Ingredion has partnered with Holobiome to use AI and a database of two million bacterial genomes to predict how specific ingredients will interact with human health before clinical trials.
Research extends beyond digestion to explore how sweeteners, plant proteins, and texture solutions affect the gut-brain axis, including sleep and mental health.
This data-driven insight allows for “made-for-me” nutrition, accelerating the discovery of sustainable, health-forward ingredients tailored to specific consumer goals.
Ingredient supplier Ingredion has teamed up with biotechnology company Holobiome to explore how various food ingredients can affect the human gut microbiome and the body’s larger health functions beyond digestive health. The collaboration aims to help R&D departments better prioritize ingredients and food matrices worth advancing to human trials based on their gut interactions.
The partnership leverages Holobiome’s proprietary resources, including large-scale human cohorts, microbiome health models, bacterial strain banks, and human gut simulators.
The companies say ongoing research into how texture solutions, sweeteners and plant proteins affect the gut microbiome has “huge potential” to accelerate preclinical testing of individual ingredients.
Nutritional Insights spoke with Eric Weisser, head of Ventures, Open Innovation, and Customer Innovation at Ingredion, and Dr. Philip Strandwitz, founder and CEO of Holobiome.
By studying how ingredients act in the gut microbiome, Weisser says this new insight can help researchers apply a “critical lens” to ingredient discovery research for new functional products.
“Supported by Holobiome’s microbiome profile, researchers gain a better preclinical understanding of how materials behave from a systems biology perspective – not just functionally,” he notes.
Bacteria mapping 90,000 people
With a database of more than two million human gut bacterial genomes and a human gut simulator, Holobiome has mapped how bacteria and their functions are associated with health and disease, trained on data from more than 90,000 people.
“Think of this as knowing potential targets of interest in the microbiome – which we continue to improve with more data,” explained Strandwitz.
“By combining this ‘map’ with the microbiome data we generate from the filter material in a human gut simulator model, we can inform hypotheses that will advance to human trials for validation.”
He noted that gut health studies often rely on in vitro or in vivo screens, “if they have access to these.” Research methods have evolved exponentially in recent years, as supercomputing is increasingly harnessed to create individual gut microbiome maps for more focused nutritional guidance.
“Advances in the generation of large-scale data will really unlock healthier food choices. We are most excited about very large-scale, multi-omic experiments,” says Strandwitz.
Ingredion actively fosters food innovation partnerships to develop multifunctional ingredients, from bio-fermentation to postbiotics and fiber.Ingredion and Holobiome have explored specific microbial pathways or metabolites when linking ingredients to health outcomes, he highlighted. “We have some in common, like short-chain fatty acids, but many of the signatures we see are novel and informed by large-scale human cohorts.”
“This resolution is further strengthened by our microbial genome database, which sits at over 2,000,000 genomes today.”
Moreover, some categories of materials interact particularly strongly with the microbiome. Strandwitz highlights: “We definitely see fiber having an effect, but what’s more interesting to me is that we broadly see materials and categories of materials that show strong effects – and in ways that are not captured by fiber alone.”
“This unlocks important creativity for formulations, including combinations and things, that are closer to the final form of the product.”
AI to find functional proteins
This month, Ingredion announced a similar strategic R&D partnership to accelerate AI-powered functional protein discovery and development with Shiru. Shiru’s own AI discovery platform is touted as the industry’s broadest searchable database of functional protein ingredients, with more than 77 million naturally occurring protein sequences cataloged and analyzed.
We asked Weisser how parallel advances in microbiome science complement that approach.
“We see Shiru and Holobiome as partners in helping us solve two parts of the same challenge,” he highlighted. “Shiru’s AI discovery capabilities and Holobiome’s microbiome expertise are completely complementary in the way they are reshaping our approach.”
“Shiru helps us explore what’s possible, using AI to identify protein-derived materials that already exist in nature with functional potential. Holobiome adds another layer to help us understand how those materials interact with human health and performance.”
Weisser says that partnerships help Ingredion connect the dots. “From identifying promising materials to helping us better understand how they might perform, we’re building a smarter, end-to-end materials discovery and functional validation process.”
Shiru recently launched uPro, a functional protein from potatoes, and OleoPro, an alternative fat that mimics animal fat. These natural ingredients discovered by AI are on the market for use in food and personal care.
Potential Personalization
Microbiome-informed ingredient discovery is an important step toward more intentional and targeted nutrition. However, Strandwitz tells us that this does not mean that Holobiome will offer personalized solutions.
Microbiome-informed ingredient discovery is an important step toward more intentional and targeted nutrition.Insights from these partnerships will likely enable the development of more tailored products — such as formulations designed for specific consumer needs, goals, or life stages, he said. “It supports a broader shift to ‘made-for-me’ nutrition, where products feel more relevant and purposeful.”
“We believe the real value lies in improving how we design ingredients and formulations from the ground up, to better align with a range of consumer needs.”
Experts suggest that insights into the microbiome could open the door to new functional benefits beyond digestion, such as cognition or metabolic health. “The Holobiome doesn’t just study how food affects digestive health; it explores the gut-brain axis — analyzing how nutrition can support mental health, pain, sleep, and overall human health outcomes,” Weisser said.
“Our focus is to equip our customers with deeper insights so they can explore new products that align with growing consumer interest in more intentional, health-forward choices.”
Gut microbiome support takes center stage at the new Natural Products Expo West 2026 trade show, with targeted benefits spanning digestion, mood, immunity, skin health, and beyond. In that event, Nutritional Insights explored post- and probiotic innovation with experts from Cargill, Kerry, and Morinaga Food Nutrition.
Recently, scientists have discovered a new way to distinguish between healthy and diseased microbiomes, based on the interactions of gut bacteria. This led to the development of the Ecological Network Balance Index, which assesses whether microbial communities are dominated by competition or cooperation.
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