The enteric virome consists largely of bacteriophages and prophages related to commensal bacteria. Bacteriophages indirectly affect the host immune system by targeting their associated bacteria; however, studies suggest that bacteriophages also have distinct pathways that enable them to interact directly with the host. Eukaryotic viruses are less abundant than bacteriophages but are more efficient in the stimulation of host immune responses. Acute, permanent, and latent viral infections are detected by different types of pattern recognition receptors and induce host immune responses, including the antiviral type I interferon response. Understanding the complex interplay between commensal microorganisms and the host immune system is a prerequisite to elucidating their role in intestinal diseases.

肠病毒主要由与共生细菌有关的噬菌体和噬菌体组成。噬菌体通过靶向其相关细菌间接影响宿主免疫系统；然而，研究表明，噬菌体也具有独特的途径，使它们能够直接与宿主相互作用。真核病毒不如噬菌体丰富，但在刺激宿主免疫反应方面更为有效。急性，永久性和潜伏性病毒感染可通过不同类型的模式识别受体进行检测，并诱导宿主免疫应答，包括抗病毒I型干扰素应答。了解共生微生物和宿主免疫系统之间复杂的相互作用是阐明它们在肠道疾病中的作用的前提。