Are you feeling down? Do you have joint pain? Are you dealing with itchy eczema? Do you feel constantly bloated? All of these issues — and more — can be traced back to your gut. It turns out that the tens of billions of microbes in your digestive tract are the master puppeteers of your health. Find out what makes these tiny bugs tick, and how you can keep your gut ecosystem healthy and thriving.

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What is the gut microbiome?

Everything You Need To Know About Gut Health_What is the gut microbiome

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 micro-organisms make up what’s known as the human microbiome.

Most of your microbes live in your gut, mainly in your intestines and colon. Bacteria are the most studied of the microbes — scientists have discovered over 1,000 species of bacteria in the gut.[1] These bugs do a lot — they digest your food, keep your immune system humming along, protect your intestines from infections, remove environmental toxins from the body, and produce B vitamins and vitamin K, which helps your blood clot.[2]

Everyone’s gut microbiome is unique, although certain combinations of microbes — and a diverse mix of them — are the hallmarks of a healthy gut.[3]

Normal gut flora contains small amounts of “bad” bacteria — microbes that cause disease when they overgrow.[4] That’s why keeping a good balance between the good and the bad guys is important — too much bad bacteria makes you sick and robs you of feeling your best. You want vibrant communities where the good and bad bacteria work together in harmony.

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.[5] This early development of intestinal flora is critical — it sets the tone for your gut health for life.[6]

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 serious diseases, including multiple sclerosis, diabetes, depression, rheumatoid arthritis, cancer, autism, heart disease, and asthma.[7] It’s actually tough to find a condition that’s not connected to gut health in some way.

The signs your gut is unhealthy

If you’re feeling or noticing any of the following symptoms, you may have a gut imbalance:

  • Food sensitivities or allergies
  • Digestive problems like gas and bloating
  • Weight gain
  • Skin issues like acne, eczema, and rosacea
  • Fatigue
  • Mood swings
  • Autoimmune disorders
  • Depression
  • Anxiety
  • Difficulty concentrating
  • Joint pain

What impacts gut health

Everything You Need To Know About Gut Health_What impacts gut health

Your gut flora, your diet, and the strength of your intestinal lining determine the health of your gut. Using antibiotics too often disrupt your gut bacteria. When you’re sick, antibiotics help clear out the bad bacteria, but in the process they wipe out the good bugs too. Some studies have shown that antibiotics can permanently alter intestinal flora.[8] [9]

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 other new environments

Stress, mood, and the gut — what’s the connection?

Have you ever felt nauseous when you’ve been worried about something? Or had “butterflies” in your stomach when nervous? The brain sends signals to the gut that produces these physical symptoms.

Scientists are discovering that it goes the other way too — when your gut is inflamed or imbalanced, it sends a signal to your brain. You then feel stressed or worried or depressed. It turns out that your gut and your brain are constantly talking to one another.

This back-and-forth communication is known as the gut-brain axis, and occurs primarily along an information superhighway called the vagus nerve. A strong vagus nerve improves the communication between your gut and your brain, so it’s vital that you keep it in working order (learn more about how to tone your vagal pathway).


Everything You Need To Know About Gut Health_stress

Stress is bad news for the brain-gut axis. Stress signals trigger the release of neurotransmitters and proinflammatory cytokines (molecules that contribute to inflammation and disease), which affect the gut in all kinds of ways.[10][11] Stress can cause:

  • Intestinal dysmotility (when the muscles and nerves of the digestive system don’t work properly)
  • Holes in the intestine, allowing toxins, bacteria, and food particles to escape and enter your bloodstream
  • An imbalance in your gut bacteria
  • Decreased blood flow and oxygenation to the gastrointestinal (GI) tract
  • Acid reflux

This digestive damage can develop into serious GI disorders including inflammatory bowel disease (IBS), peptic ulcers, and food allergies.


Everything You Need To Know About Gut Health_Mood

You’ve just come off a round of antibiotics, and at the same time you’ve been reaching for sugary foods a little too often. You notice you’re feeling more blah than usual and a bit low. That’s probably no coincidence, thanks again to the gut-brain axis.

A groundswell of research in recent years points to a strong link between what’s going on in your gut and various mood and behavioral disorders including depression, autism, and even neurodegenerative diseases.[12] [13] [14] [15] Stomach irritations and gut imbalances send signals to the brain via the central nervous system (CEN), triggering changes in your mood.

A recent study found that transferring the fecal bacteria of depressed people to rats led to depressed behavior in the rats.

