventional T cells.

The transcriptional control of CD1d-restricted NKT cell development has remained elusive. We report that PLZF (promyelocytic leukemia zinc finger; Zbtb16), a member of the BTB/POZ-ZF family of transcription factors which includes the CD4 lineage-specific c-Krox (Th-POK, Zbtb7b), is exquisitely specific to CD1d-restricted NKT cells and human MR1-specific MAIT cells. PLZF was induced immediately after positive selection of NKT cell precursors and PLZF-deficient NKT cells failed to undergo the intrathymic expansion and effector differentiation that characterize their lineage. Instead, they preserved a naïve phenotype and were directed to lymph nodes. Conversely, transgenic expression of PLZF induced CD4 thymocytes to acquire effector differentiation and migrate to non-lymphoid tissues. We suggest that PLZF is a transcriptional signature of NKT cells that directs their innate-like effector differentiation during thymic development.