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This study does not appear to address the composition of the gut biome of patients before infection, which is what I’d also be interested to know but that’s a more difficult study to conduct, I am sure.
Jack Cohen-Joppa

“The microscopic organisms living in our intestines may influence the severity of COVID-19 and the body's immune response to it, and could account for lingering symptoms, researchers reported on Monday in the journal Gut. They found that the gut microorganisms in COVID-19 patients were very different from those in uninfected individuals. "COVID patients lack certain good bacteria known to regulate our immune system," said Dr. Siew Ng of The Chinese University of Hong Kong. The presence of an abnormal assortment of gut bacteria, or "dysbiosis," persists after the virus is gone and could play a role in the long-lasting symptoms that plague some patients, she said. Her team has developed an oral formula of live bacteria known as probiotics and a special capsule to protect the organisms until they reach the gut. "Compared with patients on standard care, our pilot clinical study showed that more COVID patients who received our microbiome immunity formula achieved complete symptom resolution," Ng said, adding that those who got it had significantly reduced markers for inflammation in their blood, increased favorable bacteria in their stool and they developed neutralizing antibodies to the virus.”
link to study:
https://gut.bmj.com/content/early/2021/01/04/gutjnl-2020-323020

Abstract
Objective: Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus.

Methods: In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma.

Results: Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase.

Conclusion: Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.
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