Today, we’re diving into autoimmunity—what it actually is, why it happens, and how ultra-processed foods may be contributing to the problem.
Autoimmune disease is often misunderstood. Some will tell you diet has nothing to do with it. Others claim diet is the cure. The truth is more nuanced—and that’s exactly what we explore in this episode.
You’ll learn:
This isn’t about selling supplements or pushing extremes. It’s about understanding the science so you can make informed decisions about your health.
As always, this episode is backed by scientific literature. Full citations are included below, with abbreviated versions available on shorter clips.
If you’re dealing with autoimmune symptoms—or just want to better understand how food impacts your immune system—this episode is for you.
Full citation list:
Hall KD, et al. “Ultra-Processed Diets Cause Excess Calorie Intake and Weight Gain: An Inpatient Randomized Controlled Trial of Ad Libitum Food Intake.” Cell Metabolism, 2019.
Supports the formulation argument: UPF intake increased spontaneous calorie intake and weight gain even with diets matched for presented calories, sugar, fiber, sodium, and macronutrients. This is your anchor for “hyper-palatability and formulation change physiology, not just psychology.”
Narula N, et al. “Association of Ultra-Processed Food Intake With Risk of Inflammatory Bowel Disease: Prospective Cohort Study.” BMJ, 2021.
Best human disease-level citation for the episode. Supports the claim that higher UPF intake is associated with greater IBD risk, making the gut-immune link clinically meaningful rather than purely theoretical.
Chassaing B, et al. “Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolome.” Gastroenterology, 2022.
Best emulsifier paper for human translation. Supports the claim that CMC can perturb the microbiota and metabolome and may contribute to barrier-hostile gut ecology in susceptible individuals.
Daniel N, et al. “Human Intestinal Microbiome Determines Individualized Responses to Dietary Emulsifier Carboxymethylcellulose.” Cellular and Molecular Gastroenterology and Hepatology, 2024.
Useful nuance paper. Supports the point that emulsifier sensitivity is not identical across all people and that host-microbiome context matters.
Shil A, et al. “Artificial Sweeteners Disrupt Tight Junctions and Barrier Function in the Intestinal Epithelium Through Activation of the Sweet Taste Receptor T1R3.” Nutrients, 2020.
Best citation for the “sugar-free does not mean barrier-neutral” point. Supports direct epithelial barrier effects of common artificial sweeteners in experimental models.
Peng L, et al. “Butyrate Enhances the Intestinal Barrier by Facilitating Tight Junction Assembly via Activation of AMP-Activated Protein Kinase in Caco-2 Cell Monolayers.” Journal of Nutrition, 2009.
Classic mechanistic citation for butyrate. Supports the claim that loss of fermentable fiber and reduced butyrate production can weaken barrier function.
Kumar KP, et al. “The Interplay Between the Microbiota, Diet and T Regulatory Cells in Maintaining Intestinal Homeostasis.” Frontiers in Microbiology, 2023.
Useful for the tolerance language. Supports the argument that diet and microbial metabolites shape Treg biology and mucosal tolerance.
Haase S, et al. “Sodium Chloride Triggers Th17 Mediated Autoimmunity.” Frontiers in Immunology, 2019.
Key citation for high salt and autoimmune-prone immune skewing. Supports the claim that excess salt can promote pathogenic Th17 biology relevant to autoimmune disease.
Wilck N, et al. “Salt-Responsive Gut Commensal Modulates TH17 Axis and Disease.” Nature, 2017.
Strong bridge between salt, microbiome, and Th17 signaling. Supports the point that salt is not just a blood pressure story; it is also an immune-story.
Vitales-Noyola M, et al. “Analysis of Sodium Chloride Intake and Treg/Th17 Lymphocytes in Patients With Rheumatoid Arthritis and Systemic Lupus Erythematosus.” Journal of Immunology Research, 2018.
Helpful human-facing citation for salt and immune skewing in autoimmune populations. Use cautiously, but it strengthens translation from theory to autoimmune terrain.
Phuong-Nguyen K, et al. “Advanced Glycation End-Products and Their Effects on Gut Health.” Nutrients, 2023.
Good review for the AGE section. Supports the argument that AGE-rich processed foods may worsen oxidative stress, microbiota balance, and barrier function.
Chen Y, et al. “Dietary Advanced Glycation End-Products Elicit Toxicological Effects by Disrupting Gut Microbiota and Increasing Colon Permeability in Rats.” Journal of Toxicology and Environmental Health, 2021.
Useful mechanistic support for the processing-chemistry section. Reinforces the claim that dietary AGEs can alter microbial ecology and increase permeability.
Monteiro CA, et al. “Ultra-Processed Foods: What They Are and How to Identify Them.” Public Health Nutrition, 2019.
Dr. Brendan McCarthy is the founder and Chief Medical Officer of Protea Medical Center in Arizona. With over two decades of experience, he’s helped thousands of patients navigate hormonal imbalances using bioidentical HRT, nutrition, and root-cause medicine. He’s also taught and mentored other physicians on integrative approaches to hormone therapy, weight loss, fertility, and more. If you’re ready to take your health seriously, this podcast is a great place to start.
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