The 9 Most Beneficial Foods for Your Gut Health (and the Worst) Backed by Science
An Introduction to Our Gut Microbiome
If you’re like me, you don’t often think about the multitude of microscopic life in and on your body. I’m too busy writing, reading, and connecting with my human-sized friends to sit around contemplating the microscopic ones.
Nevertheless, they are, shall we say, abundant.
Our hands, for example, carry around 150 species of “normally present” microbes that usually don’t harm us. However, our hands also tote around “transcient” germs like Influenza, E. Coli, and Strep.
Thankfully, most of us work hard at iradicating them. I think we’re pretty good at intentionally washing these away regularly with basic soap and water.
Clearly, we actually do think about these mini-creatures on our hands.
Thank you glaucoma.uk for this magnified view of an eye mite.
Maybe eyelash mites aren’t as present on our radar. These eight-legged, cigar-shaped Demodex mites, live in our eyelash and eyebrows hairs.
{Insert me shuttering, making gagging sounds, and rolling my eyeballs back into my head}
The thought of mites living in my eyelashes makes me as sick as thinking about bed bugs, ticks, and lice.
Turns out, however, these hidden little organisms on our eyelids, according to an article by UCLA Health, are a “part of our body’s natural microbiome.”
Evidently, these eyelid buddies feast on our dead skin cells and excess oils, and by doing so, “they’re actually doing us a service.”
I’d rather not know about this friendly service; however, I am willing to live at peace with them knowing I normally don’t have to give them too much thought.
Oh, but there’s more.
Your mouth hosts 700 types of microbes. Move over, eye mites. I can’t even think about 700 types of creatures living in my mouth. More ick.
Nevertheless, most of us brush our teeth regularly, rinsing most of those colonies down the drain at least twice daily, three times if you’re really diligent about it.
You may think you’re simply washing away food particles, but what you’re also accomplishing is removing mouth bacteria, fungus, and viruses: microbes that can not only cause tooth decay, but also lead to heart disease.
According to the University of Pennsylvania’s Penn Medicine blog, “[r]esearchers suspect that bacteria present in gum disease can travel throughout the body, triggering inflammation in the heart’s vessels and infection in heart valves.”
Fresh breath, clean teeth, and a white smile for the world. A healthier heart for you.
All hidden. A hidden power that YOU harness each and every day probably without even thinking about it.
The Colony of Microscopic Tenants in Our Gut
While some hidden microbes on our bodies are out to kill us (Hello, transient hand viruses), some are helpful little scavenger buddies (Good morning, eye mites), and some are silently trying to infiltrate and inflame our blood system (I’m looking at you, plaque), our biggest colony of microscopic tenants has largely flown under the radar of scientists.
Fortunately, research has exponentially increased around our gut microbiome in the last 20 years. Yet, even though the study of our “gut biome” seems fairly recent, it actually began, not surprisingly, with the invention of the microscope.
The history of microbiota research with its significant milestones up to 2019 has been noted in this article in Nature. If you’re interested in the topic, I encourage you to plug into the creative, inquisitive right side of your brain and read the research from 2025 here.
In a nutshell, the first mainstream news reports about our human intestinal microbiome started appearing in the media around 2006. Since then, the scientific field has expanded from the fringes to the forefront, as often happens with cutting-edge functional medicine wisdom before more main-stream research jumps in to support it.
Our gut-mind axis is the perfect example of this. Despite knowing that “we are what we eat,” the science behind this didn’t “officially” back this up until 2019 when studies began proving that improving our gut health can effectively treat a robust list of seemingly unrelated illnesses from inflammatory bowel disease to depression.
Okay, so…where do we go from here?
Let’s focus on this week. Today.
If you’re working on improving your understanding of how you can take control of your own physical and mental health, then perhaps you’ll want to do more research about the hidden powers of the microbes that live in your stomach and intestines.
You might, however, just want to optimize it without understanding every little scientific detail. That’s okay, too.
Perhaps you can guess that I’m the deep-diver. And I’m happy to save you time by summarizing the research for you.
I know we have one thing in common: If you’re reading this you’re ready to pounce of life’s possibilities with me. You’re ready (or already on the journey) toward a healthier, longer lifespan and an active, pro-aging attitude.
So whether you want to know the nitty gritty details or not, I think it’s important for you to know that researchers at the University of South Carolina conducted a literature review of the gut microbiota data from 106 other studies, while citing 150 research projects in their publication.
The Dietary Index for Gut Microbiota (DI-GM)
From this massive amount of data, they developed what they call the Dietary Index for Gut Microbiota (DI-GM)
It’s not complicated, and simply boils down to this:
What you eat absolutely affects both your physical and mental health. Certain foods are very beneficial to our gut biome. Others are harmful to the sensitive balancing act that’s going on in there.
