Best Foods for the Gut Microbiome: How to Create an Environment for Healing background image
June 14, 2024

Best Foods for the Gut Microbiome: How to Create an Environment for Healing

Featured Product:

Key Takeaways:

  • When considering gut health, we must prioritize the gut microbiome. While microscopic, gut bacteria are essential to forming a healthy ecosystem free of digestive issues. It helps to support the immune system, blood sugar regulation, and digestion as a whole.
  • A diet that supports your gut microbiome is a helpful tool to improve damaged gut terrain. Ideally, your diet should consist of prebiotic, probiotic, and postbiotic foods while eliminating highly processed food groups.
  • The gut microbiome is delicate. It’s easily manipulated by inputs like physical and emotional trauma, heavy antibiotic use, and consuming processed foods. Taking proper care of your gut microbiome considers all of these elements as potential concerns.

It seems like we know a lot about gut health today, but the human gut microbiome is still practically uncharted territory. 

It’s not that scientists haven’t researched it (they have). But the gut microbiome is an entire ecosystem by itself — regulating things like the immune system and digestive tract while communicating with the brain, all on a cellular level. We’ve only scratched the surface of exactly what the gut microbiome can do.

What we do know about the gut microbiome is that an imbalance of essential bacterial species can cause symptoms like bloating, cramps, weight gain, insulin resistance, and more. 

And, with processed foods and pharmaceutical drug use on the rise, we know our microbiome is changing… and not for the better. 

There are ways we can intervene on behalf of our gut health, though.

Diet and nutrition remain one of the key pillars of health, and key elements of our diet can have a significant impact on our overall microbiome health. Let’s explore a healthy microbiome diet and why it takes a whole lot more than probiotics to cultivate a healthy ecosystem.

Table of Contents:

Key Elements of the Gut Microbiome Diet 

Before we dive into the key pillars of the gut microbiome diet, we have to understand the role the gut microbiome plays in our health. Here’s what we know:

  • Our gut microbiome helps regulate the immune system.
  • The microbiome is part of the digestive system and turns fibrous foods into essential nutrients.
  • Each person’s microbiome is as unique as their fingerprint.
  • The microbiome is an ecosystem — meaning good bacteria as well as pathogens like yeast and parasites can coexist in the same space (sometimes causing symptoms, sometimes not). 
  • Our microbiome changes based on its environment. Processed foods, pharmaceutical drugs, stress, and nutrient deficiencies may alter the microbiome and cause symptoms.
  • 95% of serotonin is made in the gut, and the gut communicates with the brain via the gut-brain axis. 

Most importantly, our gut microbiome requires many different elements to thrive, not just probiotics. Here are the three pillars of a healthy gut microbiome:

Prebiotic Fiber

Natural fibers that come from leafy greens, fruits, grains, and legumes are essential to a healthy gut ecosystem. The goal is to create an environment where healthy colonies of gut flora thrive — and they can’t do this without the proper fuel.

High fiber foods are actually broken down and digested by the microbiome. The berries, spinach, and kale you eat on a regular basis are exactly what fuel healthy bacterial colonies in your gut.

That said, people with low levels of healthy gut bacteria will probably struggle to digest fiber at first. We recommend slowly increasing your fiber intake, giving your gut time to colonize and adjust.

Probiotic Supplements and Foods

Just a few years ago, probiotic foods and supplements were considered the best resources to restore an imbalanced microbiome. While probiotics are certainly helpful, they need to be considered as just one element of a multi-step plan to restore gut health.

For instance, without prebiotics to feed your gut microbiome, your probiotic supplements may die off without doing any good. Not only that, but most probiotic supplements contain dozens of strains, which might not all benefit your unique microbiome.

If you want to supplement with probiotics, we recommend working with a functional medicine practitioner to run tests and find missing or low levels of important bacterial species. Otherwise, consuming a healthy dose of probiotics alongside prebiotic and postbiotic foods is a more well-rounded approach.

Postbiotic Support

When rebuilding your gut microbiome, it’s going to take a while before daily symptoms begin to resolve. Postbiotics can help expedite the healing of the gut. These are the metabolites left behind after the microbiome digests fiber. They’re essential substrates like butyrate, amino acids, and vitamin K that benefit your digestive health in other ways.

