Are Carbs “Bad” for Your Gut?

Written by Jennifer Chesak: Award-winning freelance science and medical journalist, editor, and fact-checker. Her work has appeared in several national and international publications, including the Washington Post and BBC. Chesak earned her master of science in journalism from Northwestern University’s Medill, and she currently teaches in the journalism and publishing programs at Belmont University. She is the author of “The Psilocybin Handbook for Women.”
Reviewed by Jennie O’Grady: Senior SciComms Specialist at Seed Health

Given the ubiquity of low-carb packaged foods and carb-restricted diets like keto, it’s easy to fall for the myth that carbohydrates are “bad” for you. In reality, carbs are like any other element of nutrition: far from black and white.

To understand how different carbohydrates impact the body, you’ll need to look at what they do to the collection of bacteria residing in your digestive tract.

In this crash course on carbohydrates, we’ll cover how carbs impact the gut microbiome, how to identify the good from the bad, and how to prepare your carbs to best support your gut health and beyond. 

How Do Carbs Affect Digestion and Gut Health?

There are two main types of carbohydrates—simple and complex—and they impact the gut in very different ways.¹

Simple Carbs:

Simple carbs are composed of 1-2 sugar molecules. Your body has no problem breaking these molecules down quickly (hence the name “simple”).

Some examples include the fructose in fruits, the lactose in dairy products, and the various sugars in processed or refined items like candy, table sugar, syrups, and sodas. 

When people say that carbs are “bad” for you, they’re likely referring to these simple carbs.

The two categories of simple carbs—monosaccharides (single sugar molecules) and disaccharides (two sugar molecules linked together)—are easily absorbed in the small intestine of the gut. While easy, speedy absorption may sound great, when it comes to digestion, you actually want your body to work a little harder.²

Since simple carbs are digested so quickly, they can lead to a sudden rise in your glucose (blood sugar) levels. (We’ll get into why this can become problematic later.) 

They’re also usually digested well before they reach the colon, where trillions of hungry beneficial, protective bacteria reside.^2,3 If these bacteria aren’t fed, they begin to die off, making our guts more susceptible to pathogenic (harmful) bacteria in their absence.⁴

Simple carbs can also weaken the gut lining, allowing toxins into the bloodstream where they can cause inflammation.² Inflammation around the gut is also linked to inflammatory bowel diseases, such as Crohn’s and ulcerative colitis.⁵

To recap, here are a few of the ways over-eating simple carbs can throw the body for a loop: 

• Simple carbs lead to blood sugar spikes and corresponding crashes.⁶
• These spikes and crashes may impair sleep quality, according to small preliminary studies.⁷
• Spikes and crashes can tank your energy, mood, and more and lead to cravings.^8,9
• Spikes overload your system with glucose, which can lead to fat storage and a slower metabolism.^10,11
• Refined and processed carbs contribute to chronic whole-body inflammation.¹²
• Refined and processed carbs can lead to poor gut health and reduced gut barrier integrity.¹³

Complex Carbs:

Complex carbohydrates, also called polysaccharides, consist of larger chains of at least three sugar molecules, so they take longer for you to break down into their constituent parts.^1,14

Some examples include starches, which are found in foods such as corn, oats, rice, and fiber, which are in whole fruits and vegetables, legumes, and whole grains.

There are two types of fiber: soluble fiber (which mixes with water in your gut to create a gel-like substance that protects your gut lining and helps you feel full) and insoluble fiber (which adds bulk to your stool to keep your bowels moving). Fiber and healthy poops go together for a reason—both types of it are important for easy, regular digestion.

Fiber and some types of starches called resistant starches reach the colon undigested, where they can feed beneficial gut bacteria.¹⁵ During this process, bacteria produce short-chain fatty acids (SCFAs)—byproducts that strengthen the lining of the gut and reduce inflammation throughout the body. These complex carbohydrates also slow down the digestion process when compared to simple carbs, leaving you feeling fuller for longer.^15,16

To visualize how fiber and resistant starches differ from simple carbs, consider what happens when you’re tired and drink a cup of coffee. You’ll get a strong jolt of energy, but it’ll be temporary. You won’t be any more well-rested in the long run, and you may find yourself crashing later. Compare this to a solid night of sleep; it’s more of a time commitment, but it will leave you with enough energy to last all day. 

