IISER research team develops AI-based tool to predict bacterial enzymes

BHOPAL: The Indian Institute of Science Education and Research Bhopal researchers have developed an artificial intelligence (AI) based method to predict how the bacteria in the gut break down various types of food and medication.

This web-based tool provides information about specific bacterial enzymes, reactions, and bacteria involved in the process of digestion and absorption of nutrients by the human gut.

IISER Bhopal team has created an AI-based tool called "GutBug” that can potentially predict all possible bacterial enzymes that act on bioactive dietary molecules as well as oral drugs. The finding of this research was published recentlyin the Journal of Molecular Biology.

The paper has been co-authored by Dr Vineet Sharma, associate professor of department of biological sciences, IISER Bhopal, along with research scholars Aditya Malwe and Gopal Srivastava. GutBug is available at https://metabiosys.iiserb.ac.in/gutbug.

The collection of good bacteria in the gut is called gut microbiome which plays a crucial role in the body processes of anything a human consumes orally. The number of microbes living in the gastrointestinal tract is greater than the number of human cells in the body.

The human gut microbiome is made of over a thousand different species of bacteria, which have more than 3.3 million unique genes. These bacteria secrete enzymes to process what a human eats and provide the body with various metabolites that are essential for health and body functions. However, studying the complex host-microbial relationships is a challenge because of the vastness of the microbiome and the fact that the collection of bacteria varies among individuals.

Explaining the technicalities of the research, Dr Vineet K. Sharma said, “GutBug uses a combination of machine learning, neural networks, and chemoinformatic methods. We used a curated database of 363,872 enzymes from ~700 human gut bacterial strains and a substrate database consisting of 3,457 enzymes to train the AI model.”

Dr Sharma said, “GutBug can help better understand how the food we eat or medicines we consume orally are processed by our gut bacteria and how this affects our health. Such understanding can be useful in designing diets, developing new prebiotics, creating nutraceutical products, and improving drug design depending on the nature of the gut bacteria each individual has, leading to personalized medicine.”