Viruses and the Microbiota

Abstract

Every surface of the human body is colonized by a diverse microbial community called the microbiota, yet the impact of microbiota on viruses is unclear. Recent research has advanced our understanding of how microbiota influence viral infection. Microbiota inhibit infection of some viruses and promote infection of other viruses. These effects can occur through direct and/or indirect effects on the host and/or virus. This review examines the known effects and mechanisms by which the microbiota influence mammalian virus infections. Furthermore, we suggest strategies for future research on how microbiota impact viruses. Overall, microbiota may influence a wide array of viruses through diverse mechanisms, making the study of virus-microbiota interactions a fertile area for future investigation.

Keywords: bacteria; innate immunity; microbiota; virus.

Figure 1

Anatomical locations of potential microbiota-viral interactions. Distinct populations of the microbiota are found across the human body. Colored boxes represent the diversity in the bacterial taxa. Predominating bacterial taxa at each location are shown, although other taxa are also present (9, 10). At each of these sites, viruses initiate infection and potentially interact with the local microbiota community. Common viruses are shown. Red text indicates viruses that have been studied in the context of the microbiota.

Figure 2

Future work on microbiota-virus interactions: From phenomenology to molecular mechanism. Top: Ideally, initial studies with a given virus would start with examining the effect of the microbiota on viral infection using an animal model. Several viral families are shown (left, nonenveloped virus families; right, enveloped virus families). Middle: If animal studies indicate that microbiota promote or inhibit viral infection, then follow-up experiments to determine whether microbiota influence the host and/or viral particle should be performed. These experiments will provide clues regarding more specific mechanisms and are typically a combination of in vivo and in vitro experiments. Bottom: Once microbiota effects on the host or virion are confirmed, additional experiments may lead to identification of specific molecular mechanisms by which microbiota promote or inhibit infection. These experiments may identify specific microbial products conferring effects, binding sites on viral particles, specific immune cascades with proviral or antiviral effects, and so forth.