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.