What are processed foods and why are they so bad for metabolic health?

Here’s what “processed” actually means, how these foods impact your metabolic health, and how to avoid the worst of them in the grocery aisles

Article highlights

  • You can classify food into unique categories based on how much its been processed—less processing generally equals better for you, with some caveats.
  • Some processed foods can still be healthy choices if they have a few, high-quality, whole ingredients and no additives.
  • Ultra-processed foods—those that least resemble whole food and pack extracted fats and synthetic ingredients—are best avoided entirely.
  • These "Frankenstein" foods impact your metabolic health in multiple ways: reducing insulin sensitivity, promoting oxidative stress and disrupting your microbiome.

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Ultra-processed foods make up 60% of the calories Americans consume and contribute to poor health outcomes like insulin resistance, inflammation, and obesity. So it’s vital to understand what happens to food at different stages of processing and how that processing impacts our bodies. 

But what counts as processed food? It’s easy to stroll through the grocery store and identify bright orange cheese dust and hot dogs as things to avoid and kale as the pinnacle of healthy eating. 

But what about all the foods that fall in between? 

The packaged crackers with just a few recognizable and healthy-sounding ingredients––are those an optimal option for health, or just less harmful than cheese dust? Granola? Canned beans? When you leave the produce section, the decisions can get overwhelming real fast.

Here, we’ll walk through some definitions and highlight some of the most damaging components of processed foods to help make your shopping a little less fraught and a little more likely to yield healthy, beneficial snacks. 

The Categories of Food Processing 

First, let’s back up and define phrases like “ultra-processed” and look at what counts as processed versus whole. 

The NOVA classification system splits all food into four categories based on how processed it is:

  • Unprocessed and minimally processed foods
  • Processed culinary ingredients
  • Processed food
  • Ultra-processed food

Food scientists at the University of São Paulo, Brazil, developed an early version of this system in 2010. It is now one of the most common food-processing classification systems used in scientific literature. NOVA’s categorization considers the physical, biological, and chemical manufacturing processes food undergoes before you buy it and what impact the byproducts have on our health. Here’s what the four categories entail.

Unprocessed and Minimally Processed Foods

Nearly all foods in a grocery store have gone through some degree of processing—even produce may be washed or chilled after harvesting. But whole foods without added ingredients, like fruits, vegetables, raw cuts of meat and fish, fungi like mushrooms, eggs, and nuts—count as unprocessed. In this category, meat and fish may be butchered, produce may be sliced, inedible husks, or shells removed. 

Minimally processed foods may also be dried, crushed, ground, filtered, roasted, boiled, fermented, pasteurized, chilled, frozen, or vacuum-packed, as long as there’s no extra salt, sugar, or other ingredients. This minimal processing makes natural food better suited for travel and storage but keeps it mostly pure. Frozen vegetables are an example of minimally processed foods that keep their integrity as whole food.

Canned vegetables and legumes like black beans can also fall into this category as long as they aren’t packaged in a brine. However, the packaging itself can contain endocrine disruptors, which have been linked to metabolic disorders. Look for packaging that says BPA-free to avoid bisphenol A (BPA), and look for the number 3 inside the recycling symbol to avoid phthalates

Foods in this group are generally the basis of a healthy diet and should fill most of your cart at the grocery store. 

Processed Culinary Ingredients

This group contains calorie-dense foods you rarely eat by themselves, such as oils, butter, sugar, and non-caloric ingredients like salt. How these ingredients impact your metabolic fitness largely depends on the context. For example, roasting fresh vegetables in olive oil will have a different effect than drinking coffee with added sugar. 

Some oils in this category are best avoided entirely. For example, processed seed oils like soybean oil are among the most common sources of fat in the American diet but are some of the worst oils for metabolic fitness. That’s because processed seed oils can contain high amounts of linoleic acid, an omega-6 fatty acid that prompts fat cells to store more fat. The ratio of omega-6 to omega-3 fatty acids used to be around 1:1 in ancient humans’ diets but is as high as 20:1 in the modern diet, which increases the risk of obesity. Research has shown that these engorged fat cells appear to spike inflammatory proteins that may lead to insulin resistance.  

Related article: What causes insulin resistance?

Processed Foods 

Manufacturers combine foods from the first two groups––for example, canned fish in a salty brine or fruit preserved in sugary syrup––to create processed foods with long shelf lives. Like minimally processed foods, processed foods may be canned, frozen, or fermented. The easiest way to tell the difference is by scanning the label for added ingredients, even just salt or oil.  