We often recommend postbiotic supplements, like butyrate, to help restore the gut ecosystem. But there are also many postbiotic foods you can consume on a microbiome diet. 

Best Foods for the Gut Microbiome

When beginning a microbiome diet, you want to shoot for prebiotic, probiotic, and postbiotic foods. These are the best foods for the gut microbiome because they work together to create a thriving gut ecosystem.

Prebiotic Foods

Typically, anything with natural, unprocessed fiber is considered a prebiotic, like…

  • Leafy greens (kale, spinach, Swiss chard, and collard greens)
  • Whole seeds (flax, chia, and hemp)
  • Root veggies (radishes, potatoes, garlic, beets, ginger, and onions)
  • Berries (raspberries, blackberries, and elderberries)
  • Whole fruits (oranges, bananas, and kiwi)
  • Foraged foods (mushrooms, dandelion roots, and rose hips) 
  • Whole grains (oats, barley, kamut, buckwheat, and rye)

The key to eating more prebiotic foods is to start slow. If your microbiome is depleted of beneficial flora, it won’t be able to digest high amounts of fiber all at once, so don’t force it. Slowly begin to increase portions of fruits and vegetables throughout a period of weeks.

Probiotic Foods

With live cultures of healthy bacteria, probiotic foods are typically fermented to draw out their cultures.

  • Kombucha
  • Kefir
  • Yogurt
  • Buttermilk
  • Kimchi
  • Sauerkraut
  • Some types of pickles
  • Miso
  • Raw dairy

We also recommend increasing your probiotic food intake slowly. If you spend a few weeks on probiotic foods with no positive results, you may need to undergo some strategic gut testing with your functional medicine practitioner.

Postbiotic Foods

Postbiotic foods are nutrient-dense and can help relieve uncomfortable gut symptoms. We can use these to support our microbiome while we increase prebiotic and probiotic intake, guiding our digestive system to create postbiotics on its own.

  • Raw cottage cheese
  • Kombucha
  • Yogurt
  • Sauerkraut
  • Kefir
  • Butyrate foods high in resistant starch
  • Since most postbiotic foods are also probiotic foods, it shouldn’t be too hard to include these in your meal plan. That said, we also recommend targeting this portion of the microbiome diet with postbiotic supplements, like butyrate. If the body is already struggling to make postbiotics, supplements can help achieve results and relieve symptoms faster.

    Food and Drugs to Avoid on the Gut Microbiome Diet

    Recovering your gut microbiome is a multi-step process and may require removing foods from your diet. Ideally, you want to eat a diet of whole foods that are minimally processed. In-season fruits and veggies from your local farmer’s market are likely to have more nutrients and fewer chemicals than grocery store foods, too.

    Here are some foods you may want to avoid on the microbiome diet: 

  • Highly processed foods
  • Fast food
  • Coffee
  • Sugar substitutes
  • Processed sugar
  • Processed grain
  • Foods pasteurized at high temperatures
  • You should also pay attention to any pharmaceutical drugs you may be taking. Antibiotics, in particular, are harmful to the microbiome as a whole. Of course, there are many cases where they’re life-saving, but they should be used sparingly. In one study, antibiotics, birth control pills, PPIs, and laxatives were shown to have the most impact on the microbiome.

    More Steps to Restoring Gut Flora

    There’s so much more to protecting the gut microbiome than diet alone. Eating diverse foods, addressing trauma, and starting slow are all important steps when it comes to caring for your gut microbiome. Targeted supplements and testing may play a role in your healing journey, too.

    Don’t Upset Your Stomach

    You may feel slight digestive discomfort in the first few days or weeks of this diet (this is a sign your microbiome population is changing–for the better), but you shouldn’t feel miserable on this diet.

    You may try foods that cause nausea, bloating, and loose stools. Excess veggies or fermented foods can be difficult to digest, especially if you’re not used to them.

    Our rule of thumb? Don’t overdo it. Introduce new foods slowly, and don’t exacerbate symptoms. This isn’t helpful.

    Focus On Food Quality Rather Than Food Elimination

    Yes, there are certainly times when foods should be avoided due to severe allergies or sensitivities. However, this doesn’t happen as often as we think. Most of the time, it’s not the food itself that causes discomfort, it’s the manufacturing process.

