The Inverted Gut
What Modern Food Overrides
Last month, I wrote about the gut as a sensor array—the body's first signal line, not just a digestive organ but a communication node. But that system doesn’t operate in a vacuum. It’s embedded in a larger context: the food supply. And if the gut is a sensor array, then modern food—particularly in industrialized nations—has become something like a filter, or worse, a signal jammer.
We’ve come to rely on an externalized digestive system: not our own bodies, but the factories, processing plants, and formulations that determine what nourishment even is. The problem isn’t just what this does to the body. It’s what it does to perception. When the input is distorted, so is the signal.
A System of Substitutions
The majority of what passes as food in a modern grocery store is the result of extraction, reconstitution, and artificial engineering. Whole ingredients—fruits, vegetables, grains, meats—are increasingly the exception. What dominates are items that have been processed to be more durable, addictive, and marketable: corn syrup in dozens of forms, seed oils that never spoil, proteins stripped from their original context and added back with flavor masking agents.
This is sometimes defended as innovation. And to a degree, it is. Industrial food production has fed billions and brought down global famine rates. But the cost has been a radical shift in what the body is exposed to, and what the gut microbiota—our internal ecosystem—must contend with.
Fiber, for example, is largely absent from ultra-processed food. Yet fiber is essential not just for digestion, but for feeding beneficial bacteria that produce anti-inflammatory compounds like butyrate¹. Without it, microbial diversity plummets. Add in emulsifiers, preservatives, and synthetic sweeteners—many of which are known to disrupt the gut barrier and microbiome²—and the result is a kind of internal confusion.
The gut still responds. But the response is misdirected, chronic, inflammatory. The system treats the noise as signal.
The Illusion of Choice
It feels like we have endless food choices. Walk into a supermarket and you're met with tens of thousands of SKUs. But look closer, and you’ll find the same base inputs repeated again and again: refined wheat, corn derivatives, industrial seed oils, sugar (often under alternative names). There’s variation in packaging and flavor profiles, but the underlying materials are few.
This is the illusion of variety. What we’re often choosing between is not foods, but formats—different arrangements of the same nutrient-poor, gut-disruptive inputs.
The systems behind this weren’t designed to harm. They were optimized—for shelf stability, transport, cost efficiency, and consumer pleasure. But in optimizing for those variables, other aspects were left out: how food interacts with the enteric nervous system, how it trains the immune system, how it feeds or starves specific bacterial communities.
Put simply: food has been flattened into a commercial product. But the body hasn’t caught up. It still expects meals grown, cooked, and eaten in context.
Food as Information
This is where the analogy of the sensor array becomes useful again. If the body is a sensing system, then food isn’t just fuel. It’s data. And traditional food cultures understood this in practice, even if they didn’t use those words.
In rural Greece, for instance, meals are made from seasonal produce, olive oil, fermented dairy, fish, and legumes. The Mediterranean diet, now widely studied, wasn’t invented in a lab. It evolved over centuries of local adaptation. The same is true of traditional Japanese cuisine—rich in fermented foods like miso and natto, small portions of rice, and sea vegetables—all of which support gut microbial health and metabolic balance³.
In contrast, a Western diet—high in ultra-processed items, low in fiber and diversity—has been consistently associated with higher rates of obesity, metabolic syndrome, depression, and inflammatory diseases⁴. The connection isn’t only chemical. It’s informational. The gut is interpreting the inputs and sending signals upstream—to the brain, the immune system, even the hormonal axis.
When those inputs are distorted, so are the outputs.
Rebuilding Signal Fidelity
This isn’t a call to purity. It's not about demonizing all processed food or romanticizing the past. The point is structural. If the goal is to live in a way that makes sense—where energy, mood, and clarity aren’t being constantly hijacked—then rebuilding the informational quality of food matters.
That might mean shifting from packaged to prepared, from shelf-stable to fresh, from uniform to varied. But more than anything, it means remembering that what we eat isn’t just about taste or calories. It’s about the signals we’re giving to the body—signals that determine how well the system functions, how clearly it can speak, and how much noise we have to live through to hear what it’s trying to say.
References
- Sonnenburg, E. D., & Sonnenburg, J. L. (2014). Starving our microbial self: The deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metabolism, 20(5), 779–786.
- Chassaing, B., Koren, O., Goodrich, J. K., Poole, A. C., Srinivasan, S., Ley, R. E., & Gewirtz, A. T. (2015). Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature, 519(7541), 92–96.
- Heiman, M. L., & Greenway, F. L. (2016). A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular Metabolism, 5(5), 317–320.
- Martínez Steele, E., Popkin, B. M., Swinburn, B., & Monteiro, C. A. (2017). The share of ultra-processed foods and the overall nutritional quality of diets in the US: evidence from a nationally representative cross-sectional study. Population Health Metrics, 15(1), 6.