Gut Microbiome Alterations in COVID-19

Abstract

Since the outset of the coronavirus disease 2019 (COVID-19) pandemic, the gut microbiome in COVID-19 has garnered substantial interest, given its significant roles in human health and pathophysiology. Accumulating evidence is unveiling that the gut microbiome is broadly altered in COVID-19, including the bacterial microbiome, mycobiome, and virome. Overall, the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19, together with a decrease in gut microbiome diversity. Beyond the existence of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria, fungi, and eukaryotic viruses, which are also associated with disease severity and presentation. Meanwhile, a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with COVID-19. Such gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution, coinciding with 'long COVID' (also known as post-acute sequelae of COVID-19). The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2infection and its downstream detrimental effects on the systemic host immunity and the gut milieu. The impaired host immunity and distorted gut microbial ecology, particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida, may hinder the reassembly of the gut microbiome post COVID-19. Future investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection, as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.

Keywords: COVID-19; Gut; Immunity; Infection; Microbiome.

Figure 1

Alterations in the gut bacterial, fungal, and viral microbiome in patients with COVID-19 The gut bacterial microbiome in COVID-19 is characterized by decreased diversity and richness, and persistent bacterial microbiome dysbiosis even after disease resolution. The gut mycobiome in COVID-19 is characterized by increased fecal fungal load and increased beta-diversity (more heterogeneous), and it is unstable over time and also persistently altered after disease resolution. SARS-CoV-2 shows infectivity in the gut. Delayed SARS-CoV-2 viral shedding and persistent gut virome dysbiosis are both present after disease resolution. The gastrointestinal tract epithelial barrier is impaired in a subset of COVID-19 patients. The figure is created with BioRender.com.