It’s up to you if you’d like to harness the power of your little helpers or not. It’s also up to you if you want to take the time to understand exactly what’s happening at a molecular level. I encourage you to learn more if you’d like to spend more time reading about it.
Regardless of how deep you want to dig into the whys and hows of it all, I know you can use the information to your benefit.
This all begins with how you fuel your journey and if you decide that YOU ARE WORTH harnessing the hidden powers of your gut-mind axis.
Here are the foods in the DI-GM. You’ll also find these and similar foods across various other types published lists, which I will explore in greater detail in future blog posts. When you get right down it, the best foods for humans regardless of what you’re trying to achieve (a better gut biome, a healthy weight, lower inflammation, lower cholesterol, a healthier heart, sharper brain, longevity) are actually basically about them same.
In the center of a giant Venn diagram, we will repeatedly see the same beneficial foods: leafy greens, cruciferous vegetables, whole grains, fermented items, berries and other colorful fruits, nuts and seeds, avocadoes, lean meats, beans & lentils, and fish rich in omega-3 oils. Add in coffee, green tea, dark chocolate, and spices for some flavor and sizzle.
Let’s start with the MOST BENEFICIAL FOODS for your gut health:
In no particular order, the winners are:
Fermented dairy (low or no sugar Greek yogurt, lower fat cheese such as Swiss, low or no sugar kefir, sour cream, buttermilk, cottage cheese)
Chickpeas (also known as garbanzo beans)
Soybeans (including tofu, miso, soymilk) Read here if you’re worried about soy and breast cancer.
Whole grains (like brown rice, oatmeal, whole grain breads, quinoa, etc.)
Cranberries (not the sugar-coated dried ones)
Avocados (For the love of all that’s good and right, you need my favorite avocado cutter.)
Broccoli (Why is steamed is best?)
Coffee (Again, watch the sugar which negates the positive effects of the coffee.)
Green tea (Try a mint/green tea blend)
and a bonus 10th: Fiber (Remember from biology class how plant cells have cell walls and animal cells don’t? Plants provide us with fiber from their cell walls; animals have zero fiber to share with us.)
Worst Foods for a Healthy Gut
And here are the WORST FOODS for your gut health:
In no particular order, the foods that disrupt the balance of our healthy microbiome are:
Red meat (beef, veal, pork, lamb, game meat, excluding organ meat)
Processed meats (frankfurters “hotdogs”, sausages, corned beef, luncheon meat from beef, pork, or poultry)
Refined grains (white bread, white flour, white rice)
High-fat diet (≥40% of energy from fat -- not exactly a “food” but let’s call it high-fat foods such as donuts, ice cream, cheesecake, cakes, french fries, palm oil, etc.)
Let’s quickly touch on red meat. If you want to eat red meat, do it. Just be aware that a diet heavy on red meat without thoughtful consideration of trying to balance it out with foods beneficial to your gut health is going to decrease the amount bacteria that you need.
Think of it as a balancing act. If a round of antibiotics for an infection is about to wipe out your gut biome, then focus on building it back up with the top beneficial foods. It wouldn’t be the best time for a week of hamburgers, lamb chops, and steaks as your main focus.
But what about so many influencer medical experts saying we should be eating a high-fat diet? Here’s a great article from Dr. Mark Hyman called, “Why Fat Doesn’t Make You Fat” that might help to explain it.
Yes, science is messy. It’s supposed to be. Research often back-tracks and frequently contradicts itself. That is the nature of the scientific method. So, yes, there are indeed healthy high-fat foods.
That’s not what I’m talking about here in the worst foods for your gut health list.
I’m talking about the high-fat, highly-processed junk that is just “food-like products” that most Americans eat in our SAD (Standard American Diet). They aren’t really food, are they? They are chemically processed, highly-refined yuck that cannot support the health of your hidden gut biome or the health of your body and mind.
Think about it: If that kind of “food” cannot keep microscopic bacteria alive and thriving, it surely isn’t going to keep your fabulously complex body alive and thriving!
Keep away from that high-fat junk as much as you can based on where you live and your budget. It’s hard sometimes to find food that isn’t processed and high in unhealthy fat, but I know that you’ll do your best given your life circumstances. You’ve got this. Make the best choices that you can with what you’ve got. Your future self is counting on you.
What You Can Achieve Today
If you can replace even one item from the WORST list with one item from the MOST BENEFICIAL list, you’ll be taking a step in the right direction for making your gut biome a home for happy little creatures.
After all, we cannot deal with our digestive super colony with soap and water. We’ve got to actively feed the good ones and starve the harmful ones.
That takes some thought and planning. You’re worth the effort.
Let’s pounce on this together. Let’s keep exploring the list of hidden powers in your body that you can tap into to help you thrive. The list is astounding, amazing, and awesome.
And so are you.
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