    There’s almost always a solution to food sensitivities. Here are a few we love:

    • Gluten Sensitivity — Find a source of flour that doesn’t contain glyphosate, like European imported flour or an ancestral grain like kamut.
    • Bean, Legume, or Rice Sensitivity — While these are known to cause bloating, a simple preparation process can help with this. Try soaking your grains in water and a tablespoon of vinegar for a few hours before cooking.
    • Fresh Fruit or Veggie Sensitivity — When trying to recover your microbiome, we recommend using the freshest and cleanest produce available. Find in-season organic fruits and veggies at your local farmer’s market and introduce them slowly.

    Consider a Low FODMAP Diet

    If you don’t have enough healthy gut microbes to break down prebiotic fiber, you may experience symptoms of irritable bowel syndrome (IBS) when eating certain fruits, veggies, and legumes. If this is the case, we recommend trying the low FODMAP diet to help restore the natural microbiome before going crazy with new food introductions.

    Take Action For Better Microbiome Health

    The goal of the microbiome diet is to improve your overall gut health while managing symptoms. In addition to a gut friendly diet, there are a number of supplemental resources that can help reduce current symptoms while nurturing a healthy long-term gut ecosystem. One of them is butyrate – a short-chain fatty acid that’s also a postbiotic.

    Butyrate supplements can help support a more resilient gut.* This supplement has also been shown to shift the bacterial colonies in the gut, which is helpful when you’re rebuilding your gut ecosystem.*

    Support Your Gut Microbiome — Take Action with Butyrate

    Related Articles

    Ashley Palmer | 10.27.2026

    Semaglutide Can Change What People Want to Eat. Here's What Your Gut Has to Do With It.

    Imagine you order the meal you've loved for a decade, and a few bites in, you realize you just don't care about it. You're not full, exactly. Just uninterested.

    Many people taking semaglutide (a GLP-1 medication) describe this experience. Foods that were reliable favorites suddenly seem greasy, or too sweet, or just vaguely off. Scientific American captured the strangeness: a former food writer losing interest in cooking, longtime favorites tasting wrong.

    The obvious explanation is that these medications make you feel full sooner. But fullness doesn't explain why a specific curry tastes bitter now, or why a go-to wine suddenly tastes off. Something more is happening, and it points to a hormone your body has been producing your whole life.

    In this article, we'll look at what the newest research suggests semaglutide does to food preferences, what GLP-1 actually does inside the body, and where your gut microbiome and a short-chain fatty acid called butyrate fit into that system.

    Table of Contents:

    • Semaglutide Isn't Only Changing How Much People Eat
    • Your Gut Was Making GLP-1 Long Before Ozempic
    • Where the Microbiome Comes In
    • Can Butyrate Support Natural GLP-1 Production?
    • Why Butyrate Matters Beyond One Hormone
    • Support the System, Not Just the Signal
    • The Bigger Story Your Gut Was Already Telling

    Semaglutide Isn't Only Changing How Much People Eat

    Researchers are starting to document what users have been describing anecdotally.

    A 2026 observational study of hospitalized Japanese patients with type 2 diabetes found that those on semaglutide showed significantly reduced preference for sweet carbohydrates, non-sweet carbohydrates, and non-sweet fats — while preferences for protein and dietary fiber stayed essentially unchanged. This wasn't a blanket loss of interest in food. It was a selective shift.

    For someone focused on weight loss, eating less may be the point. Still, a reduced appetite for fats is worth paying attention to, since dietary fats supply essential fatty acids and help the body absorb fat-soluble vitamins.

    Taste perception may also contribute. In a 16-week, randomized, placebo-controlled study of 30 women with obesity and PCOS, semaglutide improved overall taste recognition scores and altered brain activity in response to both food images and a sweet solution. In other words, participants' sense of taste sharpened, which may help explain why some foods suddenly seem too strong.

    A 2025 study found the opposite: reduced sensitivity across all five basic tastes in people taking GLP-1 medications compared with matched non-users. That means the more accurate takeaway isn't "Ozempic makes food taste different" so much as "GLP-1 signaling reaches further into how we experience food than many researchers expected."

    None of these studies settles the question on its own. But together they point somewhere useful: GLP-1 isn't only a satiety signal. It appears to play a role in how appealing food seems in the first place.