Another study divided 40 healthy women into two groups based on their gut bacteria composition (this after analyzing the women’s stools). The women with a prevalence of one type of bacteria reported feeling less anxious, stressed, and irritable after looking at negative images compared to the other group, whose guts were dominated by a different kind of bacteria. Scans also showed differences in the women’s brains — those who said they felt less stressed showed lower brain volume in areas like the hippocampus than the other group.[16]

Related: How Your Gut Bacteria Control Your Mind

How the gut impacts your weight

Everything You Need To Know About Gut Health_How the gut impacts your weight

You can now blame your gut flora for your excess weight. Research has found that obese people and lean people have different types of microbes in their guts.[17]

One study put genetically-similar mice on a high fat diet. The mice gained or lost weight depending on the types of bacteria in their gut.[18]A diverse mix of bacteria in the gut is also key to staying thin.[19]

Another study looked at 77 pairs of twins — one twin was obese, the other wasn’t. The researchers found that the obese twin had different gut bacteria — as well as less bacterial diversity — than their non-obese twin.[20]

Naturally slender people have more of a bacteria from the Bacteroidetes phylum. You can’t buy this species as a supplement, but you can hack it by eating foods bursting with antioxidants called polyphenols — found in brightly colored vegetables, coffee, and chocolate.

Gut microbes also make a hormone called FIAF (fasting-induced adipose factor) which tells the body to stop storing fat and burn it instead. To ramp up FIAF production, you want to starve the bacteria of starch and sugar. When bacteria are “hungry,” they make more FIAF and you burn fat.[21]

The different digestive conditions

Everything You Need To Know About Gut Health_The different digestive conditions

When your gut bacteria is out of balance, your body isn’t able to digest food as well, which can lead to various digestive conditions:

IBS: Irritable bowel syndrome (IBS) occurs when the gut and the brain don’t communicate properly. Stress or certain foods cause the colon to spasm, so food either gets pushed through the intestines too quickly (diarrhea) or it gets stuck and you get constipated. One theory says that IBS is caused by an overgrowth of bacteria in the small intestine (more on that below). You feel pain and cramping, bloating, and fatigue.[22] [23] [24] It’s a vicious cycle — the constant discomfort and embarrassment (IBS sufferers report a lot of gas) makes you feel even more stressed and anxious, but this stress and anxiety makes the symptoms worse. Note that IBS is different from irritable bowel disease (IBD) — a more serious disorder that causes severe inflammation in the bowel. A large study funded by the US government found that cognitive behavioral therapy (CBT) helped IBS sufferers control their mental stress, which eased their symptoms in the long term.[25]

SIBO: Too much bacteria in the small intestine causes small bacterial overgrowth, or SIBO. Symptoms include gas, bloating, diarrhea, autoimmune diseases, and nutrient malabsorption. Recent research suggests that SIBO may be responsible for nearly 80 percent of IBS cases.[26] The small intestine connects the stomach and the large intestine (which includes the colon). Normally, muscular contractions push food through the small intestine to the colon. When these muscles don’t work properly, your intestines can’t efficiently move bacteria into the colon for elimination. That means the bacteria remains in the small intestine, upsetting the microbial balance. Low stomach acid is another possible cause of SIBO. Doctors prescribe antibiotics to clear out the excess bacteria, but studies show that herbal antimicrobials treat SIBO just as well.[27] Learn more about how to treat SIBO.

Crohn’s: Crohn’s is a form of irritable bowel disease (IBD) that causes chronic inflammation to your digestive tract. Crohn’s typically occurs in the ileum — the final part of the small intestine — although it can affect any part of the GI tract, from the mouth to the anus. Common symptoms include diarrhea, nausea, weight loss, anemia, and stomach pain. This long-term inflammation can lead to ulcers, fistulas, and malnutrition.[28] It’s not clear what causes Crohn’s — it may be an autoimmune reaction, where your immune system attacks your own intestinal cells, triggered by bacteria in your digestive tract. A recent study found high amounts of three types of gut bacteria in people with Crohn’s, suggesting that the right mix of probiotics could control the bad bacteria, and therefore control Crohn’s symptoms.[29] Note that the other form of IBD is ulcerative colitis — it has similar symptoms to Crohn’s, but only affects the large intestine, while Crohn’s can develop anywhere in the GI tract.

