The current coronavirus disease (COVID-19) pandemic poses a significant challenge for human microbiota researchers around the world, as the causes and long-term repercussions of infection at the gastrointestinal (GI) level are still unknown. Original research publications, clinical investigations, epidemiological reports, and review-type articles about human intestine infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the possible repercussions on the microbiota were reviewed in the current study. Furthermore, the following aspects of COVID-19 have been discussed: Epidemiology, human sensitivity, the impact of dietary habits on the intestinal microbiota, and the impact of comorbid metabolic disorders like obesity, inflammatory bowel disease (IBD), and diabetes on the intestinal microbiota. According to the studies, health, age, and nutritional condition are linked to specific bacterial populations in the gut, which may influence the clinical course of COVID-19 infection. Changes in the faecal microbiota were linked to the severity of SARS-CoV-2 and COVID-19 infections. Patients with metabolic and GI issues are likely to have a moderate-to-high risk of SARS-CoV-2 infection, implying that gut dysbiosis plays a direct role in COVID-19 severity. However, further work is needed to identify COVID-19's initial GI symptoms so that early management can be attempted.