How Can Fungi Address the Global Food Waste Problem?

Tucked away on the kitchen countertop sits a bubbling, living goop in a jar. Each day, a mixture of flour and water feeds the beige concoction, commencing a ritualistic dance that summons wild yeast and bacteria from the air. This transformation turns simple ingredients into a tangy, fermenting marvel embraced by professional bakers and home chefs alike to create rustic bread loaves.

Cooking is deeply rooted in science. Replacing eggs in baking with aquafaba from cooked legumes or using baking soda to increase the pH of onions for faster caramelization are just a couple examples of how a deeper understanding of physical and chemical principles can transform the cooking process. 

In his laboratory at Stanford University, chef-turned-scientist Vayu Hill-Maini loves to experiment with the science of food. He draws on his experiences in the kitchen and scientific training in biochemistry and microbiology to address challenges facing the food system. Specifically, his team uses filamentous fungi—molds and mushrooms—as a platform to address these goals and transform food waste into tasty meals. He believes that mastering food preservation, waste minimization, and alternative ingredients can lead to more sustainable culinary practices, reducing the environmental impact of the modern food system. For Hill-Maini, one manâ€s trash is another manâ€s dinner. 

From Chef to Scientist, Food is a Common Ground

For many, the kitchen is a sacred space, a warm haven where the scents of simmering spices and baked bread mingle with laughter, familiar faces, and memories. “Food is deeply meaningful and deeply personal and deeply connected to who I am and how I see the world,†said Hill-Maini, who noted the influence of his global upbringing. Born in Stockholm to a Cuban and Norwegian father and an Indian mother raised in Kenya, food became his bridge to connecting with these diverse cultures. 

At the age of 18, Hill-Maini moved to the US to pursue a career as a chef. After a few years working in a sandwich shop in New York City, Hill-Maini returned to school, enrolling at Carleton College. He recalled how difficult it was to connect with the overly theoretical material taught in the introductory biology, chemistry, and physics classes; he craved more hands-on learning that would allow him to tap into his creative side. During the summer after his freshman year, he visited the Fundación Alícia, started by Ferran Adrià, a three-star Michelin chef and pioneer in molecular gastronomy, a scientific approach to cooking that explores the chemical and physical properties of food to create innovative dishes.

“It was a space that really embraced science as a way to create new food innovations,†said Hill-Maini. 

He returned to university with a fresh perspective on his studies, recognizing that science served as a lens through which he could understand and connect with his passion; organic chemistry provided a foundation for understanding smell and sensation while biology was a vehicle for exploring the human experience and nutrition. His budding interests were met with support from mentors who encouraged him to continue his studies, which led him to pursue a PhD in biochemistry at Harvard University. 

“I never really dreamt or considered it, until these experiences led me there,†said Hill-Maini. 

“What if we actually reimagine those waste products…and we think of them as opportunities, as ingredients?†
– Vayu Hill-Maini, Stanford University

There, he studied how gut bacteria break down food and drugs and explored how the emergence of cooking in human evolution may have shifted the structure and function of the gut microbiome.^1,2 His graduate studies led him to a postdoctoral fellowship at the University of California, Berkeley (UC Berkeley), where he worked with bioengineer Jay Keasling to develop synthetic biology tools for manipulating microbial metabolism.

As he continued to immerse himself in the realms of biochemistry and microbiology, Hill-Maini saw an opportunity to combine his passions for science and cooking, envisioning innovative solutions to the pressing challenges facing the food system.

Fungal Fermentation for Tackling Food Waste

What happens to the spent grain used for producing beer, the remaining whey from cheesemaking, or the leftover soybeans and oats from making plant-based milks? The global food supply chain creates one-fourth of the total human-generated greenhouse gas emissions, with significant contributions from food loss and waste.^3,4 Furthermore, modern food production is making soils more acidic and bodies of water more nutrient-dense, which negatively impacts biodiversity and natural ecosystems.

“Food waste isn’t just a home problem with eggshells in your trashcan,†said Hill-Maini. “It’s really an industrial scale [problem].†These byproducts, which are produced en masse all over the world, are also packed with essential nutrients like fiber, fat, and protein, and therefore offer a unique opportunity to tackle two issues facing the worldâ€s food systems: sustainability and food insecurity. 

“What if we actually reimagine those waste products…and we think of them as opportunities, as ingredients?†said Hill-Maini. 

During his fellowship at UC Berkeley, he became increasingly interested in how microbes could transform food waste into tasty, nutritious, foods that carry a smaller carbon footprint.⁵ Fermentation is an age-old tradition in many cultures, from cheese to soy sauce to tempeh. 

