The role of the microbiota in infectious diseases

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The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation.

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Fig. 1: Disruptions to the microbiota alter mechanisms of colonization resistance and affect infection outcomes.
Fig. 2: Example of how the indigenous microbiota influences infectious disease susceptibility in the female genital tract.
Fig. 3: Hypothesized mechanisms for therapies preventing the colonization or clearance of pathogens.


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The authors thank D. R. Hill, K. Rao and C. M. Bassis for helpful feedback on earlier versions of this manuscript, and D. R. Hill for many helpful conversations regarding this manuscript. This work was supported by a grant awarded to V.B.Y. from the National Institute of Allergy and Infectious Diseases at the National Institutes of Health (U01-AI124255).

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All authors contributed to the conceptualization, writing and preparation of this manuscript, as well as the creation of the figures.

Correspondence to Vincent B. Young.

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Libertucci, J., Young, V.B. The role of the microbiota in infectious diseases. Nat Microbiol 4, 35–45 (2019) doi:10.1038/s41564-018-0278-4

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