COVID-19 disrupts balance of faecal microbiome

Patients with the coronavirus disease 2019 (COVID-19) have an altered faecal microbiome, characterized by enrichments in opportunistic pathogens, and depletions of beneficial commensals, according to a recent study.

“These findings indicate the prolonged effect of SARS-CoV-2 infection on the gut microbiomes of patients with COVID-19,” researchers said. “Strategies to alter the gut microbiome might be developed to manage gastrointestinal effects of the virus in these patients.”

Fifteen COVID-19 patients participated in the pilot study, from whom around 0.1 g of faecal sample was collected, prewashed, and subjected to DNA extraction and amplification. The resulting libraries were trimmed and filtered, and reads were mapped to markers specific to bacterial clades. The researchers also evaluated the microbiota of six pneumonia and 15 healthy controls.

Only one COVID-19 patient presented with diarrhoea, and none developed gastrointestinal symptoms while hospitalized. Eight patients had received empirical antibiotics at baseline, while seven had not. Those who were antibiotic-naïve saw an enrichment of opportunistic pathogens in their stool samples at baseline relative to controls. These included Clostridium hathewayi and Actinomyces viscosus, among others. [Gastroenterology 2020;159:944-955.e8]

In comparison, those who were on baseline antibiotics showed a reduction in multiple beneficial symbiotic species, such as Faecalibacterium prausnitzii, Eubacterium rectale, and Dorea formicigenerans.

Being positive for COVID-19 emerged as the strongest host factor associated with alterations in the gut microbiome, according to permutational multivariate analysis of variance (p=0.002). Other significant factors included pneumonia, hyperlipidaemia, and antibiotic use. Age and sex showed no such impact.

Notably, even after the clearance of the SARS-CoV-2 virus the gut microbiome of COVID-19 patients remained markedly different from that of healthy controls. By the final follow-up, the gut microbial community in five cured COVID-19 patients grew to resemble the healthy controls’ but remained substantially altered in the remaining 10 patients.

By testing on the seven antibiotic-naïve COVID-19 patients, the researchers also found 23 bacterial taxa that interacted significantly with disease severity. Majority belonged to the Firmicutes phylum but exerted diverse effects on COVID-19. In addition, 14 bacterial species also appeared to influence the faecal viral load of SARS-CoV-2.

“[O]ur study provides evidence of prolonged gut microbiome dysbiosis in COVID-19 and its association with faecal SARS-CoV-2 virus shedding and disease severity,” the researchers said, noting that empirical antibiotics, which were in common use during the initial COVID-19 outbreak, could have worsened the situation, depleting microbial communities of beneficial symbionts and aggravating dysbiosis.

“[O]ur data support avoidance of unnecessary antibiotics use in the treatment of viral pneumonitis, as antibiotics can eliminate beneficial bacteria and weaken the gut barrier,” they added. “Improving efficacy of future immune interventions such as vaccines, through modulating the gut microbiome, in combating COVID-19 should be considered.”