Leaky gut: Too much bad bacteria and not enough good bacteria can cause leaky gut — when cracks or holes develop in your intestinal lining, allowing toxins, undigested food particles, and bacteria to pass through and enter your bloodstream. This creates inflammation in the body and over time leads to autoimmune disease. Leaky gut has been linked to type 1 diabetes, IBD, celiac disease, multiple sclerosis, and asthma.[30]

Ways to test your gut

Everything You Need To Know About Gut Health_Ways to test your gut

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 be looking 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).

Take a gut test: You can now send a fecal sample 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 bacteria healthy with supplement and diet recommendations. You can test again — whenever you want really — to monitor your progress and see if any changes you made are working to heal your gut.

What to eat for a better gut

Everything You Need To Know About Gut Health_What to eat for a better gut

Cleaning up your diet is the most powerful way to starve the bad bacteria and feed the good guys. Read more on how to balance your gut flora. In the meantime, follow these gut-friendly diet tips:

Quit sugar: If you make one change to improve your gut health, make it this. Bad bacteria love sugar and feed off of it. Excess sugar is the prime culprit behind small bacterial intestinal overgrowth (SIBO) and candida (a type of yeast overgrowth). Cut out sugar (that includes the fructose in fruit), low-nutrient carbs, conventional dairy, and alcohol. Learn more about how to kick your sugar habit with Bulletproof-approved alternative sweeteners.

Choose a variety of foods: The hallmark of a thriving gut is a diverse mix of good bacteria. So eating a variety of low-toxin, anti-inflammatory foods ensures no one bacterial strain dominates over the others. Focus on vegetables, high-quality protein, and omega-3 fats. Read more about cleaning up your diet here.

Add MCT oil: Medium-chain triglycerides — the saturated fatty acids found in coconut oil — are strong antifungals, antibacterials, and antivirals.[31][32] Try Brain Octane Oil — it’s the most potent extract of coconut oil. Use it in your Bulletproof Coffee, drizzle it over sushi, or blend it in a smoothie.

Feed your good bacteria prebiotics: Prebiotics are what good bacteria (aka probiotics) feed on.[33] This process produces short-chain fatty acids like butyrate, which strengthens your brain and your gut[34][35] (grass-fed butter is full of butyrate — one reason why it’s such a big part of the Bulletproof Diet.) You can get prebiotics from vegetables rich in soluble fiber like sweet potatoes, brussels sprouts, and asparagus, as well as coffee and chocolate. Also experiment with foods high in prebiotic resistant starch, like plantain and green banana flour, cooked and cooled white rice, and raw potato starch. Not everyone can tolerate resistant starch, so start slowly and track how you feel (one tablespoon of potato starch a day is a good starting point).

Try this resistant starch recipe: White Chocolate and Raspberry Keto Cake

Get more collagen: Collagen heals and repairs the gut lining, making it easier for your body to absorb nutrients.[36] Eat collagen-rich foods such as bone broth and organ meats, or add a hydrolyzed collagen protein powder to your smoothie (try Collagen Protein.) You can also use Collagelatin to make puddings and jellies, or to thicken soups and sauces.

Related: How to Get More Collagen, and Why Your Skin Needs It to Stay Young

Other ways to heal your gut

Everything You Need To Know About Gut Health_Other ways to heal your gut

Watch out for histamine: Taking probiotic supplements can be a good thing for your gut, but 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. Avoid probiotic supplements that contain Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus. These histamine-producing bacteria are also present in so-called health foods like conventional yogurt and aged or fermented foods. Learn more about the best and worst probiotics.

Be cautious with antibiotics: Western doctors tend to over-prescribe antibiotics for illnesses like the common cold and ear infections that don’t even respond to these drugs. The Centers for Disease Control and Prevention (CDC) estimates that physicians are handing out roughly 50 million unnecessary prescriptions each year. Antibiotics kill the pathogenic bacteria in your gut but at the same time sweep away healthy microbes too. If you’re on a necessary course of antibiotics, load up on anti-inflammatory foods and prebiotics to get your gut thriving once again.

Related: How to Restore Your Gut After Taking Antibiotics

Hack stress: Stress can impact the gut in all sorts of ways (see above). Learning to manage your stress is a powerful way to heal your microbiome. Carve out time each day to meditate — even just a five-minute meditation can calm your nervous system and give you a sense of wellbeing. Find out more here on how to hack your stress.

Take activated charcoal: Activated charcoal — a form of carbon — has been used for thousands of years to detoxify the body and improve digestive health.[37] Activated charcoal binds to toxins and chemicals in the gut, stopping your body from absorbing them. Take it slowly — too much activated charcoal can give you constipation. Start with 1 or 2 capsules a day. Try: Coconut Charcoal.

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