    Your Gut Was Making GLP-1 Long Before Ozempic

    Here's what often gets lost: GLP-1 wasn't invented by a pharmaceutical company.

    GLP-1 is a hormone your intestines release on their own, produced mainly by specialized cells called enteroendocrine L-cells. These cells sit in the gut lining, acting as sensors that detect what's arriving from your meal and releasing hormones that coordinate the response.

    GLP-1 helps regulate insulin release, slows how quickly the stomach empties, contributes to satiety, and carries information from the gut to the brain. GLP-1 medications didn't create a new pathway. They target one your body was already running.

    But there's an important difference, and a lot of wellness marketing glosses over it. Your body's own GLP-1 is broken down within minutes of release. Semaglutide is engineered to resist that breakdown and activate GLP-1 receptors far more strongly, for far longer.

    Supporting your body's own GLP-1 signaling through food or the microbiome isn't a lesser version of taking semaglutide. It's a different thing entirely.

    Where the Microbiome Comes In

    Your gut bacteria eat what you don't digest.

    When fermentable fibers and resistant starch reach the colon, bacteria ferment them and produce short-chain fatty acids (SCFAs), mainly acetate, propionate, and butyrate. These aren't waste products. They're signaling molecules, and the cells lining your intestines are built to receive them.

    Intestinal cells carry receptors, including FFAR2 (also called GPR43) and FFAR3, that detect short-chain fatty acids. When SCFAs bind these receptors on L-cells, they trigger an internal cascade that can influence the release of gut hormones, including GLP-1 and a related satiety hormone called PYY.

    So the pathway is real: fiber arrives, microbes ferment it, metabolites are produced, gut cells sense them, hormones get released, and the gut communicates with the pancreas and the brain. That last link is worth sitting with — your gut and brain are in constant conversation, and food-derived microbial metabolites are part of what they're saying to each other.

    The quick version of this compresses to: fiber → butyrate → GLP-1 → less hunger. The actual biology is an ecosystem with many signals, of which butyrate is one.

    Can Butyrate Support Natural GLP-1 Production?

    The mechanistic evidence is strong. The human evidence is thinner, but still developing.

    A small 2026 study in adults with obesity found that oral sodium butyrate combined with L-arginine significantly increased circulating GLP-1. That's encouraging, but the study had only seven participants, butyrate wasn't tested on its own, and participants reported no difference in hunger or fullness.

    By contrast, in a 2025 randomized controlled trial of 50 adults with obesity, people taking sodium butyrate alongside a reduced-calorie diet saw reductions in weight, BMI, and waist circumference, but their serum GLP-1 didn't change significantly.

    A 2026 randomized, double-blind trial of 46 adults added more nuance. After 12 weeks of sodium butyrate plus a moderately reduced-calorie diet, participants with obesity lost a meaningful amount of weight. Participants who also had type 2 diabetes did not, although their blood sugar control improved.

    That pattern echoes an earlier finding. In a 2018 study, four weeks of oral butyrate improved insulin sensitivity in lean men but not in men with metabolic syndrome.

    Together, these suggest butyrate's effects depend heavily on metabolic context: who you are, what your microbiome looks like, and where the butyrate ends up. But GLP-1 is only part of the story.

    Why Butyrate Matters Beyond One Hormone

    Focusing only on GLP-1 undersells what butyrate does.

    Butyrate is the primary fuel source for colonocytes, the cells lining your colon. Not a supporting nutrient. Their main energy supply. Those cells use butyrate to power the work of maintaining a functioning gut lining, the barrier that decides what passes from your digestive tract into your body and what doesn't.

    This is where the cellular health picture comes together. A well-fueled intestinal lining supports a healthy gut barrier. A healthy barrier supports a stable environment for the microbial community living there. And that community produces metabolites that signal to the rest of the body — including the gut-to-brain communication involved in appetite and satiety.

    Butyrate sits at the center of that loop as both fuel and message. That role holds regardless of what the GLP-1 research eventually concludes.

    Support the System, Not Just the Signal

    The takeaway isn't that you should be trying to maximize GLP-1. Your metabolism and gut function are more complex than one signal.

