Scientists make bacteria dependent on squid pigments

In a bioreactor no bigger than a glass of water, the once-elusive pigment suddenly appears in vivid abundance. Xanthommatin is the molecule behind some of nature’s most dramatic colour tricks – the near-instant camouflage of squid and the shimmering eyes of insects – yet producing it in the laboratory has long been nearly impossible.

“We thought it would be cool to produce these pigments in bacteria,” says Pablo Ivan Nikel from the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark. “They are everywhere in the animal world – in squid, in butterflies and in our own eyes – but no microbe has ever been found that naturally makes them.” Xanthommatin is complex, expensive and normally extracted only in tiny amounts from animals or through inefficient chemical synthesis.

“The breakthrough came from an unexpectedly simple idea,” Nikel says. “We rewired the bacteria so that their survival requires producing the pigment. In practical terms, they are addicted,” Nikel explains. “They die if they do not make the pigment.”

The first experiment offered a moment of disbelief. “Either we messed up big time and this is pure contamination – or things were working on the first try,” Nikel recalls. But as the culture in the flask deepened into a vivid purple, the team realised that they had done something extraordinary. “Bacteria can be extraordinary chemists, and here you can actually see the colour.”

“By tying growth directly to pigment production, we suddenly had a general blueprint,” Nikel says. “A way to turn microbes into factories for whole new classes of high-value compounds.”

Why this pigment has been out of reach

For decades, biotechnology has promised to replace harsh chemical synthesis with cleaner, living cell factories. Nevertheless, even the most elegant engineering often collapses under evolutionary pressure. When researchers install a foreign biosynthetic pathway in a bacterium, the microbe typically treats it as a burden.

“The new product is not part of the microbe’s natural programme,” says Pablo Ivan Nikel. “It is very easy for the microbe to suppress it, mutate it or simply get rid of it.”

Xanthommatin, the pigment behind squid camouflage and butterfly wing colours, illustrates the challenge. It is a high-value molecule used in cosmetics, sunscreens, speciality dyes, wearable sensors and optical coatings. Nevertheless, there is no scalable, sustainable source: chemical synthesis is inefficient and expensive, and natural extraction requires killing animals.

One gram of xanthommatin can cost thousands of dollars, which has kept it from being used more widely.

“If you need to extract the pigment from animals, the yields are close to zero,” Nikel notes. In the case of squid, it also raises ethical questions: harvesting hundreds of animals for milligrams of pigment is neither sustainable nor humane.

“Producing xanthommatin in bacteria could reshape the entire materials pipeline,” Nikel says. “We replace animal extraction and polluting chemistry with microbes grown on sugar.”

But the biological challenge runs deeper.

“How can the whole animal change colour in the blink of an eye? It is still a matter of debate,” Nikel says. “The molecules are known, but not the physiological details. I always found it extremely interesting that we still do not know exactly how squids change colour so fast. The molecules are known, but the physiological trigger behind those instantaneous whole-body transformations is still to be elucidated.”

The trick that makes bacteria “need” colour

To overcome these barriers, the team turned to Pseudomonas putida, a bacterium that thrives under harsh conditions and can withstand the metabolic strain of complex engineering.

By reimagining what a “must-produce” molecule can be, the researchers opened the door to using microbes for compounds that previously seemed biologically out of reach.

“At the heart of the study is a simple but ingenious trick,” Nikel says. “Create a metabolic hole that only the pigment pathway can fill.”

The team engineered a precise deficiency in P. putida’s one-carbon metabolism – the system the cell uses to shuffle tiny one-carbon building blocks around – so that the strain cannot grow on its own. This is like removing a crucial Lego piece the cell needs to build with.

“We then introduced the entire biosynthetic route for xanthommatin, and one step in that pathway releases the exact missing ‘Lego block’ – just enough to patch the engineered defect – making pigment production the cell’s lifeline.”

This inversion – turning a molecule the cell normally does not care about into something it must make to survive – is at the core of the platform’s elegance.

“As soon as you know what needs to be modified to create the deficiency, you are in business,” Nikel says. “The activity of the pathway rescues the growth, and cells that do not keep it active simply do not grow.”

A purple flask that changes everything

To fine-tune the system, the researchers subjected the strain to adaptive laboratory evolution. In practice, this is automated Darwinian selection: robots grow the microbes through hundreds of generations and subtly change the conditions so that only the best pigment-producing cells thrive. It is evolution on rails.

“As the bacteria evolved, they strengthened the flow through the pigment pathway,” Nikel says. “Cells that produced more pigment grew better, and those that produced less fell behind.”

By wiring metabolism so neatly that a pigment becomes as essential as an amino acid, the researchers created a blueprint that could be reused for fragrances, cosmetic actives, antioxidants, agents that protect against ultraviolet light, speciality dyes or even drug precursors – all with the same growth-coupling logic.

The first indication that the strategy worked was not a graph or a sequencing readout – it was colour. Deep, unmistakable colour. “That was our eureka moment,” says Pablo Ivan Nikel.

That moment produced a rare mix of excitement and disbelief. As the culture deepened into a vivid purple, the team realised they had done something extraordinary: the engineered strain thrived while the control remained nearly colourless.

“The pigment is secreted directly into the surrounding broth,” Nikel says. “This prevents toxic build-up and makes purification surprisingly simple.”

Scaling up: a glass of water that replaces hundreds of animals

The performance exceeded expectations. In a 250-millilitre bioreactor – roughly a glass of water – the engineered bacteria produced pigment at levels once obtainable only from large numbers of animals.

“In the lab, the purified xanthommatin shows the same redox-driven colour shift we see in nature,” Nikel says.

Spectroscopy confirmed that it was chemically indistinguishable from the authentic molecule – produced here using only water, salts and sugar. The economics are equally striking: xanthommatin is a high-value specialty molecule with applications ranging from cosmetics and dyes to advanced materials.

“Because the pigment is tied to survival, the bacteria cannot turn off production – even if mutations arise. The strain stays genetically stable, becoming a reliable, self-maintaining factory.”

They produce a molecule that no microbe has ever produced naturally.

The bigger picture: when survival drives production

Xanthommatin may be the first showcase molecule of this system, but its significance extends far beyond pigments. By turning a complex animal metabolite into a requirement for life, the team has created a biomanufacturing logic in which evolution and engineering push in the same direction.

“Xanthommatin and its derivatives sit at the intersection of cosmetics, dyes, ultraviolet light protectants and advanced materials, and fermentation replaces both harsh chemical synthesis and ethically fraught extraction from animals.”

The deeper shift, however, is the platform itself. The same trick can be reused: if survival depends on making a molecule, the microbe keeps the pathway running. In principle, this could be applied to fragrances, antioxidants, dyes or even drug precursors.

The pigment’s natural roles hint at other possibilities. The pigment naturally switches colour depending on its chemical state – the same trick squid use. That behaviour could inspire colour-changing textiles, adaptive coatings or even biodegradable display components – ideas that become feasible once the biological supply barrier falls.

Engineered strains often lose their synthetic pathways over time, but these microbes retain pigment production because their survival depends on it – turning genetic stability into a built-in feature.

“Seen from this perspective, xanthommatin is just the opening act,” Nikel says.

The deeper achievement is a kind of programmable biology: a way to make microbes care about producing molecules they never evolved to make, because their survival depends on it – a shift that moves biomanufacturing into an era of truly evolution-friendly engineering.