Researchers explore microbial ecosystem in search of drugs to fight SARS-CoV-2

Previous clinical findings have shown that some patients with moderate to severe COVID-19 have gastro-intestinal symptoms, while others showed signs of infection solely in the lungs.

"We wondered whether gut resident bacteria could protect the intestine from invasion of the virus," said Mohammed Ali, a Ph.D. student in Medicine at Yonsei University, Seoul, South Korea.

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 H. pylori and have proven active against irritable bowel syndrome, had such activity, said Ali.

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. "To train our model we leveraged previous coronavirus datasets in which several compounds were tested against targets from coronaviruses," said Mr. Ali. "This approach seems to be significant as those targets share features in common with SARS-CoV-2."

Ali emphasized the ecological nature of his approach to this work, observing 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.

Junebeom Kim, a master's candidate, also contributed to this research. Ali and Kim were supervised by Sang Sun Yoon, Professor, Department of Microbiology and Immunology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea.

World Microbe Forum is a collaboration between the American Society for Microbiology (ASM), the Federation of European Microbiological Societies (FEMS), and several other societies, which is breaking barriers to share science and address the most pressing challenges facing humankind today.