Processed foods usually have at least three ingredients but can have several more––slightly modified versions of recognizable foods. Most cheeses, tofu, and processed meats like ham, bacon, smoked fish, and pastrami also fall into this category. Whole-grain bread that only has the same ingredients you’d use to make bread at home (flour, yeast, salt) would fall into this category; a bread that also had emulsifiers, coloring, or other additives would fall into the ultra-processed group.

Whether or not processed foods can be part of a healthy diet comes down to context and ingredients. For example, flaxseed crackers have just a few ingredients that are themselves healthy, don’t have added sugar or salt, and are not heavily processed—given this, you can still get the health benefits of the whole food from the processed version. 

However, it’s easy to end up eating too much fat, salt, and especially sugar from foods in this category. Look at labels carefully, as there are dozens of ways sugar can hide in everyday foods like peanut butter and ketchup. 

Ultra-Processed Foods

A study that looked at Americans’ eating habits over six years found that ultra-processed foods comprised the majority of calories in most Americans’ diets and increased across nearly all demographics during that time (2007-2012). It’s not just fast food, frozen meals, or breakfast cereal, either. This category can include seemingly healthy energy bars and protein shakes. Manufacturers create these products by combining extracted parts from many different foods or synthetic ingredients like preservatives—a bit like building Frankenstein. 

First, manufacturers break down whole foods to create raw materials like oil, sugar, starch, protein, and fiber—often extracted from just a few types of plants (corn, wheat, soy, sugarcane, or beets). Foods in this category may also have trans fats, which manufacturers often create through a chemical process called hydrogenation. Adding hydrogen to the oil makes the fat solid at room temperature and significantly extends shelf life, but with significant health costs (more on that below). 

Next, some of these products undergo chemical modifications to break them down further. Hydrolysis uses enzymes to extract protein, carbohydrates, natural flavoring, and coloring from ingredients. These parts then mix with other food derivatives and synthetic additives.

The result is ultra-processed foods: mass-produced versions of pastries, breads, cakes, cookies, as well as nut milks, “nuggets” made of ground meat, fish, or soy meat substitutes, and most chips, crackers, and other snack foods.

A healthy, clean diet should avoid these foods. Not only do they have little nutritional value, but regularly consuming their excess salt, sugar, and unhealthy fats increases your risk for diabetes, heart disease, obesity, and even depression. Specifically, in a review of studies linking processed food intake with health, the highest levels of ultra-processed food intake across studies increased risk of overweight/obesity by 39% and metabolic syndrome by 79%, while also being associated with low HDL levels.  

Studies have shown a correlation between eating ultra-processed foods and high consumption of refined sugars, saturated and trans fats, as well as a lack of protein, fiber, and vital vitamins and minerals. 

(It’s worth noting that there’s also an environmental cost to some of this ultra-processing. For example, it takes more than 94 pounds of corn to make a bottle of corn oil.)

How Ultra-Processed Foods Impact Metabolic Health

Trans Fats Alter Insulin Sensitivity

Although natural trans fats from meat and industrially created trans fats have a similar impact on plasma lipoproteins, including HDL and LDL cholesterol, research shows that industrial trans fat is more likely to promote inflammation and cellular stress, which are linked to insulin resistance and other metabolic diseases. Trans fats tend to disrupt liver function and have been shown to cause liver damage in mice. Trans fats also inhibit insulin sensitivity, possibly by altering insulin receptor signaling. 

Because of these strong links to disease, the Food and Drug Administration (FDA) banned artificial trans fats, also known as partially hydrogenated oils, in 2018, but most countries have not taken that step. 

Refined Grains Spike Blood Sugar

Refined grains also count as ultra-processed food. While whole grains like corn kernels, wheat, and brown rice contain three key parts––the bran, germ, and endosperm––the refining process removes the bran and germ, leaving just the endosperm. 

Removing the germ extends shelf life since fat stored in the germ can spoil quickly. Refining grain also creates an end product with a soft, chewy texture, which is only possible if you remove the fibrous bran. But by doing so, the carbohydrates can be broken down more quickly when digested, which translates to increased blood glucose levels sooner after eating. Even if manufacturers enrich the refined grain with synthetic versions of the vitamins stripped away by processing, it still doesn’t contain fiber. Fiber helps slow the body’s breakdown of starches into glucose, helping keep blood sugar stable. 

Related article: What is glucose?

Processed Foods Promote Oxidative Stress

Many of the techniques used in food processing, like exposure to heat or light or adding iron to fortify grains, promote lipid oxidation in the foods, which increases the number of free radicals in the fats (lipids). Many seed oils are also easily oxidized. Eating too many of these foods can cause oxidative stress in your body, in which excess free radicals can cause damage to tissue and DNA.

