Written by Bulletproof
There’s a universe of living organisms in your digestive tract, and the little critters can do a ton for you. The cells in your gut biome can do everything from making you happier to clearing up acne to fixing autoimmune issues – when they’re not trying to control your biology for their own benefit. This post is about how to make your gut bacteria behave so you can reap the many benefits of a balanced gut biome.
Up to 100 trillion cells live in your gut microbiome, forming a world that scientists are still working to understand.  Your gut microbiome is home to a rich variety of bacteria, viruses, and other microorganisms, as well as a wide array of fungi that we’re just beginning to identify. 100 trillion cells – that’s enough microbes to make it the highest density natural bacterial ecosystem that we know of. Way more than your compost bin.
If all is going well, these organisms live in perfect homeostasis with you, their host. Gut bacteria play a beneficial role in countless bodily functions and can help you perform at your maximum level, if the right kind is proliferating in the right environment. From regulating your immune system to keeping the lining of your gut strong, these organisms can be a part of how you take control of your own biology.
Just don’t let them do it without your permission. When your gut bacteria are out of balance, it makes you weak, tired, and inflamed – and it can even change your personality. It’s important to know how to hack these little bastards, because they’re already hacking your body for their own survival!
Here are the top things to know about your gut microbes:
Gut bacteria influence your nutrition
Gut bacteria produce and help absorb key nutrients. About 75% of the Vitamin K made in your body each day is produced by gut bacteria, with the rest coming from food.  Vitamin K is a fat-soluble vitamin essential for blood coagulation and bone health.
Since your body doesn’t store Vitamin K well, the intestinal factory is crucial to keeping your Vitamin K2 levels optimal. It’s hard to get from food, although grass fed butter has lots of it. Vitamin K2 holds a place of honor on the top 10 Bulletproof Supplements list.
Your gut bacteria also heavily influence your B vitamins, helping your body make and absorb the Vitamin B12 that you get from food and produce biotin, another important B vitamin. [3, 4]
The gut-brain axis: conversations between your gut and mind
Heard of the gut-brain axis? Researchers only discovered it recently, and it’s a hot topic in medicine right now. Your intestines and brain talk to each other via the endocrine system (hormones released into the bloodstream) and the nervous system (nerve signals triggered in the gut and transmitted to the brain, and vice versa).
The gut-brain axis is an important messaging system that oversees your satiety, food intake, glucose regulation, fat metabolism, insulin secretion and sensitivity, and bone metabolism.
Sounds like something you want working properly, right?
Gut bacteria keep your tract intact
Your GI tract acts as a barrier that protects you from the outside world. If things are working the way you want, your GI tract allows nutrients in and keeps disease-causing pathogens out, at least most of the time. Gut microbes play a big role in maintaining the integrity of the gut lining and allowing this barrier system to work as it should.
As you might have read in The Bulletproof Diet, when bacteria ferment fiber (or collagen protein) in the colon, they produce short chain fatty acids. These are an important fuel for the cells that line the intestinal wall, keeping it strong and helping your body avoid leaky-gut syndrome. The most common short chain fat is butyric acid, which is also found in butter. In fact, it gets its name from butter because that’s where it was first discovered.
The right gut bacteria also help strengthen the intestinal wall through a process that prevents the production of inflammatory TNF-?, while also increasing the amount of intestinal wall-strengthening proteins. 
At the same time, out of balance fermentation can result in the formation of endotoxins, which means the bacteria in your gut form toxins that make you weak and tired. If your gut is weakened, these toxins are more easily make it into your bloodstream.
How the gut biome “trains” your immune system
Your ability to fight illness starts in your gut. Roughly 70% of your body’s immune cells live in your intestines, and contact with your microbiome “programs” your immune cells to behave in a certain way before they go out into circulation.
For example, immune cells called T cells can either suppress inflammation or promote it, depending on whether your gut is thriving or imbalanced. The microbiome begins training immune cells at birth and continues to help your developing immune system distinguish between friendly and harmful bacteria.