    Lasting metabolic regulation runs on an ecosystem: microbial diversity, adequate fermentable fiber, well-nourished intestinal cells, an intact gut barrier, and steady communication between gut and brain. Semaglutide shows what happens when you push one signal in that system very hard. It doesn't show that one signal is the whole system, or the only way to modulate it.

    Feeding that ecosystem starts with fiber-rich whole foods: vegetables, legumes, cooked-and-cooled potatoes and rice (good sources of resistant starch), and other plant foods your gut bacteria can thrive on. Give it time. Gut environments shift over weeks and months, not days.

    For targeted support, BodyBio Butyrate provides butyrate in supplement form to support the gut lining and a healthy microbiome.*

    The Bigger Story Your Gut Was Already Telling

    Semaglutide has taught researchers a great deal about how strongly GLP-1 signaling can influence not just hunger but desires: what sounds good, what tastes right, and what gets left on the plate.

    And yet, the more interesting revelation may be how much was already happening without it. Every meal you eat feeds a microbial community that turns fiber into signaling molecules, which intestinal cells read and translate into messages sent onward to your pancreas and your brain. That conversation has been running your entire life.

    Butyrate is one voice in that conversation. It fuels the cells that hold your gut barrier together and takes part in the signaling between your microbiome and the rest of your body. Supporting butyrate production in the gut won't replicate a pharmaceutical. It doesn't need to. Feeding the system well is its own goal, and the benefits build gradually, often in small shifts that are easy to miss at first.

    Support your gut at the cellular level with BodyBio Butyrate.*

    *These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease.

    This article is for educational purposes only and is not a substitute for medical advice. If you're taking semaglutide or another GLP-1 medication, talk with your healthcare provider before adding new supplements.

    Ashley Palmer | 06.16.2026

    Comprehensive Guide to Butyrate: What it is, Benefits, Side Effects, & More

    Butyrate is a necessary component to a balanced microbiome, also working as an inflammation guard*. One of several, short-chain fatty acids created from fermented resistant starches, low butyrate levels have been associated with serious health concerns.

    Ashley Palmer | 04.24.2026

    Butyrate and IBS: What Your Gut Cells Actually Need

    You've tried the probiotics. You've cleaned up your diet. You're doing everything you're supposed to do, and your gut still isn't cooperating.

    If you have IBS, that frustration is familiar. Bloating, urgency, unpredictable mornings, the constant guessing game of what's going to set things off.

    What often gets missed in the conversation around IBS isn't a trendy new supplement or a stricter elimination diet. It's something more foundational: what your gut's own cells actually need to function.

    Here's a closer look at what butyrate does, why IBS and low butyrate levels are closely linked, and how supporting the gut at the cellular level can make a difference.

    Table of Contents:

    • Understanding Butyrate

    • How Butyrate Works in the Gut

    • Why This Becomes an Issue for People With IBS

    • Supporting the Body More Effectively

    • Butyrate, IBS, and the Cellular Health Connection

    • How Butyrate Supports IBS Comfort Long-Term

    Understanding Butyrate

    Butyrate is a short-chain fatty acid (SCFA) produced in the colon when beneficial gut bacteria ferment dietary fiber, specifically resistant starch. It belongs to a class of compounds called postbiotics, the functional byproducts of a healthy microbiome.

    Unlike probiotics, which are living bacteria, butyrate is a metabolite. It's a compound your body puts to work directly at the cellular level. Understanding the difference between probiotics and postbiotics, like butyrate, is a useful shift you can make when thinking about gut health.

    Why the Body Relies on Butyrate

    Your colon is lined with specialized cells called colonocytes. These cells run almost entirely on butyrate, providing up to 90% of their energy needs.

    When colonocytes have what they need, they do their job well. They maintain the integrity of the gut lining, regulate what passes into the bloodstream, support a healthy inflammatory response, and help keep gut motility on track. Without enough butyrate, the gut’s main source of energy, the gut simply can't do its job well.

    How Butyrate Works in the Gut

    Butyrate supports three interconnected systems in the gut: the gut lining, the immune environment, and gut motility.

    The gut lining is just one cell layer thick. Butyrate fuels those cells and supports the tight junctions between them, the structural connections that keep the barrier intact and functioning.