In this case, simple carbs are coffee—satisfying, but ultimately a band-aid solution—and complex carbs (specifically, fiber and resistant starches) are sleep—longer-term investments in energy and overall functioning.

The benefits of fiber and resistant starches include the following:

• Fiber helps increase the population of beneficial bacteria in the gut.^17,18
• Fiber helps blunt potential blood sugar spikes, aiding with metabolic health.^17,19
• SCFAs help reduce inflammation and support the immune system.²⁰
• Fiber and SCFAs support the health and function of your gut barrier.²⁰
• SCFAs support the production of glucagon-like peptide 1 (GLP-1) a hormone that helps control blood sugar and helps with fullness signals to prevent overeating.²¹ (It’s the hormone mimicked in anti-obesity medications like Ozempic.) 

What Are Some Gut-Friendly Carbs?

Here are a few healthy carbs that can feed the beneficial microbes in your gut, and some tips on how to work them into your diet:

1. Whole Fruits

While the fructose in fruit is a simple carb, the fiber in fruit is a good-for-your-gut complex carbohydrate. Whole fruits also carry a host of phytonutrients including polyphenols like stilbenes, and flavonoids. These plant compounds help combat inflammation in the gut and beyond.²⁵ 

2. Whole Vegetables

Like fruits, vegetables are also a source of fiber and gut-healthy plant compounds. 

3. Whole Grains

Whole grains like oats, brown rice, quinoa, and barley are high in dietary fiber, vitamins, and minerals. They promote the growth of beneficial gut bacteria and improve bowel regularity.¹⁷ 

Whole grains differ from refined grains like white bread, which is often made from wheat flour (both a starch and a fiber). Processing wheat into flour involves removing the bran and germ.²⁶ This strips out much of the fiber content, leaving you with a refined carbohydrate that will likely be absorbed quickly, spiking your blood sugar. So while bread is structurally a complex carb, it acts more like a simple carb after processing.

4. Legumes

Legumes like lentils, chickpeas, black beans, and kidney beans are packed with fiber that feeds beneficial gut bacteria. 

5. Resistant Starches

You can find slow-digesting resistant starch in plantains, legumes, nuts, seeds, whole grains, unripe (green) bananas, and more.¹⁵ 

6. Honorable Mention: Some Types of Dairy 

Existing studies indicate dairy has both beneficial and negative impacts on the gut microbiome, so we’re placing this one in the “honorable mention” category.²⁷ Fermented dairy products, such as yogurt and kefir seem to be better at boosting beneficial bacteria than non-fermented dairy, according to preliminary research.²⁸ 

Carbs That Harm Gut Health

Here are a few types of refined and processed carbs to avoid or limit for the sake of your gut:

• Refined Grains: White bread, white rice, pastries, and many breakfast cereals
• Sugary Foods and Beverages: Sodas, candies, cakes, cookies, and other sweets
• Processed Snacks: Chips, crackers, pretzels, and other packaged snacks
• High-Fructose Corn Syrup: Found in many sweetened beverages, candies, and processed foods

Can Carbs Help With Weight Loss?

Yes and no. Eating fewer simple carbohydrates, especially those that are refined or processed, and swapping them for gut-friendly complex carbohydrates can help with weight management and keep you off the blood sugar spike-crash rollercoaster.

Let’s break down this carb-weight connection a little more: When we eat a meal, our glucose (blood sugar) begins to rise.²⁹ How fast and how high it rises and how long it stays elevated will depend on various factors, including the type of carbs consumed. Simple carbs have a high glycemic index, meaning they cause more glucose to be rapidly released into the blood.³⁰

In response to the rise in blood sugar, your pancreas will release insulin, which acts as a signal to your body’s cells to take in the extra circulating glucose and use it as energy.