The early “training” can help your immune system function properly for a lifetime. On the flip side, people with diminished exposure to gut microbiota (for example, as a result of even a single antibiotic use, or from eating antibiotic-tainted non-organic meat) are more likely to develop illnesses, especially allergies and asthma. [9, 10] Your gut health is yet another reason to use antibiotics with caution and avoid industrially produced meat. Choose a Bulletproof-inspired vegetarian diet when grass-fed or wild-caught meat is unavailable.
The gut biome regulates energy balance
Gut bacteria influence how your body uses energy and whether you store that energy as fat. They metabolize and extract energy from food components that aren’t digestible to humans. Depending on the makeup of your microbiome, you’ll extract different amounts of energy from the food you eat. Some research suggests that this is the link between the gut microbiome and obesity. It turns out that obese people lose less energy in their feces than lean people do, due to the ability of their gut bacteria to “harvest” more energy from their diet. 
In the Bulletproof Diet, you can read about how fat people have more of one species of bacteria than thin people, and how you can hack it by eating more polyphenols – found in dark leafy vegetables, purple stuff, and coffee, chocolate, vanilla, and some spices. This may be one mechanism that explains how Bulletproof Coffee may work in humans, but we’re not sure yet. Believe it or not, there is a mouse study of butter and coffee which showed that buttered coffee helps mice have more of the “thin people bacteria” called bacteroidetes. 
We also know that bacteria make a hormone called FIAF (Fasting Induced Adipose Factor) which amplifies your fat storage or fat loss, depending on how many carbohydrates your gut bacteria get from your diet, and when you eat them .
Basically, your gut microbiota has a powerful influence over genes that govern energy use and fat storage. If your gut bacteria are out of balance, these microbes will cause your body to store more fat than necessary. If you rebalance your gut, the microbes will burn fat for you all day long. So you can see the importance of keeping these guys happy.
Dysbiosis: the gut microbiome out of balance
It’s a delicate balance in your gut — and almost never a perfect one. In fact, we have no idea what perfect would look like, given the extensive use of antibiotics and herbicides has forever altered the microbial landscape of our soil and our bodies.
The composition and overall health of the gut microbiome (and how it makes you feel) will shift with changes in diet, bouts of illness, periods of drinking alcohol or taking drugs, stress, body weight, age, and exposure to new environments (traveling overseas, for example).
Given the important functions of your gut microbiome, it’s not hard to imagine the biological chaos that can result when things in the gut are out of balance. A significant body of research demonstrates the link between gut bacteria imbalance (dysbiosis) and many diseases common in Western society. In fact, it’s tough to find a condition that’s not in some way linked to gut health.
Bacterial imbalances make you weak
Since gut bacteria can be good or bad, imbalances in the types and amounts of gut microbes that cause a bunch of different problems. For example, you can find identical imbalances (greater-than-average amounts of the Firmicutes type and too little of the Bacteroidetes type) in both obese people and mice bred to be obese, and other connections to autism.[11, 15, 16, 17]
The other little problem is that a less-than-optimal balance of gut bacteria can make your body intolerant to glucose, whether you’re overweight or not. High glucose can age you and makes you put on weight.
You see these imbalances in people with Type 2 Diabetes, too. Studies also show a high correlation between that the ratio of Firmicutes to Bacteroidetes in diabetics with reduced glucose tolerance, but not with BMI. In other words, gut bacteria affected glucose tolerance independent of weight. That’s why you shouldn’t trust those little bastards in your gut or assume they’re behaving themselves.
