Covid-19 & the gut microbiota

Covid-19 is a respiratory illness caused by a novel coronavirus (SARS-CoV-2) and is still affecting tens of millions of people worldwide today. Although most of Covid-19 patients present respiratory symptoms, up to 20% of them have gastrointestinal (GI) symptoms including diarrhea [1], suggesting that the digestive tract is an extrapulmonary site of disease expression and SARS-CoV-2 infection. In addition, Covid-19 presents a wide spectrum of disease severity, varying from asymptomatic, mild, severe, and up to critical resulting in respiratory failure or even death [2].

The GI tract is the largest immune organ in humans, playing critical roles in host defense against pathogens infections. Trillions of microorganisms live and colonize the human gut – bacteria, fungi, viruses, and other life forms that are collectively known as the microbiota – regulating the host immunity. Therefore, it is of paramount importance to understand if the gut microbiota modulates the host susceptibility to and severity of SARS-CoV-2 infection, as well as the impact of SARS-CoV-2 infection on the host GM and its downstream long-term effect on human health.

The gut bacterial microbiota and Covid-19

Covid-19 patients had significant alterations in the gut bacterial microbiome compared with healthy individuals, characterized by depletion of beneficial commensals and enrichment of opportunistic pathogens in the gut (Figure 1) [3]. Depletion of gut symbionts persisted even after the resolution of Covid-19. The baseline (at hospitalization) abundance of the bacteria Coprobacillus, Clostridium ramosum and Clostridium hathewayi showed positive correlation with Covid-19 severity, whereas there was an inverse correlation between the abundance of Faecalibacterium prausnitzii (known as an anti-inflammatory bacteria) and the disease severity.

SARS-CoV-2 uses the angiotensin converting enzyme 2 (ACE2) receptor to enter the host and this receptor is highly expressed in both the respiratory and gastrointestinal tracts [4]. ACE2 is important in controlling intestinal inflammation and gut microbial ecology [5]. Four Bacteroides species : B. dorei, B. thetaiotaomicron, B. massiliensis, and B. ovatus, were reported to inversely associate with ACE2 expression in murine gut [6]. Interestingly, their abundances in faecal microbiome also showed inverse correlation with faecal SARS-CoV-2 viral load in Covid-19 patients during the disease course. These findings suggest that the human bacterial GM is affected by Covid-19 and might calibrate the host defense against SARS-CoV-2 infection.

The fungal microbiome and Covid-19 

The GI tract also harbors a large number of fungi, collectively known as the mycobiome (fungal microbiome), which have been shown to be causally implicated in GM assembly and immune development [7]. Patients with Covid-19 also had altered gut mycobiomes, characterized by enrichment of Candida albicans and highly heterogeneous mycobiome configurations (Figure 1) [8]. The diversity of the fecal mycobiome in patients with Covid-19 at discharge was 2.5-fold higher than that in healthy individuals. Opportunistic fungal pathogens, Candida albicans, C. auris, and Aspergillus flavus were highly present in faeces of Covid-19 patients during the disease course. Two respiratory symptom- associated fungal pathogens, A.flavus and A. niger, were detected in faecal samples from a subset of patients with Covid-19, even after disease resolution. Unstable gut mycobiomes and prolonged dysbiosis persisted in approximately 30% of patients with Covid-19.

The gut virome and Covid-19 

Through shotgun RNA viral sequencing, a signature of active gut viral infection were found in 47% of patients with Covid-19, even in the absence of gastrointestinal symptoms and after respiratory clearance of SARS-CoV-2 [9], suggesting “quiescent” SARS-CoV-2 infection in the GI tract and potential faecal-oral transmission risk. Patients with such gastrointestinal SARSCoV- 2 activity harboured abnormal GM compositions and functions, featured by high abundances of opportunistic pathogens and enhanced capacity for biosynthesis of nucleotide and amino acid and carbohydrate metabolism (glycolysis) [9].

The human GI tract also harbours abundant viral/phage members collectively known as the gut virome. Covid-19 patients had under-representation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-Covid-19 subjects (Figure 1) [10]. Faecal virome in SARSCoV- 2 infection showed more stress-, inflammation- and virulence-associated gene encoding capacities. At patient baseline, faecal abundances of the RNA virus, Pepper chlorotic spot virus, and multiple bacteriophage species inversely correlated with Covid-19 severity. These viruses were also inversely associated with blood levels of pro-inflammatory proteins, white cells and neutrophils, indicating gut resident viruses might tune host immune response to SARS-CoV-2 infection. Among Covid-19 severity-associated DNA virus species, 40% species showed inverse correlation with age, which may underlie the observation that elderly subjects are at a higher risk for a more severe Covid-19.