Association of Intestinal Dysbiosis with Clinical Outcomes in COVID-19 Patients

Bacteria and viruses are fundamentally different forms of life.  Bacteria typically have all the machinery for their own metabolism and reproduction, while viruses multiply through hijacking the host cell biochemical machinery. 

Infections in people can be caused by certain bacteria and certain viruses. Examples of infections caused by bacteria include C. difficile colitis, Strep throat, cellulitis, urinary tract infections, etc. Examples of viral infections include influenza, HIV, Zika, and most recently COVID-19.

At first glance, it is hard to imagine how antibiotics, drugs that kill bacteria, can affect outcome of viral infections. In fact, doctors generally advise against using antibiotics for uncomplicated viral infections because they do not help to facilitate recovery and only promote antibiotic resistance. However, a viral infection can weaken the host and a person can get a bacterial superinfection on top of the viral one. In fact, most deaths associated with influenza happen in patients that develop bacterial superinfections.

Importantly, antibiotics also kill many of the normal bacteria that live in the intestinal tract. This is a potential problem because the intestinal bacteria continuously interact with the host immune system and help to calibrate all immune responses. For example, a research group at Stanford University showed that antibiotic treatment lowers protective immune responses to novel viruses and at the same time heightens inflammation.1 In multiple animal models administration of antibiotics made viral infections more severe and caused increased mortality.2


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  1. Hagan T, Cortese M, Rouphael N, et al. Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans. Cell 2019;178:1313-1328 e13.
  2. Winkler ES, Thackray LB. A long-distance relationship: the commensal gut microbiota and systemic viruses. Curr Opin Virol 2019;37:44-51.
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