There’s also leaky gut
Unhealthy bacteria in the gut don’t just bring on weight and metabolic disorders. An unhealthy gut microbiome can give you leaky gut, which is just what it sounds like — a condition where holes develop in the walls of your gut allowing intestinal contents to “leak” through into the bloodstream. This includes proteins that can trigger allergies or autoimmune disease. Bacteria and bacterial neurotoxins called lipopolysaccharides (gut researchers call it LPS because it’s so common) also leak through, and they definitely don’t belong in your bloodstream. Once they leak out, they can impact other organs like the liver, kidneys, and heart, causing widespread inflammation and disease. Leaky gut has been linked to type 1 diabetes, inflammatory bowel disease, celiac disease, multiple sclerosis, and asthma, among others. Less serious but more common issues caused by leaky gut include acne, rosacea (red skin), stomachaches, headaches, and fatigue.
Food particles – particularly gluten, casein, and soy – have proteins similar to proteins found in your body. When your immune system sees gluten from your leaky gut, it may accidentally begin attacking your thyroid gland in a condition called Hashimoto’s. Does gluten contribute most to Hashimoto’s thyroiditis, or does leaky gut? It’s hard to say. Best to avoid both.
Gut bacteria also have a proven effect on your mood and are linked to neurological conditions. Bacteria leaving the gut (when they’re not supposed to) can prompt or worsen a chronic inflammatory response that leads to depression. The movement of bacteria and toxins from the gut to the rest of the body is one of the most significant and preventable causes of disease in modern society.
The Bulletproof Leaky Gut Syndrome Protocol
Diet is by far the most important factor in making your gut work. Just one day of eating a Western-style diet can dramatically alter the gut microbiota in mice (and not in a good way) , and in humans, too. A pillar of the Bulletproof Diet is to prevent inflammation, and that includes gut inflammation. By keeping the gut microbiota in healthy balance you can prevent illness. You can also achieve optimal metabolic and immune function.
Common symptoms of leaky gut syndrome or an imbalance in gut bacteria include:
- Food sensitivities
- Persistent acne or other skin problems
- Autoimmune disorders (hypothyroidism, Hashimoto’s thyroiditis)
- Weight gain
- Digestive issues/bloating
- Mood swings
- Joint pain
As you can see, leaky gut syndrome can affect most of the systems in your body. If you suspect you have leaky gut syndrome, try the following protocol.
Choose low-toxin, low-inflammation, high-nutrient foods
The Bulletproof Road Map illustrates a hierarchy of foods from superhero to toxic. The Bulletproof Diet is both low-histamine and anti-inflammatory, so eating foods from the green zone will help good bacteria proliferate while also fighting off the bad guys. Below you’ll find the breakdown of targeted food tips to address leaky gut.
- Cut out sugar: This should be your first priority. Sugar feeds bad bacteria and promotes yeast and candida overgrowth, all of which damage your gut.
- Make food diversity a priority: Eating a variety of high-quality foods introduces not just good bacteria, but many different good bacteria into your biome, making your gut more likely to thrive. Balanced gut diversity also leads to strong gut integrity and a properly functioning immune system. Diversity starts with eating a variety of whole, unprocessed foods. It also means avoiding inflammatory foods including the industrialized sugars, starches, and oils that comprise the Western Diet.[26, 27]
- Avoid anti-nutrients: Anti-nutrients are food toxins that cause inflammation and in some cases, lead to severe gut and autoimmune reactions.  The main naturally occurring antinutrients are mold toxins (mycotoxins), lectins, phytates, and oxalates. Foods with antinutrients include wheat, spelt, soy, nuts, seeds, beans, seeds, and raw cruciferous vegetables such as kale and spinach.
- Stay away from grains: Grains not only contain a large amount of gut irritating lectin, but several also contain gluten and other hard to digest proteins. Once your gut is back to a hundred percent, you can give fermented and sprouted grains a try if you really miss them. While I still don’t recommend eating them regularly, they contain fewer lectins and phytates.   Still skip the gluten-containing grains, though.
- Buy local, fresh food: I’m a huge fan of fresh, organic, local meat and vegetables because our gut bacteria is also related to our soil bacteria. Large-scale commercial agriculture has changed soil organisms for good, producing more toxins than ever before. The genes that develop these toxins get shared with your gut bacteria.
