Certain commensal bacteria that reside in the human intestine produce compounds that can inhibit SARS-CoV-2, the virus causing COVID-19, researchers have found.

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Previous clinical findings have shown that some patients with moderate to severe COVID-19 have gastrointestinal symptoms, while others showed signs of infection solely in the lungs. "We wondered whether gut resident bacteria could protect the intestine from the invasion of the virus", said Mohammed Ali, a doctoral student at Yonsei University in Seoul.

To investigate this hypothesis, the researchers screened dominant bacteria inhabiting the gut for activity against SARS-CoV-2. Their search revealed that Bifidobacteria, which have previously been shown to suppress other bacteria such as Helicobacter pylori (H pylori) and have proven active against irritable bowel syndrome, had such activity, said Ali. H pylori can cause sores, called ulcers, in the lining of the stomach and also lead to stomach cancer.

The investigators also used machine learning to search for potential illness-fighting compounds in databases containing microbially produced molecules, discovering some that might also prove useful against SARS-CoV-2. "We leveraged previous coronavirus datasets in which several compounds were tested against targets from coronaviruses", said Ali. "This approach seems to be significant as those targets share features in common with SARS-CoV-2". Ali observed that many existing antibiotics and cancer therapies are compounds that bacteria use to compete with each other within the gastrointestinal tract and that these were initially purified from microbial secretions. "Finding microbes that secrete anti-coronavirus molecules will be a promising method to develop natural or engineered probiotics to expand our therapeutics prevention techniques, to provide a more sustainable way to combat the viral infection", said Ali.

The research will be presented at the World Microbe Forum, taking place online from June 20 to 24.