Exploring multi-omics tools and sharing research insights to improve nutrition

Food systems are under growing pressure to support human and planetary health. The Periodic Table of Food Initiative (PTFI) explores cutting-edge science to reshape nutrition, such as multi-omics tools — technologies that map food at the molecular level. PTFI states that these tools and collaborative research among its partners enable a holistic understanding of food composition and lay the groundwork for transformative innovations.

Nutrition Insight continues our talk with Selena Ahmed, PTFI’s global director, and Mariana Barboza, research program manager for the Innovation Institute for Food and Health (IIFH) at the University of California (UC), Davis. 

Both highlight the synergies and collaborations between PTFI Centers of Excellence, which champion food quality research and focus on translating science to impact regional landscapes. 

These centers tackle specific research questions, which often align with the initiative’s focus on determining food composition, how this changes based on product, and how it impacts people’s and planetary health. 

Barboza says that UC Davis IIFH is highly interested in advancing the understanding of food and developing new foods that can solve humanity’s problems.

“The majority of our society is suffering from diet-related disorders, and we need to provide solutions. Food is at the center of this issue and should also be part of a solution.” 

Multi-omics tools

Barboza says that UC Davis and its IIFH have developed several omics tests to map food components, holistically and synergistically tackling food analysis in multi-omics. These tests combine data from different biological molecules of one specific type. 

“The tool that we use in multi-omics is mass spectrometry, which has been historically used in biomedicine to identify biomarkers for cancer diagnostics, and at some point, some pivoted and started applying the tools developed for biopharma to characterize food.” 

She explains that from 2009 onward, researchers started using these tools developed to study blood to instead analyze food. This was defined as foodomics — applying omics technologies to food and nutrition to improve consumer well-being and health. 

Food products are sources of protein, lipids, carbohydrates, and small molecules. Barboza says researchers need specific methods to understand and analyze each compound. 

“To study proteins, we use proteomics. In carbohydrates, we normally talk about glycans and thus glycomics when we characterize carbohydrates.”

Barboza says that PTFI has at least five different omics that together provide a holistic analysis of food at the molecular level.“Small molecules are all under metabolomics, which you might intuitively think means metabolites. But it’s anything that is a small molecule,” she continues. “For fats or lipids, we do lipidomics.”

PTFI omics tools to measure micronutrients are called ionomics because these elements are ions. 

“We have at least five different omics that together provide a holistic analysis of food at the molecular level in a manner that has never been done before,” underscores Barboza. “People have been doing proteomics, glycomics, and metabolomics, but PTFI is doing all of that together.” 

“The food that we are characterizing and making available in the database has each of those components, which is unique, and that is part of the innovation of our initiative.”

Researchers and experts at UC Davis have helped develop these tests as leaders in their field, such as its West Coast Metabolomics Center focusing on food metabolomics or Dr. Justin Siegel, advancing the efficacy of proteins through enzymes. 

Dr. Carlito Lebrilla helps to dissect carbohydrates, developing three platforms to characterize these for PTFI. As carbohydrate molecules in foods are so complex, “nobody has studied them,” says Barboza. 

Transforming the food system

PTFI and UC Davis aim to achieve solutions that transform the global food system and make it more resilient. Barboza says these solutions need to be healthier than current offerings. 

“Most of the outcomes of the research in UC Davis IIFH ended up being companies,” she adds. “We have many in our portfolio, and some of them use the technologies we use with PTFI.” 

We recently met with Davis-born Rivalz Snacks to discuss its high-fiber and high-protein snacks.For example, some companies are commercializing sources of fiber that were discovered to modulate the gut microbiome. 

“There’s also a snack company that has become the snack company for the university, which spun out from UC Davis IIFH. It is a plant-based food, and at this moment, we are trying to increase the consumption of plant-based meals.” 

Ahmed adds that the Wellvine ingredient and Vine to Bar premium chocolate are interesting examples. This ingredient uses grape pomace — pulp, skin, and seeds — leftover from the wine industry. 

“While it doesn’t use PTFI tools, it’s a cool example of how multi-omics analysis from UC Davis was utilized to repurpose a prominent waste stream in California,” she says. “It enhances this chocolate and brings bioactives, but also enhances the flavor.”  

Barboza says that grape pomace is “rich in molecules that are feeding the microbiota in our gut, and the properties of these oligosaccharides combine perfectly with the chocolate. They provide the needed sweetness but reduce the total content of carbohydrates.” 

PTFI as an enabling platform

Ahmed and Barboza underscore the synergies and ongoing collaboration between PTFI’s Centers of Excellence. Each conducts its work but often tackles similar research questions with the same PTFI tools, allowing researchers to share and combine findings into place-based and global insights. 

Ahmed illustrates: “For example, saying, ‘I’m looking at this question over here, and you’re going to do that there.’ What are the differences? Is it very dependent on agro-climatic conditions? How is it based on the population in our place?” 

Synergies and collaboration between PTFI’s partners allow researchers to share and combine findings into place-based and global insights.Barboza says the different centers meet monthly, where participants share data and tools, troubleshoot issues, and provide solutions. “It’s a collaborative experience where everyone can understand what everyone is working on and support each other’s needs.” 

For example, she highlights a close collaboration between UC Davis and the Mexico Center of Excellence, where UC Davis can provide tools to analyze sources of protein that the Mexican center is interested in studying. 

“Those collaborations spontaneously happen when we are together, and we see how we can collaborate or help another project to begin.”

The case for dietary diversity

Although PTFI Centers of Excellence have access to the standardized multi-omics tools, unlike UC Davis, not all are running all omics platforms yet. 

Ahmed says that some centers in low- and middle-income countries do not have high-resolution mass spectrometry, which is needed to run these tests. “Part of our capacity-building efforts have been to work with funders to provide mass specs and the training for generating that data and meeting each center where they are in terms of their expertise.” 

PTFI also has standardized protocols for food system attributes to provide a context for where the food was grown. Thus, the centers can compare an apple grown in Davis with an apple from Fiji, comparing climate or agricultural conditions. 

Ahmed illustrates that apples vary significantly in composition between cultivars, where, and how they were grown.“I think the insights are that not all apples are the same,” says Ahmed. “There’s this tremendous diversity in composition, so when we make our dietary recommendations, such as eating more fruits and vegetables, while that’s good nutritional advice, we can even be more precise based on this type of data — what type of apple or how that apple was grown.” 

She highlights significant composition differences, especially with small metabolites, across apple cultivars and between apples grown in regenerative or non-regenerative agriculture. Similarly, there are more unique compounds in each dark, leafy green vegetable than in the whole category. 

Ahmed says these findings underscore the importance of increasing dietary diversity. “I’m not going to eat kale every day because it is quite different from spinach or chard.”

Nutrition diversity also adds to planetary health, she explains. “It’s about bringing biodiversity back to our agricultural systems so they can be more resilient in the face of climate change and planetary health, with biodiversity being such a core determinant of ensuring that the earth operates within a safe space for humanity.”