The intestinal immune system recognizes and responds to the vast diversity of microbes present within the gut. Highly sophisticated cellular and molecular networks are continuously coordinated to tolerate the presence of a large number and diversity of bacteria on mucosal surfaces. Different types of bacteria induce different immune responses, and bacterial metabolism of dietary factors generates metabolites that have significant effects on host immune responses. Dendritic cells, epithelial cells, innate lymphoid cells, T-regulatory cells, effector lymphocytes, natural killer T cells, and B-cell responses can all be influenced by the microbiome. Many of the mechanisms being described are bacterial strain or metabolite-specific. A better understanding of the mechanisms governing microbiome-host immune responses will likely lead to novel therapeutics for inflammatory disorders.