(NIH) The trillions of microbes living in the gut—bacteria, fungi, and viruses—are known collectively as the gut microbiome. Research has shown that changes in gut microbes may contribute to a variety of diseases and conditions.
COVID-19 patients often have imbalances in their gut microbes that allow antibiotic-resistant bacterial infections to take over. These patients also have a high rate of secondary bacterial infections that may be life-threatening. However, it hasn’t been clear how SARS-CoV-2, the virus that causes COVID-19, affects the gut microbiome. Many critically ill COVID-19 patients receive antibiotics. These can also affect gut microbes. So, it’s not clear if COVID-19 or antibiotic treatment causes the microbiome disruptions in these patients.