Revisiting COVID-19; faecal microbiome and the possible consequences of dysbiosis

For May’s blog we are going to focus on a single article from BMJOG, getting a lot of social media attention! In their article on the Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity Hazan et al have clearly tapped into a huge area of interest in the wider COVID-19 and microbiome community.

As always, have a read of the previous blog posts here and have a look at the latest journal content on the website.

The study aimed to compare microbiome diversity, alongside composition, in asymptomatic to severe COVID-19 positive patients, exposed controls. The researchers performed shotgun metagenomic sequencing on stool samples from patients presenting to healthcare from March 2020-October 2021. Patients were grouped by severity based on NIH criteria. Importantly for microbiome studies, the controls were individuals who had prolonged or close contact with the positive patient, but tested negative themselves. In total 50 patients (of whom 28 were classified as severe) and 20 controls were recruited. Vitally, no patients were on ‘antibiotics, SARS-CoV-2 infection treatments, over the counter (OTC) remedies (e.g., vitamins, antipyretics, analgesics) or supplemental oxygen’ between confirmed COVID-19 positivity and sample collection.

In terms of the results, the 28 severe patients had significantly reduced bacterial diversity (Shannon Index, p=0.0499; Simpson Index, p=0.0581) compared to controls. Positive patients overall had lower relative abundances of a number of bacteria including Bifidobacterium, Faecalibacterium and Roseburium, but they had increased abundances of Bacteroides. Patients with positive PCRs had an inverse association between disease severity and abundance of the same bacteria.

The clinical implications of these results is interesting, and debatable. The authors hypothesise that low bacterial diversity, and potentially the depletion of specific bacterial genera led to reduced immune function and more severe disease. However, it could also be interpreted as a pattern of faecal bacteria resulting from COVID-19 infection and with limited possibility for therapeutic intervention. The authors propose that modulation of specific bacteria might reduce susceptibility to COVID-19, although this is highly speculative.

On the topic of COVID-19, an excellent review published in Gut has updated management of IBD in COVID-19, specifically aiding with risk stratification and vaccine response. This excellent paper, with practical points, is well worth the read.

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