“We’re not the first ones to think about it,†said Hill-Maini. “This is thousands of years of human ingenuity that we’re building on.†

Around this time, a chef colleague introduced him to a book on traditional Southeast Asian fermentations and pointed him to oncom (pronounced ahn†cham), a kind of meat substitute found in Western Java that is produced from soy pulp. He thought this was the perfect starting point for diving into the molecular biology underlying fungal fermentation.

To study the practice of fungal fermentation, tease apart the biochemistry, and explore new culinary dimensions, Hill-Maini teamed up with oncom experts in Indonesia, a Michelin-star chef in Copenhagen, and scientists at UC Berkeley. Their collaboration culminated in a paper published in Nature Microbiology, and a crowd-pleasing meal.⁶

When the team ran a metagenomic survey of oncom, they were surprised to find that the food source was dominated by a single fungus: Neurospora intermedia. In some samples, it was the only fungus they detected, suggesting that it is probably sufficient to turn waste into food. Curious how a single fungus achieves such a feat, the researchers explored the biochemical and genetic changes that occur during the fermentation process. When they cultivated N. intermedia on soymilk byproducts, they found that N. intermedia secretes enzymes that break down pectin and cellulose, two abundant biopolymers in plant waste. The biochemical reactions also altered the nutritional value and flavor profile of the products: The team observed an increase in protein content and antioxidants and a significant reduction in hexanal, a compound that creates an “off-note†flavor. 

When Hill-Maini and his team sequenced different strains of N. intermedia, including those found in the wild and those associated with oncom, they discovered that the fungal species exists as two different groups in nature: One is associated with food waste and the other grows in the path of a fire. When they looked deeper into the data, they found that the waste-associated strains were better at cellulose degradation than their wild counterparts. Whole-genome phylogenetic analyses confirmed that oncom-associated strains were genetically distinct from wild strains. This suggested to the researchers that some strains of N. intermedia have undergone genomic adaptations in response to human-generated byproducts. 

“It’s a beautiful story of the genetic adaptations and domestication that might have happened when humans actually took wild fungi and turned them into these powerful [fermentation] factories,†said Hill-Maini.

Hill-Maini and his team wondered whether N. intermedia could also give other common food waste products a second chance. They cultured N. intermedia with 30 different industrial byproducts, including hemp, apple pomace, banana peels, coffee grounds, and pumpkin seed, and found that the fungus grew on 27 of the plant-based byproducts. 

N. intermedia-fermented foods proved to be safe and nutritious, but how did they taste? To find out, Hill-Maini worked with the Danish chef Rasmus Munk to create oncom prototypes. Then, 60 guests rated these for flavor, texture, and appearance. “Everybody was very positive towards it,†he said. “Nuttyâ€, “mushroomâ€, and “earthy†are just a few of the words that the participants used to describe the flavor. “This is not only a cool science innovation; this is something that people might actually want to eat.†

Now, at Stanford University, where he recently started his own lab, Hill-Maini is looking to cook up new collaborations and engineer edible solutions for a more sustainable and equitable food system. 

A Science Lab to Let Him Cook

Historically, Hill-Maini noted, academia has been a “dead zone of innovation for food,†something he hopes to revitalize with his new research program. He is eager to scale up his research on filamentous fungi and leverage advances in human biology and medicine to push the boundaries of food innovation and fuel advances in planetary health. He noted, “Thatâ€s where the next food innovation is going to come from.â€

Recently, he developed a synthetic biology toolkit for the edible fungus Aspergillus oryzae, incorporating genetic tools like CRISPR-Cas9.⁷ This toolkit will allow scientists to bioengineer fungi for applications in food production, like improving nutritional value, and sustainability, such as bioremediation.⁸

Hill-Maini is also excited to continue working with chefs on projects for food waste conversion. “Every year, we are proving that there is magic at this interface,†said Hill-Maini. “Michelin star chefs [are] authored in Nature Microbiology, and top-level scientists are authored in chef journals and so we’re proving the power of this collaboration over and over again, and I’m excited to keep scaling that connection.â€

Previously, these collaborations occurred beyond the academic laboratory. Soon, he will have a research and development kitchen next door to his microbiology and synthetic biology lab. “What we’re hoping to do is to say, let’s bring in a chef to a biotechnology lab for three months, and let’s have them share their skills and perspectives around food, but let’s also bring them into the world of microbiology and biochemistry,†said Hill-Maini.