AI could Run a Million Microbial Experiments per Year

An artificial intelligence (AI) system enables robots to conduct autonomous scientific experiments - as many as 10,000 per day - potentially driving a drastic leap forward in the pace of discovery in areas from medicine to agriculture to environmental science.

Reported today in Nature Microbiology, the team was led by a professor now at the University of Michigan.

That artificial intelligence platform, dubbed BacterAI, mapped the metabolism of two microbes associated with oral health - with no baseline information to start with. Bacteria consume some combination of the 20 amino acids needed to support life, but each species requires specific nutrients to grow. The U-M team wanted to know what amino acids are needed by the beneficial microbes in our mouths so they can promote their growth.

"We know almost nothing about most of the bacteria that influence our health. Understanding how bacteria grow is the first step toward reengineering our microbiome," said Paul Jensen, U-M assistant professor of biomedical engineering who was at the University of Illinois when the project started.

Figuring out the combination of amino acids that bacteria like is tricky, however. Those 20 amino acids yield more than a million possible combinations, just based on whether each amino acid is present or not. Yet BacterAI was able to discover the amino acid requirements for the growth of both Streptococcus gordonii and Streptococcus sanguinis.

To find the right formula for each species, BacterAI tested hundreds of combinations of amino acids per day, honing its focus and changing combinations each morning based on the previous day's results. Within nine days, it was producing accurate predictions 90% of the time.

Unlike conventional approaches that feed labeled data sets into a machine-learning model, BacterAI creates its own data set through a series of experiments. By analyzing the results of previous trials, it comes up with predictions of what new experiments might give it the most information. As a result, it figured out most of the rules for feeding bacteria with fewer than 4,000 experiments.

"When a child learns to walk, they don't just watch adults walk and then say 'Ok, I got it,' stand up, and start walking. They fumble around and do some trial and error first," Jensen said.

"We wanted our AI agent to take steps and fall down, to come up with its own ideas and make mistakes. Every day, it gets a little better, a little smarter."

Little to no research has been conducted on roughly 90% of bacteria, and the amount of time and resources needed to learn even basic scientific information about them using conventional methods is daunting. Automated experimentation can drastically speed up these discoveries. The team ran up to 10,000 experiments in a single day.

But the applications go beyond microbiology. Researchers in any field can set up questions as puzzles for AI to solve through this kind of trial and error.

"With the recent explosion of mainstream AI over the last several months, many people are uncertain about what it will bring in the future, both positive and negative," said Adam Dama, a former engineer in the Jensen Lab and lead author of the study. "But to me, it's very clear that focused applications of AI like our project will accelerate everyday research."

The research was funded by the National Institutes of Health with support from NVIDIA.

Dama AC, Kim KS, Leyva DM et al.
BacterAI maps microbial metabolism without prior knowledge.
Nat Microbiol, 2023. doi: 10.1038/s41564-023-01376-0

Most Popular Now

Mahana Therapeutics Signs Agreement with…

Mahana Therapeutics, a leading provider of prescription digital therapeutics, announced today that the company has entered into a multi-million-dollar distribution and marketing partnership with the Consumer Health division of Bayer...

ChatGPT can Outperform University Studen…

ChatGPT may match or even exceed the average grade of university students when answering assessment questions across a range of subjects including computer science, political studies, engineering, and psychology, reports...

NHS AI Diagnostic Funding: Five Things t…

Opinion Article by Guilherme Carvalho, Sales & Contracts Manager, Sectra. A new £21 million fund for AI was announced by the UK government in June, with the intention of providing NHS...

ChatGPT Shows Limited Ability to Recomme…

For many patients, the internet serves as a powerful tool for self-education on medical topics. With ChatGPT now at patients’ fingertips, researchers from Brigham and Women’s Hospital, a founding member...

Combining AI Models Improves Breast Canc…

Combining artificial intelligence (AI) systems for short- and long-term breast cancer risk results in an improved cancer risk assessment, according to a study published in Radiology, a journal of the...

AI Predictions for Colorectal Cancer: On…

Colorectal cancer (CRC) ranks second in leading causes of cancer-related deaths globally, according to the WHO. For the first time, researchers from Helmholtz Munich and the University of Technology Dresden...

Healthcare Chatbot: Expand Support with …

The Danish eHealth platform, sundhed.dk, has faced a substantial surge in requests from Danish citizens and has swiftly expanded its support and effectively adapt to the ongoing changes in queries due...

ChatGPT Shows 'Impressive' Acc…

A new study led by investigators from Mass General Brigham has found that ChatGPT was about 72 percent accurate in overall clinical decision making, from coming up with possible diagnoses...

WiFi SPARK's Healthcare Business Re…

Leading WiFi provider WiFi SPARK is rebranding its healthcare arm as SPARK Technology Services Limited. The new identity marks the completion of the integration of the former Hospedia bedside unit...

AI Performs Comparably to Human Readers …

Using a standardized assessment, researchers in the UK compared the performance of a commercially available artificial intelligence (AI) algorithm with human readers of screening mammograms. Results of their findings were...

ChatGPT is Debunking Myths on Social Med…

ChatGPT could help to increase vaccine uptake by debunking myths around jab safety, say the authors of a study published in the peer-reviewed journal Human Vaccines and Immunotherapeutics. The researchers asked...

Online AI-Based Test for Parkinson'…

An artificial intelligence (AI) tool developed by researchers at the University of Rochester can help people with Parkinson's disease remotely assess the severity of their symptoms within minutes. A study...