Processed Foods Disrupt the Gut Microbiome 

Your diet also determines the makeup of your gut microbiome. There are trillions of microbes living in your gut, and scientists know that this web of life has a significant impact on your metabolic fitness

How much processed food you eat is one major factor determining what kind of bacteria and other microbes thrive in your gut.

In one study, researchers analyzed the gut microbiomes of more than 1,000 people. They tracked how different eating habits correlate with certain gut microbes and markers of heart health and metabolic fitness. People who mainly ate more healthy, plant-based, unprocessed foods––which tend to be nutrient-dense––had gut microbes associated with metabolic markers of lower risk of heart disease and Type 2 diabetes. On the other hand, eating a diet with fewer of these whole foods fostered microbes linked to metabolic markers of poorer health.  

Why do processed foods so negatively affect our gut microbiomes?

  • Processed Foods Promote Inflammation
    In this literature review, researchers present evidence linking highly processed foods with gut microbes associated with obesity and metabolic disease. Although we don’t yet understand all the mechanisms involved (and a lot of the research is in mice), one plausible connection is inflammation. Gut bacteria respond to what you eat, with a changing roster of bacteria based on the nutrients available and the chemicals produced by the bacteria around them. Ingredients in heavily processed foods like artificial sweeteners and emulsifiers can encourage gut bacteria that produce a more pro-inflammatory environment.
  • Processed Foods Lack Metabolism-Regulating Fiber
    Processed food doesn’t contain the nutrition that whole grains and vegetables provide––nutrients the body evolved to metabolize. One essential nutrient directly linked to both the gut microbiome and insulin is fiber. Fiber plays a crucial role in determining which microbiota thrive in the gut, and the typically low fiber content of ultra-processed food can foster a less diverse microbiome. On top of that, dietary fiber isn’t hydrolyzed, or broken down, by digestive enzymes. Instead, gut microbes ferment dietary fiber, producing metabolites like the short-chain fatty acids (SCFA) acetate, propionate, and butyrate. These work their way into the liver, where some get used for energy, and a small number circulate throughout the body’s blood and tissues. Studies show that these circulating gut-produced SCFAs help regulate metabolism and improve insulin resistance. 

Nutrients in Processed Foods are Acellular 

The nutrients in whole foods are typically contained within cells (with a few exceptions). The digestive tract has to release these nutrients before the body can use them. But the energy in ultra-processed foods is largely acellular or not contained within a cell. Acellular nutrients are more easily accessible, so gut microbes can take them up before they are absorbed in the small intestine. 

We see this idea most easily in whole grains. When we mill whole grains into flour, the result is a mixture of cellular and acellular nutrients. But as we refine those grains further, as is the case with white flour, more and more cellular nutrients get released. The same is true of oils and starches extracted from seeds––most of these nutrients are acellular. 

Acellular nutrients also contain less variety and therefore don’t require the same gut microbes that whole foods do. Studies in mice found that this can transform the microbial landscape of the colon. 

Researchers fed mice the equivalent of a Western diet high in simple sugars, starches, and fats. They saw a dramatic reduction in microbial diversity and a bloom of sugar-metabolizing bacteria in the distal colon, where they don’t usually occur. This may cause a domino effect of molecules released by bacteria entering the bloodstream or intestinal wall—a process linked to Type 2 diabetes

Five Takeaways for Thinking about Processed Foods

  • Whole, unprocessed foods are best as they pack the most micronutrients and healthy fiber. Opt for choices that look like real food.
  • Minimally processed foods can also be a nutrient-rich option if you avoid certain packaging types that are harmful to health, like those that include BPA or phthalates.
  • Avoid canola oil, corn oil, soybean oil, and other processed vegetable oils, which contain linoleic acid. Keep your eyes peeled for these—they are pervasive. 
  • Processed foods are trickier. If you’re picking up something in a box or bag, scan the label first. Look for short ingredient lists that include whole grains, seeds, nuts, no added sugar, and low sodium. If you can easily recognize all of the ingredients as individual foods that you could buy on their own, it’s a safe bet that the food hasn’t gone through a lot of processing. Look at the nutritional information and avoid high levels of salt, sugar, or refined seed oils. 
  • Avoid ultra-processed foods altogether. Even a little bit can have a significant impact on metabolic fitness. Studies have shown that the types of microbes living in your gut can quickly change with even temporary diet shifts. You can recognize ultra-processed foods by their long ingredient lists, including telltale additives like dextrose, maltose, or artificial sugars, and their lack of resemblance to whole foods.