Food Allergy Fund Launches Microbiome Collective to Tackle Root Causes of Food Allergies and Related Immune Disease
First-of-its-kind research network aims at the gut microbiome, positioning food allergy science as the front line in tackling today’s fastest-growing immune diseases
Washington, D.C. (November 17, 2025) — Today, the Food Allergy Fund launched its multimillion-dollar, multi-institution Microbiome Collective. This first-of-its-kind framework aims to uncover the root causes of food allergies and related immune-driven gut diseases. Food allergies and immune-related gut conditions are among today’s fastest-growing health challenges. By uniting leading scientists and new biotechnologies under a single, coordinated effort, the FAF Microbiome Collective aims to deliver earlier diagnostics and disease-modifying treatments to millions of people worldwide.
"Food allergies may be the canary in the coal mine for a much larger health crisis tied to the microbiome,” said Ilana Golant, FAF founder and CEO. “Solving allergies could reveal how to prevent and treat a range of diseases—from autoimmune disorders to neurodegeneration—that impact millions of lives."
Unlike traditional funding models, the Food Allergy Fund Microbiome Collective creates a shared research infrastructure where teams share data, and co-develop hypotheses tested both from the bottom up (through controlled lab studies) and top down (in human trials). This approach eliminates the reproducibility crisis that has plagued previous microbiome research and accelerates the translation of therapeutic outcomes and findings into patient tools.
“Previous microbiome studies have been limited by small sample sizes, different methodologies, and isolated datasets,” said Dr. Rima Rachid, director, Food Allergy Program, Boston Children’s Hospital. “FAF’s Collective model creates the scale and standardization needed to link specific microbiome mechanisms to disease, and, more importantly, to develop precision treatments.”
Built on Breakthrough Results
The Global Microbiome Research Collective includes and builds on cutting-edge research funded by FAF:
Diet–Microbiome Interactions to Predict Food Allergy Severity and Treatment Response — In this upcoming study, researchers will analyze stool samples from peanut-allergic children to identify which gut bacteria patterns are linked to more severe allergic inflammation and how different foods interact with those microbes. By mapping these “diet to microbiome relationships,” the researchers aim to develop personalized nutrition strategies for reducing allergic reactions and allergic disease. If successful, this approach will be expanded to include patients of different ages and additional food allergies. (University of California San Francisco - Dr. Susan Lynch)
First-in-human fecal microbiota transplantation (FMT) trial and Phase II Trial Evaluating the Safety and Efficacy of MTT in Children — In the first clinical trial of FMT (a therapy that transfers healthy gut bacteria from a donor into a patient’s digestive system) delivered in oral capsule form, 40% of participants increased their threshold reactive dose from traces to 1.5–3 peanuts after a single treatment. Adult results advanced into phase II pediatric trials, testing a shelf-stable oral version of encapsulated microbiota transplantation therapy (MTT) (Boston Children’s Hospital - Dr. Rima Rachid & Dr. Talal Chatila).
Engineering Probiotics to Build Food Tolerance — A new collaboration is combining Memorial Sloan Kettering’s Chrysothemis Brown Lab’s discovery of Thetis cells—immune cells that help the body learn tolerance in early life—with the Ronda Lab’s microbiome engineering and AI tools. This two-phase program will first build an atlas of tolerance pathways and then develop safe probiotic-based therapeutics to both prevent and treat food allergies. (Innovative Genomics Institute, UC Berkeley – Dr. Carlotta Ronda & MSK Cancer Center – Dr. Chrysothemis Brown)
A Synbiotic for the Prevention of Food Allergies — Researchers developed a novel synbiotic that combines prebiotics (fibers that feed good bacteria) with butyrate-producing probiotics. This next-generation approach strengthens immune regulation and prevents food allergy in animal models. (Pritzker School of Molecular Engineering - Dr. Cathryn Nagler)
Decoding the Gut: How Microbes and Metabolites Shape Food Allergy Treatments — Research revealed that bile acids and an increase in protective gut bacteria (Bacteroidales) play a key role in helping the body build tolerance to food, pointing to new ways to prevent or reverse food allergies. Boston Children’s Hospital (Dr. Rima Rachid & Dr. Talal Chatila)
The Food Allergy Fund Microbiome Collective will drive innovation across five priority areas, including advanced in vitro models and immune profiling, as well as early detection and clinical trials. FAF will accept research proposals focused on developing new diagnostics, treatments, and prevention strategies for food allergies, and will prioritize funding for projects that can be replicated across multiple sites and translated into patient care quickly.
"We believe food allergies are just the tip of the iceberg," said Dr. Susan Lynch, director, Benioff Center for Microbiome Medicine, professor of medicine, University of California San Francisco. "How we understand and modulate the microbiome could transform how we prevent and treat a whole spectrum of inflammatory and autoimmune diseases."
“Our goal is to design safe probiotics that deliver signals directly to Thetis cells (recently identified immune cells that help teach tolerance in early life), training the immune system to tolerate foods that would otherwise trigger allergy,” said Dr. Carlotta Ronda, Innovative Genomics Institute, UC Berkeley. “Dr. Brown and I first connected at FAF’s exclusive research retreat, and this collaboration shows the power of the Food Allergy Fund and its Microbiome Research Collective to spark partnerships that move science toward therapies.”
Addressing a Growing Health Crisis
Food allergies affect 1 in 10 adults and 1 in 13 children in the U.S., and an estimated 250 million to 300 million globally. Current diagnostics often miss at-risk individuals, and most available treatments manage symptoms rather than the underlying immune dysfunction.
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About the Food Allergy Fund
The Food Allergy Fund (FAF) is the leading nonprofit dedicated to funding cutting-edge research to prevent, diagnose, and treat food allergies—a growing public health crisis affecting 10 percent of people in the United States and more than 300 million worldwide. Through competitive research grants and convening global thought leaders at its annual summits, FAF unites scientists, policymakers, industry leaders, and entrepreneurs to accelerate breakthroughs. FAF's mission is to create a future where no one has to suffer from food allergies. Learn more at www.foodallergyfund.org.
Media Contact: Amy DiElsi, Director of Communications, amy.dielsi@foodallergyfund.org