Homeostatic Immunity and the Microbiota

Abstract

The microbiota plays a fundamental role in the induction, education, and function of the host immune system. In return, the host immune system has evolved multiple means by which to maintain its symbiotic relationship with the microbiota. The maintenance of this dialogue allows the induction of protective responses to pathogens and the utilization of regulatory pathways involved in the sustained tolerance to innocuous antigens. The ability of microbes to set the immunological tone of tissues, both locally and systemically, requires tonic sensing of microbes and complex feedback loops between innate and adaptive components of the immune system. Here we review the dominant cellular mediators of these interactions and discuss emerging themes associated with our current understanding of the homeostatic immunological dialogue between the host and its microbiota.

Figure 1. The microbiota plays a fundamental role in the induction, education and function of the mammalian immune system

Equally, evolution of the mammalian immune system has coincided with the acquisition of a complex microbiota, demonstrating a symbiotic relationship between the host immune system and its commensal microbiota. A self-reinforcing, dynamic dialogue ensures that commensal colonization occurs as a state of mutualism, the breakdown of which can result in chronic inflammatory disorders, including autoimmunity, allergies and metabolic syndromes. Conversely, selective modulation of the microbiota presents immense therapeutic potential for bolstering tumor immunotherapy, vaccination and resistance to antibiotic-resistant microbes.

Figure 2. Microbiota controls hematopoiesis and systemic hematopoietic cell education

(1) Microbiota-derived TLR and NOD ligands and metabolites (SCFA and AhR ligands) can act directly on local intestinal tissue cells, but also penetrate beyond the mucosa, into circulation to tune immune cells in peripheral tissues. (2) SCFA promote DC precursor activation and release into bloodstream. Microbiota-derived NOD1 ligands activate mesenchymal stem cells (MSC) to produce hematopoietic growth factors (IL-7, SCF, THPO, Flt3L, IL-6), and commensal-derived TLR ligands trigger MCP1 production by MSC and their progeny, thereby promoting monocyte exit into the bloodstream. (3) Diet-derived AhR-ligands promote continued tissue residency of Dendritic Epidermal T cells (DETC) within the skin epidermis. Local skin commensals engage local immune responses. Lipoteichoic acid (LTA) derived from S. aureus limits T cell activation by TLR2/6-dependent generation of myeloid-derived suppressor cells (MDSC). Conversely, colonization with S. epidermidis promotes cognate CD8⁺ T cell seeding of the epidermis, licensing of cytokine production by myeloid-derived IL-1, and engagement of antimicrobial pathways by keratinocytes. (4) SCFA-elicited DC precursors traffic to the lung and limit Th2 cell reactivation to dampen experimental asthma. Antibiotic-dependent dysbiosis elicits PGE₂ production which promotes M2 polarization of alveolar macrophages.

Figure 3. Commensal colonization differentially regulates innate and innate-like lymphoid cells

(1) Microbe-derived riboflavin metabolites promote development of mucosal-associated invariant T (MAIT) cells. (2) Commensal-induced cytokines IL-1β and IL-23 promote IL-17A production from γδT cells. (3) ILC3-derived IL-22 prevents translocation of Alcaligenes spp. to lymphoid architecture and promotes epithelial cell production of serum amyloid A (SAA)1/2 to license IL-17A production from Th17 cells. (4) ILC3-expressing MHC-II delete activated commensal-specific CD4⁺ T cells. (5) Early life colonization limits iNKT expansion and pathogenic function within the colonic lamina propria and lungs.

Figure 4. Commensal colonization promotes effector and regulatory T cell responses

(1) Intestinal colonization by Segmented Filamentous Bacteria (SFB) or Bifidobacterium adolescentis promotes local Th17 cell differentiation. (2) SFB colonization drives an ILC3/IL-22/SAA1/2 axis that licenses IL-17A production from ROR0γt⁺ Th17 cells within the terminal ileum. (3) Clostridia colonization promotes RORγt⁺ Foxp3⁺ pTreg cell accumulation, which in turn, limit colonic Th2 and Th17 cell responses. (4) Foxp3⁺ T_reg cells and ex-Th17/Tfh cells localize in the Peyer’s patches and promote B cell class-switch and production of IgA, which fosters a diverse microbiota and ensures commensal compartmentalization from the intestinal epithelium.