    At the immune level, butyrate helps the body maintain a balanced inflammatory response in the colon without triggering overactivation. And because it directly influences the rhythmic contractions that move contents through the digestive tract, it plays a meaningful role in the irregular patterns that so many people with IBS experience.

    What Happens When Butyrate Levels Are Supported vs. Strained

    When butyrate is available in adequate amounts, the gut lining stays resilient, motility is more regular, and digestive comfort improves, whether you have a diagnosis of IBS or not.

    If butyrate levels fall short, the gut barrier may become less stable, motility can become unpredictable, and the colon's immune environment may shift. How pronounced these patterns are varies from person to person. Diet, stress, genetics, and microbiome composition all play a role in your body’s patterns too.

    Why This Becomes an Issue for People With IBS

    Modern Stressors on Butyrate Production

    Butyrate is made by gut bacteria that ferment resistant starch, a type of fiber found in foods like cooked and cooled potatoes, legumes, and underripe bananas. The modern diet is low in these foods. That means many people simply aren't giving their gut bacteria the raw materials they need to produce adequate butyrate levels.

    Antibiotic use, chronic stress, and certain medications can also reduce the population of butyrate-producing bacteria in the colon. Over time, that compounds the butyrate production gap.

    Why Common Approaches Often Fall Short

    Probiotics can be a valuable part of gut health support, but most probiotic strains are not butyrate-producing species. They can shift the microbiome, but they don't directly address the fuel shortage that many IBS-related symptoms may stem from.

    Fiber-based approaches come with a similar challenge. In some people with IBS, increasing fermentable fiber can worsen bloating and gas before it helps, because a disrupted microbiome may not efficiently use that fiber to make butyrate.

    Since butyrate works at the cellular level, the signs of low butyrate can overlap common IBS symptoms, which is part of why the connection between the two gets overlooked.

    Supporting the Body More Effectively

    Foundational Support for Butyrate Production

    Diet is the first step to improving the body's natural butyrate production. Foods high in resistant starch give butyrate-producing bacteria what they need to function properly.

    Foods that naturally support butyrate production include cooked and cooled rice, potatoes, and legumes. A steady intake of resistant starch over time does more for the microbiome than occasional high-fiber days followed by low-fiber ones.

    Stress management and adequate sleep can also support a more stable gut environment. Chronic stress directly affects microbiome composition and motility through the gut-brain axis. 

    When Targeted Butyrate Support Makes Sense

    For people whose microbiome is disrupted or whose diet can't consistently provide enough resistant starch, direct butyrate supplementation is another option for long-term support.*

    Supplemental butyrate delivers the short-chain fatty acid directly to the colon, where colonocytes can put it to use.* Clinical research has shown that sodium butyrate supplementation is associated with improvements in abdominal comfort and bowel regularity in people with IBS.

    Sodium butyrate and calcium magnesium butyrate are both effective options, and the differences between which works best for your body often come down to your individual health history and mineral needs.*

    Butyrate, IBS, and the Cellular Health Connection

    IBS is complex, and its causes vary from person to person. But one consistent finding in the research is that people with IBS tend to have lower levels of butyrate-producing bacteria and overall reduced short-chain fatty acids in the gut. That points to a cellular resource problem as much as a microbiome problem.

    When the cells lining the colon are undersupported, the entire digestive environment becomes less stable. Gut barrier function, motility, immune signaling, and communication along the gut-brain axis all depend on colonocytes having what they need to function.

    Supporting the gut at the cellular level is not a replacement for other gut health practices (whole food probiotics, exercise, etc.). It’s the foundation that makes those practices more effective. When your cells are supported, the body functions more efficiently as a whole.

    How Butyrate Supports IBS Comfort Long-Term

    IBS can feel like a moving target, and the path toward better digestive comfort is rarely a straight line or a quick fix. Supporting your gut at the cellular level creates a more stable foundation, and that starts with making sure colonocytes have the fuel they need.*

    Butyrate works best as part of a consistent approach that includes diet, lifestyle, and targeted support where needed. Progress tends to be gradual, and that's expected. It reflects the time it takes for the gut lining to strengthen and the microbiome to rebalance.

    IBS makes a lot more sense when you know what the gut's cells actually need. And that clarity is often where real progress begins.

    Support your gut at the cellular level with BodyBio Butyrate.*