This is a positive thing if you’re mid-marathon or in the last few minutes of a soccer game and have run out of glycogen (a form of stored glucose) needed to power your movements. 

But in the absence of endurance sports, frequent rises and falls in insulin harm metabolic health.¹¹ This is because after a spike, our bodies tend to overcorrect with insulin. This may lower your blood sugar below your baseline, leading to a blood sugar crash (a phenomenon called postprandial reactive hypoglycemia³¹). Crashes can leave you feeling fatigued, jittery, and craving more carbs to get back to your baseline. 

This kicks off a vicious cycle in which more and more insulin is released, but your cells become less responsive to it over time (it’s a bit of a Boy Who Cried Wolf situation). Although insulin is necessary for life, too much of it will drive the storage of excess glucose as fat. Therefore, insulin surges from repeated blood sugar spikes can slow your metabolic rate, reducing how much energy you burn and making it more difficult to utilize the nutrients you eat to fuel important cellular processes.^11,32

Over time, this impaired response to insulin—called insulin resistance—can also lead to metabolic disorders like prediabetes and type 2 diabetes, as well as weight gain.³³ 

Carbs and the Brain

How do complex carbs influence our ability to combat stress and anxiety? Can simple carbs increase our risk of dementia? These types of questions are fueling fascinating ongoing research into how different carbohydrates impact the brain.

So far, diets that are high in refined carbohydrates have been linked to an increased risk of depression and anxiety, potentially because of the way these carbs increase inflammation in the gut.^34,35 The brain and gut are connected through the gut-brain axis, so the health of the gut microbiome likely plays a role in mental health and cognition.³⁶ 

Experts are also increasingly referring to Alzheimer’s disease as Type 3 diabetes since insulin resistance appears to accelerate brain aging and neurodegeneration.^37,38 Higher fructose consumption (primarily from ultra-processed foods that contain high-fructose corn syrup) has been associated with a higher risk of dementia, though more research is needed.^39,40 

How Many Carbs to Eat Per Day

According to the Dietary Guidelines for Americans, 45% to 65% of an adult’s daily calories should come from carbohydrates.⁴¹ One gram of carbs is equal to 4 calories, so for someone eating 2,000 calories a day, this breaks down to 225 to 325 grams of carbs. (For context, one cup of cooked brown rice has 45 grams of carbohydrates, a banana has 27 grams, and a piece of white bread has 15 grams.)

Ideally, no more than 5 to 10% of your daily calories are added sugars. Instead, they should come from the gut-friendly carbs listed above, including 19 to 38 grams of fiber. It’s best to combine a plant-rich, high-fiber diet with other strategies for promoting gut health, such as taking a well-formulated probiotic, getting your stress levels in check, getting enough sleep, and prioritizing daily movement. 

Note: There are also certain times when your body will require more carbohydrates—such as when you’re pregnant or lactating.

Are Low-Carb Diets Good for the Gut?

Low-carb diets like the ketogenic diet generally limit carb consumption to 20 to 50 grams per day. This type of carbohydrate restriction forces the body to utilize fat (instead of glucose) for fuel. 

Low-carb diets have been shown to be beneficial for certain conditions such as epilepsy, and research finds they can boost fat loss and improve insulin sensitivity in the short term.^42,43

However, their impact on gut health is still up for debate. One major concern is that since they are so low in carbs, these diets are also lacking in fiber and phytonutrients, potentially contributing to vitamin and mineral deficiencies and negatively affecting gut health.⁴⁴

The Key Insight

Not all carbohydrates are the enemy that the diet industry makes them out to be. Yes, we in the Western world tend to overeat certain carbs (like refined sugars), but at the same time, we’re under-eating other carbs (like fiber). 

By villainizing all carbs, we’re throwing the baby out with the bathwater—and starving our body’s essential microbial workforce in the process. Instead, we can focus on consuming more of the complex carbs that feed our beneficial gut bacteria while reducing the processed and refined simple carbs that starve them.