Behind Every Breakthrough

UC San Diego-led team discovers new method for producing large amounts of color-changing, nature-inspired pigment in the lab

An octopus camouflages itself with the seafloor. UC San Diego scientists have discovered a new way to produce large amounts of xanthommatin, a natural pigment used in animal camouflage, in a bacterium for the first time. Photo: Charlotte Seid

November 03, 2025

Scientists at UC San Diego have moved one step closer to unlocking a superpower held by some of nature’s greatest “masters of disguise.”

Octopuses, squids, cuttlefish and other animals in the cephalopod family are well known for their ability to camouflage, changing the color of their skin to blend in with the environment. This remarkable display of mimicry is made possible by complex biological processes involving xanthommatin, a natural pigment.

Because of its color-shifting capabilities, xanthommatin has long intrigued scientists and even the military, but has proven difficult to produce and research in the lab — until now.

In a new study, a team led by UC San Diego’s Scripps Institution of Oceanography describes a major breakthrough in understanding nature’s ability to camouflage, as they successfully developed a new way to produce large amounts of xanthommatin pigment.

Their nature-inspired method massively over-produced the pigmented material for the first time in a bacterium, opening new possibilities for the pigment’s use in a wide range of materials and cosmetics — from photoelectronic devices and thermal coatings to dyes and UV protectants. The new approach produces up to 1,000 times more material than traditional methods.

“We’ve developed a new technique that has sped up our capabilities to make a material, in this case xanthommatin, in a bacterium for the first time,” said Bradley Moore, the study’s senior author and a marine chemist with joint appointments at Scripps Oceanography and UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences. “This natural pigment is what gives an octopus or a squid its ability to camouflage — a fantastic superpower — and our achievement to advance production of this material is just the tip of the iceberg.”

Published Nov. 3 in Nature Biotechnology, the study was funded by the National Institutes of Health, the Office of Naval Research, the Swiss National Science Foundation and the Novo Nordisk Foundation.

The study authors said their discovery is significant, not just for understanding this unique pigment — which sheds light into the biology and chemistry of the animal kingdom — but also because the technique they used could be applied to many other chemicals, potentially helping industries move away from fossil fuel-based materials toward nature-based alternatives.

A promising pigment

Beyond cephalopods, xanthommatin is also found in insects within the arthropod group, contributing to the brilliant orange and yellow hues of monarch butterfly wings and the bright reds seen in dragonfly bodies and fly eyes.

Cephalopods like this southern reef squid can change their skin color in an instant using xanthommatin, a natural pigment. Photo: Luca Davenport-Thomas

Despite xanthommatin’s fantastic color properties, it is poorly understood due to a persistent supply challenge. Harvesting the pigment from animals isn’t scalable or efficient, and traditional lab methods are labor intensive, reliant on chemical synthesis that is low yielding.

Researchers in the Moore Lab at Scripps Oceanography sought to change that, working with colleagues across UC San Diego and at the Novo Nordisk Foundation Center for Biosustainability in Denmark to design a solution, a sort of growth feedback loop they call “growth coupled biosynthesis.”

The way in which they bioengineered the octopus pigment, a chemical, in a bacterium represents a novel departure from typical biotechnological approaches. Their approach intimately connected the production of the pigment with the survival of the bacterium that made it.

“We needed a whole new approach to address this problem,” said Leah Bushin, lead author of the study, now a faculty member at Stanford University and formerly a postdoctoral researcher in the Moore Lab at Scripps Oceanography, where her work was conducted. “Essentially, we came up with a way to trick the bacteria into making more of the material that we needed.”

Typically, when researchers try to get a microbe to produce a foreign compound, it creates a major metabolic burden. Without significant genetic manipulation, the microbe resists diverting its essential resources to produce something unfamiliar.

By linking the cell’s survival to the production of their target compound, the team was able to trick the microbe into creating xanthommatin. To do this, they started with a genetically engineered “sick” cell, one that could only survive if it produced both the desired pigment, along with a second chemical called formic acid. For every molecule of pigment generated, the cell also produced one molecule of formic acid. The formic acid, in turn, provides fuel for the cell’s growth, creating a self-sustaining loop that drives pigment production.

“We made it such that activity through this pathway, of making the compound of interest, is absolutely essential for life. If the organism doesn’t make xanthommatin, it won’t grow,” said Bushin.

To further enhance the cells’ ability to produce the pigment, the team used robots to evolve and optimize the engineered microbes through two high-throughput adaptive laboratory evolution campaigns, which were developed by the lab of study co-author Adam Feist, professor in the Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering and senior scientist at the Novo Nordisk Foundation Center for Biosustainability. The team also applied custom bioinformatics tools from the Feist Lab to identify key genetic mutations that boosted efficiency and enabled the bacteria to make the pigment directly from a single nutrient source.

“This project gives a glimpse into a future where biology enables the sustainable production of valuable compounds and materials through advanced automation, data integration and computationally driven design,” said Feist. “Here, we show how we can accelerate innovation in biomanufacturing by bringing together engineers, biologists and chemists using some of the most advanced strain-engineering techniques to develop and optimize a novel product in a relatively short time.”

Leah Bushin and María Alván-Vargas hold samples of xanthommatin in solution freshly harvested from bacteria. Adding a reducing agent to the solution turns xanthommatin bright red. Photo: Pablo I. Nikel

Bacteria producing xanthommatin on a petri dish in the lab. Photo: Leah Bushin

Traditional approaches yield around five milligrams of pigment per liter “if you’re lucky,” said Bushin, while the new method yields between one to three grams per liter.

Getting from the planning stages to the actual experimentation in the lab took several years of dedicated work, but once the plan was put into motion, the results were almost immediate.

“It was one of my best days in the lab,” Bushin recalled of the first successful experiment. “I’d set up the experiment and left it overnight. When I came in the next morning and realized it worked and it was producing a lot of pigment, I was thrilled. Moments like that are why I do science.”

Next steps

Moore anticipates that this new biotech methodology, which is fully nature-inspired and non-invasive, will transform the way in which biochemicals are produced.

“We’ve really disrupted the way that people think about how you engineer a cell,” he said. “Our innovative technological approach sparked a huge leap in production capability. This new method solves a supply challenge and could now make this biomaterial much more broadly available.”

While some applications for this material are far-out, the authors noted active interest from the U.S. Department of Defense and cosmetics companies. According to the researchers, collaborators are interested in exploring the material’s natural camouflage capabilities, while skincare companies are interested in using it in natural sunscreens. Other industries see potential uses ranging from color-changing household paints to environmental sensors.

“As we look to the future, humans will want to rethink how we make materials to support our synthetic lifestyle of 8 billion people on Earth,” said Moore. “Thanks to federal funding, we’ve unlocked a promising new pathway for designing nature-inspired materials that are better for people and the planet.”

Additional study authors are Tobias Alter, María Alván-Vargas, Daniel Volke, Òscar Puiggené and Pablo Nikel from the Novo Nordisk Foundation Center for Biosustainability; Elina Olson from UC San Diego’s Shu Chien-Gene Lay Department of Bioengineering; Lara Dürr and Mariah Avila from Scripps Institution of Oceanography at UC San Diego; and Taehwan Kim and Leila Deravi from Northeastern University.

Samples collected throughout the bacterial fermentation show a gradual accumulation of the xanthommatin pigment over time. Photo: María Alván-Varga

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