Microkines offer promising new approach to cholera treatment

More than a million people die each year from infections with antimicrobial-resistant pathogens, and the problem is growing. Meanwhile, the discovery of new antimicrobials that can help stem the tide has not kept pace.

Researchers at the University of Texas at Austin see promise in a class of natural antimicrobials called microcins, which are produced by bacteria in the gut and help them compete with rival bacteria. In a pair of recent papers, researchers identify the first known microkinin that targets strains of bacteria that cause cholera and describe a method of finding microkinins in bacterial genomes with the help of artificial intelligence.

Imagine one day eating yogurt containing probiotic strains of microkine-producing bacteria to prevent or treat cholera, pathogenic E. coli, inflammatory bowel disease, or colon cancer. The idea is to put healthy bacteria that will then be able to continuously produce microkines in the gut to fight the pathogen of interest.”

Bryan Davies, professor of molecular life sciences and senior author on both papers

The cholera survey, published in Cell Host and Microbe, was led by Sun-Young Kim, Ph.D. candidate at UT.

Cholera, the deadly diarrheal disease caused by the bacterium Vibrio cholerae, causes severe dehydration and can kill in just a few hours. According to the World Health Organization, each year cholera is responsible for 21,000 to 143,000 deaths worldwide. Another type of gut bacteria is thought to trigger inflammatory bowel disease flare-ups. And yet another type of gut bacteria is associated with the development of colon cancer. Each is a potential target for microkinin.

Microkines are highly selective, meaning they usually target specific bacteria, unlike traditional antibiotics that generally kill both wanted and unwanted bacteria. This means they could potentially remove unwanted bacteria without disturbing the delicate balance of the human gut microbiome that is vital to overall health. And because their mechanism of action is different from that of traditional antibiotics, they can still be effective against pathogens that have developed antibiotic resistance.

It is difficult to identify microkines in the genome of a bacterium because their genetic sequences are very short and diverse. Instead, the team began searching the genomes of V. cholerae for a larger protein called PCAT, which is associated with microkines and helps export them from the bacteria that produce them so they can reach other bacteria. It’s like using a neighborhood landmark to help your friends find your house (“I’m two doors down from the fire station.”).

The researchers found about two dozen candidate microkines, all from nonpathogenic strains of V. cholerae. They showed that one of these microkines, named MvcC, kills pathogenic strains of V. cholerae. In other words, it’s a natural weapon that a bacterial strain uses to outsmart its henchmen.

“You have bacteria in your gut right now that are producing microkines,” Davies said. “They are a natural part of how your bacterial communities organize and compete.”

So how do strains of V. cholerae that produce microkines not become poisoned?

The researchers discovered that strains of V. cholerae that produce microcin also produce a type of antidote, called an immune protease. They showed that -? in mice whose intestines were infected with pathogenic and non-pathogenic strains of V. cholerae -? Microcin-expressing bacteria outcompeted non-expressing strains.

The researchers plan to continue the cholera work in three ways:

• Mutation of their anti-Vibrio microcin MvcC to be more lethal to V. cholerae and better resist degradation in the human body.
• Development of combinations of different anti-Vibrio microkines to prevent the development of antimicrobial resistance.
• Find out which microkinin-producing bacterial strains are best at producing and delivering microkines to pathogens in the gut.

In a related paper soon to be published in a peer-reviewed journal and available as a preprint, the researchers describe a new artificial intelligence-based approach to finding more candidate microkineses. The approach uses protein LLMs -? biologically analogous to the generative models of large AI languages ​​behind chatbots like ChatGPT -. to find sequences that are similar to known microkines. This is one of several AI-based approaches the team is experimenting with that they hope will lead to more microkinematic discoveries.

“The biology of the microkine is very unique and extremely understudied,” said Claus Wilke, professor of integrative biology and statistics and data science at UT, and a co-author on the forthcoming paper. “And so, it’s a good field to be in, where there’s still a lot to be done and discovered.”

This research was supported by The Welch Foundation, the National Institutes of Health, the US Army Research Office, the Winkler Family Foundation, and Tito’s Handmade Vodka.