By Alison Moodie
Reviewed by Emily Gonzalez, ND for Scientific Accuracy

Article at a Glance:

  • Everyone’s gut microbiome is unique. Certain combinations of microbes, and a diverse mix of them, define a healthy gut.
  • Your gut health plays a role in everything from your mood to your immune function. Cleaning up your diet is the most powerful way to starve the bad bacteria and feed the good guys.
  • Find out how to support optimal gut health, from gut health foods to daily supplements like Bulletproof InnerFuel Prebiotic.

Are you feeling down? Are you dealing with skin problems? Do you feel constantly bloated? All of these issues—and more—can be traced back to your gut health. It turns out that the tens of billions of microbes in your digestive tract are the master puppeteers of a healthy gut. Find out what makes these tiny bugs tick, and how you can support healthy digestion with the right gut health foods and wellness supplements.


Your body is home to trillions of microscopic organisms: bacteria, fungi, viruses and other microbes that inhabit almost every part of you. This busy ecosystem of microorganisms make up what’s known as the human gut microbiome.

Most of your microbes live in your gut. Bacteria are the most studied of the gut microbes. Scientists have discovered over 1,000 species of bacteria in the gut. These bugs do a lot—they digest your food, keep your immune system humming along, protect your intestines, remove environmental toxins from the body, produce B vitamins and generate vitamin K, which helps your blood clot.

Human health is complicated, to say the least. Similarly, everyone’s gut microbiome is unique, although certain combinations of microbes (and a diverse mix of them) are the hallmarks of a healthy gut.

Your gut flora also contains small amounts of “bad” bacteria. Their presence is totally normal, but we don’t want these microbes to take over.  That’s why keeping a good balance between the good and the bad guys is important. You want vibrant communities where the good bacteria thrive and the bad bacteria are kept in check.


You get your first dose of microbes as you’re being born, when you pass through your mother’s birth canal. From there, your microbiome changes during the first couple of years of life, influenced by microbes in breast milk, antibiotics and your first solid foods. Your gut microbiota stabilizes around the age of 3. This early development of intestinal flora is critical because it sets the tone for your gut health…for life.

Scientists have started taking a much closer look at the gut microbiome and its connection to almost everything in the body. A gut that’s out of balance can lead to all kinds of challenges. It’s actually tough to find a condition that’s not connected to gut health in some way because it can impact everything from your weight to your well-being.


When your gut bacteria is out of balance, your body isn’t able to digest food as well. If you’re feeling or noticing any of the following symptoms, you may have a gut imbalance:

  • Food sensitivities or allergies
  • Digestive problems like occasional gas and bloating
  • Weight changes
  • Skin issues
  • Fatigue
  • Mood swings
  • Difficulty concentrating

Did you know? Studies show that gut health impacts metabolic health. If you want to increase your metabolism, your diet is one of the key places to start.


Your gut flora, your diet and the strength of your intestinal lining determine the health of your gut (and your overall health). Keeping your gut in balance is a delicate dance, and there’s a lot that can tilt it in the wrong direction. As an adult, the health of your gut microbiome shifts when you:

  • Eat processed foods
  • Get sick
  • Drink alcohol or take drugs
  • Experience stress
  • Lose or gain weight
  • Get older
  • Travel overseas or to new environments
  • Take medication that affects the microbiome


Improving your gut health starts with what you eat. It’s the most natural way to support your good gut bacteria. They eat what you eat, so feed them well. Keep reading to learn how to nourish good gut bacteria.


  • Cut back on sugar: If you make one change to improve your gut health, make it this. Bad bacteria love sugar and feed off of it. Cut back on sugar (that includes the fructose in fruit), low-nutrient carbohydrates, conventional dairy and alcohol.
  • Eat more whole foods: The hallmark of a thriving digestive system is a balanced gut microbiome. Have a hard time eating your greens? Here’s how to eat more vegetables.
  • Up your fiber intake: We’re not talking about cardboard cereal made with whole grains. Although grains and legumes are sources of fiber, but they’re also sources of antinutrients that can contribute to inflammation and impede nutrient absorption. We recommend reaching for leafy greens, nuts, root vegetables and prebiotics like what you’ll find in Bulletproof InnerFuel Prebiotic.


Not all gut health supplements are the same. Some will help balance beneficial gut bacteria. Others might actually make you feel lousy. Here’s what you should know about how to improve gut health with targeted supplements.


Probiotic supplements help support gut health by adding beneficial bacteria to your gut microbiome. You can get probiotics in fermented foods like kimchi, sauerkraut and kefir, as well as probiotic supplements.

One caveat here—not all probiotics are the same. Some strains can increase your levels of histamine, the same chemical your body produces during an allergic reaction. Too much histamine causes inflammation in the body. This largely depends on your own biology; some people tolerate fermented foods like tempeh and miso, while others feel bloated, sluggish or foggy after eating histamine-rich foods.

Learn everything you need to know about probiotics, how they work and which strains to avoid. (We suggest starting with Bifidobacterium infantis, Bifidobacterium longum, and Lactobacillus plantarum.)


Probiotics need to eat. You need PREbiotics to feed your good gut bacteria. You can get prebiotics from vegetables rich in soluble dietary fiber (like sweet potatoes, brussels sprouts and leeks), chocolate and prebiotic supplements like Bulletproof InnerFuel Prebiotic. Also, experiment with foods high in resistant starch, like plantain and green banana flour, raw potato starch and cooked and cooled white rice.


Collagen is one of the building blocks of your gastrointestinal tract. Eat collagen-rich foods such as bone broth and organ meats. Try Bulletproof Collagen Protein Gut Health, made with beneficial ingredients to support a healthy gut microbiome.


Activated coconut charcoal is a form of carbon that has been used for thousands of years to detoxify the body and improve digestive health. Activated charcoal binds to toxins and chemicals in the gut. Read more about the benefits of activated charcoal and how to work it into your diet.


  • Get to know your poop: It might sound funny, but becoming an expert on your own stools tells you a lot about what’s going on in your gut. Check out this handy poop chart to help you identify any problem areas. You want to look at the stool’s consistency, whether it floats or sinks, its color and how often you go (once or twice a day is a sign of strong digestion, while constipation is a red flag).
  • Talk to your doctor: Talk to your healthcare provider about your gut health and digestion. They can help you understand your gut, suggest lifestyle and dietary changes and refer you to a gastroenterologist.
  • Take a gut test: You can now send a fecal sample from home to a company like Viome. They send you a test kit in the mail, and you pay them a fee to analyze your stools. You’ll receive a detailed report with a list of all the bacteria in your gut, how your microbiome compares to other people’s, and how to keep your healthy bacteria thriving with supplement and diet recommendations. You can test again to monitor your progress and see if any changes you made are working to heal your gut.

It might surprise you to think that mental health, energy and immunity all interact with digestion. But it makes sense, when you think about it—your gut microbiome is responsible for breaking down the food you turn into energy that powers your entire body, from your muscles to your brain. So, if you want to take care of your health, feel great and build a strong foundation for overall wellness, go with your gut.