Understanding the Holobiont: How Microbial Metabolites Affect Human Health and Shape the Immune System

Abstract

The human gastrointestinal tract is populated by a diverse, highly mutualistic microbial flora, which is known as the microbiome. Disruptions to the microbiome have been shown to be associated with severe pathologies of the host, including metabolic disease, cancer, and inflammatory bowel disease. Mood and behavior are also susceptible to alterations in the gut microbiota. A particularly striking example of the symbiotic effects of the microbiome is the immune system, whose cells depend critically on a diverse array of microbial metabolites for normal development and behavior. This includes metabolites that are produced by bacteria from dietary components, metabolites that are produced by the host and biochemically modified by gut bacteria, and metabolites that are synthesized de novo by gut microbes. In this review, we highlight the role of the intestinal microbiome in human metabolic and inflammatory diseases and focus in particular on the molecular mechanisms that govern the gut-immune axis.

Keywords: atherosclerosis; commensals; indole; inflammatory bowel disease; metabolic syndrome; microbiome; obesity; polyamine; polysaccharide A; short-chain fatty acids.

Fig. 1. Intestinal bacteria convert dietary nutrients to immunomodulatory metabolites

Polysaccharides that cannot be digested by host enzymes, such as cellulose, are metabolized by the intestinal microbiota to short-chain fatty acids (SCFAs, green). These exert a plethora of anti-inflammatory effects, such as inducing the expansion and de novo differentiation of regulatory T cells; enhancing the barrier function of the intestinal mucosa through epithelial cells and goblet cells; facilitating production of antibodies by B cells; inhibiting the maturation of dendritic cells and promoting an anti-inflammatory phenotype; and reducing production of pro-inflammatory cytokines by innate immune cells. Dietary tryptophan is degraded to indole derivatives (blue). Indoles promote epithelial barrier function, e.g. by supporting the maintenance of type 3 innate lymphoid cells, which are the primary producers of IL-22. Dietary arginine is metabolized to polyamines (red), which promote the integrity of the intestinal epithelium and reduce the production of pro-inflammatory cytokines by macrophages. See text for details. DC, dendritic cell; EC, epithelial cell; GC, goblet cell; ILC3, type 3 innate lymphoid cell; MΦ, macrophage; NΦ, neutrophil; Treg, regulatory T cell.

Fig. 2. Immunomodulatory function of primary and secondary bile acids

Primary bile acids (green), such as cholic acid and chenodeoxycholic acid, are synthesized by the host in the liver and conjugated to glycine or taurine before secretion into the duodenum. In the intestinal tract, primary bile acids are converted by the microbiota to secondary bile acids (blue), such as deoxycholic acid and lithocholic acid, through a multi-step process that involves deconjugation and dehydroxylation. Primary and secondary bile acids can inhibit the secretion of pro-inflammatory cytokines by macrophages, dendritic cells and hepatocytes, as well as the production of osteopontin by NKT cells. During the deconjugation process, free taurine (red) is released into the intestinal lumen, where it can promote the integrity of the mucosal epithelium by increasing autocrine production of IL-18. See text for details. DC, dendritic cell; EC, epithelial cell; MΦ, macrophage.

Fig. 3. The effects of ATP and Polysaccharide A on the immune system

Extracellular ATP (green) secreted by bacteria of the intestinal tract has pro- and anti-inflammatory effects. While it promotes secretion of pro-inflammatory cytokines, chemotaxis and differentiation of naive T cells into T_H17 cells, ATP also inhibits release of IgA into the intestinal lumen by reducing the number of B-cell-activating T follicular helper cells. Polysaccharide A (PSA, blue) is produced by the intestinal bacterium Bacteroides fragilis. It promotes production of the anti-inflammatory cytokine IL-10 by T cells directly and indirectly through dendritic cells. See text for details. DC, dendritic cell; MΦ, macrophage; NΦ, neutrophil; Tfh, T follicular helper cell; Treg, regulatory T cell. Chemical structure of PSA subunit based on (Mazmanian and Kasper, 2006). [r]_n indicates where PSA subunit repeats branch off.