The human gut microbiome contains trillions of microorganisms — bacteria, fungi, viruses, and other microbes — that collectively perform functions essential to human health. They help digest food, regulate the immune system, produce vitamins, and communicate with the brain through pathways that researchers are only beginning to understand.
What you eat shapes this ecosystem. And a growing body of research suggests that many common food additives are shaping it in ways that are not beneficial.
The Microbiome and Food
The gut microbiome is not static. Its composition shifts in response to diet, stress, medications, and environment. Research consistently shows that diverse, fiber-rich diets support a more diverse microbiome — and that microbiome diversity is associated with better health outcomes across a range of conditions.
Ultra-processed foods tend to work in the opposite direction. They are typically low in fiber, high in refined ingredients, and formulated with additives that the microbiome has not evolved to handle.
Emulsifiers
Emulsifiers are among the most studied food additives in the context of gut health.
Their function is straightforward: they help ingredients that would normally separate — oil and water — stay mixed. They create smooth textures in processed foods. They are found in ice cream, salad dressings, margarine, baked goods, and energy bars.
A 2015 study published in Nature found that two commonly used emulsifiers — carboxymethylcellulose (CMC) and polysorbate 80 — altered the gut microbiome composition in mice, promoted intestinal inflammation, and contributed to metabolic syndrome. A 2022 analysis of human data from the NutriNet-Santé cohort found associations between emulsifier consumption and increased risk of cardiovascular disease.
The proposed mechanism involves the mucus layer that lines the gut. This layer serves as a protective barrier between gut contents and the intestinal wall. Research suggests that certain emulsifiers may degrade or thin this layer, allowing bacteria to make closer contact with the intestinal lining — potentially triggering inflammatory responses.
Artificial and "Natural" Sweeteners
Sugar alcohols — erythritol, xylitol, sorbitol, maltitol — are commonly used in "low sugar" and "keto" snack bars as alternatives to cane sugar. A 2023 study published in Nature Medicine found that erythritol was associated with increased risk of cardiovascular events. Earlier research suggested that some sugar alcohols may alter microbiome composition and, in some individuals, cause gastrointestinal distress.
"Natural flavors" are complex compounds that can contain dozens of chemical components. Their effects on the microbiome are largely unstudied, in part because manufacturers are not required to disclose their composition.
Refined Ingredients and Fiber Deprivation
Beyond specific additives, the broader pattern of ultra-processed food consumption affects the microbiome through what it lacks as much as what it contains.
Fiber is the primary food source for beneficial gut bacteria. Whole foods — fruits, vegetables, legumes, whole grains, nuts, seeds — provide diverse types of fiber that support diverse microbial communities. Refined ingredients, from which fiber has been removed, provide energy but little microbiome support.
A diet heavy in refined sweeteners, protein isolates, and processed starches feeds human cells but starves the microbiome.
What Whole Food Does Differently
Whole food ingredients arrive in the gut with their fiber, phytocompounds, and complex carbohydrates intact. Medjool dates bring fiber and polyphenols. Michigan tart cherries carry anthocyanins — compounds that research has associated with positive microbiome effects. Almonds, seeds, and oats provide diverse fiber types that feed different microbial populations.
The microbiome research is evolving. Not every finding will replicate. Not every additive will prove harmful at the doses found in food.
What the research does suggest, consistently, is that the gut microbiome responds to the difference between whole food and processed food — and that the response matters for long-term health.
The simplest intervention available is also the oldest: eat food that looks like food. Ingredients you recognize, minimally processed, without a list of stabilizers, emulsifiers, and flavor compounds to hold them together.
That is what real food is. That is what the microbiome was built for.
Patterbar contains no emulsifiers, no artificial sweeteners, no sugar alcohols, and no "natural flavors." Every ingredient is a whole food. Ranked #1 by Consumer Reports for Nutrition and Taste (December 2024). Try the Variety Pack →