HMN 2026: How Exploring metabolic noise opens new paths to better biomanufacturing

Much like humans, microbial organisms can be fickle in their productivity. One moment they’re cranking out useful chemicals in vast fermentation tanks, metabolizing feed to make products from pharmaceuticals and supplements to biodegradable plastics or fuels, and the next, they inexplicably go on strike.

Engineers at Washington University in St. Louis have found the source of the fluctuating metabolic activity in microorganisms and developed tools to keep every microbial cell at peak productivity during biomanufacturing.

The work, published in Nature Communications, tracks hundreds of E. coli cells as they produce a yellow food pigment—betaxanthin—while growing, dividing and carrying out normal metabolic activities.

Understanding metabolic noise in microbes

“Like the behavior of a person, sometimes microbes are motivated to work hard, but they ‘get tired’ much more quickly and easily,” said Fuzhong Zhang, the Francis F. Ahmann Professor in energy, environmental and chemical engineering (EECE) and co-director of the McKelvey School of Engineering’s Synthetic Biology Manufacturing of Advanced Materials Research Center. Zhang is the corresponding author of the research, along with Ph.D. students Xinyue Mu and Alexander Schmitz.

Bioengineers and biologists have long observed large cell-to-cell variations in microbial metabolism, often called metabolic noise, or more generally, cellular noise. However, it has remained unclear what caused these differences and how frequently highly productive cells switch to low-productivity states. This lack of understanding has limited engineers’ ability to develop effective strategies to enrich hardworking, high-producing cells for biomanufacturing.

Answers lie in single cells’ fluctuating behavior, which is extremely challenging to study. Researchers must be able to measure a low-abundant metabolite along with the enzyme that produces it inside a tiny single cell while that cell grows and divides. To address this challenge, the team built microfluidic devices and engineered E. coli to produce a unique, bright-yellow metabolite—betaxanthin—that can be easily distinguished from thousands of other cellular metabolites.

New tools and strategies for productivity

These new advances allowed them to discover that betaxanthin production fluctuates rapidly, with cells switching from high-production to low-production states within a few hours. Approximately 50% of this betaxanthin noise comes from fluctuations in the enzyme responsible for producing betaxanthin, which arise from natural randomness (stochasticity) in gene expression. Fluctuations in cell growth rate account for less than 10% of the betaxanthin variability.

Using experimental data, the team developed computational models to test four different control strategies to ramp up bioproduction. The models showed that enriching cells that stochastically overproduce the enzyme leads to substantial increases in betaxanthin production. The team later confirmed this prediction in fermentation experiments.

“We create a gene circuit that allows cells with higher stochastic enzyme expression to grow faster,” Zhang said. “These cells also become high betaxanthin producers, giving us more product overall.”

The work is part of ongoing efforts at the McKelvey EECE department to develop new biomanufacturing capabilities in support of a zero-waste circular economy. This includes the challenging task of keeping microbial “workers” focused on making renewable products.

The content is provided for information purposes only.