Figure 3.

Microbial functions have many effects within the intestinal tract. (A) Bile acids (BA) emulsify lipids and vitamins, improving absorption by the host. Bile salt hydrolases produced by members of the microbiota deconjugate BAs, reducing their solubility and increase their excretion in the feces. Loss of BAs inhibits nutrient absorption and reduces BA recycling. (B) Short chain fatty acids (SCFA) are bacterial fermentation products that can be an energy source for colonocytes and impact immune cell development. Butyrate and propionate have been shown to inhibit nuclear histone deacetylases (HDAC) in macrophage and CD4 cells, prompting the generation of regulatory T cells (Treg). These Treg cells modulate the immune system, maintaining self-tolerance; suppression of allergy-, asthma- and pathogen-induced immunopathology; etc. Each unique arrow (back, gray, or dashed) from each SCFA, shows the respective downstream effects of each SCFA. (C) Tryptophan can be degraded by microbes into a variety of intermediates including indole and serotonin. These molecules are endogenous ligands for the aryl hydrocarbon receptor (AHR) that is present on multiple adaptive and innate immune cells. When AHR is signaled in interepithelial type 3 innate lymphoid cells, these cells produce IL-22. This cytoprotective cytokine supports the acts to strengthen epithelial barrier functions by inducing the secretion of antimicrobial peptides from epithelial cells, production of mucins (MUC-2), and proliferation of intestinal goblet cells.