- Dodge heavy fiber: Most people associate fiber with a healthy gut. Did you know our systems are not designed to break down fiber? It just sits undigested in our gut, feeding bad microbes. Heavy fibers like psyllium husks can do more harm than good.
- Eat prebiotic-rich foods that feed good bacteria: Sweet potato, carrots, asparagus, and squash contain fibrous prebiotic carbs that support good bacteria growth.
- Ditch drinking: Limit your alcohol as drinking alcohol in excess diminishes the diversity of bacteria in your gut.
- Fermented foods may help: Although these foods are rich in probiotics, fermented foods like sauerkraut, kombucha, and pickles can also cause a histamine reaction for certain individuals. It’s key to be aware of the bacteria and yeasts used to make them. More on histamine in a moment.
- Skip conventional dairy: Dairy contains the protein A1 casein that is harmful to your gut. Also, commercial pasteurization eradicates vital enzymes, making lactose difficult to digest. That is why I recommend only grass-fed organic, raw milk or yogurt from A2 cows.
- Microbiologically produced foods: If you can tolerate dairy, foods like yogurt and kefir are high in nourishing bacteria.
Support the good guys with supplements
Give the good bacteria in your gut plenty of food to keep them strong, and to keep the bad bacteria at bay.
- Prebiotics: Prebiotics feed intestinal bacteria that produce short-chain fatty acids (SCFA). These nutrients fuel the intestinal mucosal cells that keep the lining of the gut intact and healthy. Thin people have more of a bacterial species called Bacteroidetes. Bacteroidetes thrive when fed prebiotic polyphenols from green vegetables, coffee, and chocolate. You can also experiment with Bulletproof prebiotics, including resistant starches like banana flour, plantain flour, and raw potato starch.
- Digestive enzymes: Your small intestine, pancreas, stomach, and salivary glands produce enzymes that help break down our food so we can absorb its nutrients. The enzymes often stop working in the face of leaky gut. Removing enzyme inhibitors like grains and legumes and using a high-quality digestive supplement can improve overall digestion and vitamin absorption.
- Betaine HCL: Betaine HCL can improve fat breakdown and protein digestion for people who have low stomach acid due to autoimmune disease or age. 
- Activated Charcoal: Activated charcoal is ancient and scientifically backed remedy. It’s successful at absorbing endotoxins that cause gastrointestinal disease and removing toxins from processed, low-quality foods. Charcoal is a great go-to supplement if you are eating in a restaurant. 
- Collagen: Collagen is the connective tissue for most of our biological structures. By adding Upgraded Collagen or bone broth to your protocol, you’re getting vital amino acids necessary for tissue repair in healing the stomach and digestive tract lining. Collagen also improves the production of hydrochloric acid as well as attracting water into the GI tract to help move along food.
- L-Glutamine: This anti-inflammatory amino acid is imperative to fix a leaky gut by promoting growth and repair of your GI tract. It’s like a bodyguard for your gut, covering cell walls and getting rid of unwanted pests.
Take control of histamine
Prebiotics are one thing, but if you’re thinking of taking probiotics, you may want to think again. While there are some strains that can be beneficial to the gut, many, including those found in yogurt, can increase histamine levels that lead to inflammation. Be careful with your choice of probiotic and avoid supplements that contain Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus, as they can contribute to excess fat storage and weight gain. High histamine levels and/or histamine intolerance can increase inflammation.
Use antibiotics with caution
Regardless of how hard you’re working on your diet, you’ll undo those efforts if you rely heavily on certain medications. Western medicine is fond of prescribing gut-damaging antibiotics for everything from acne to the common cold. These drugs not only kill the pathogenic bacteria but a host of other important microbes with them. If you’re on a temporary and necessary course of antibiotics, follow the suggestions listed above on how to re-populate your gut bacteria in a healthy and productive way.
Your gut microbiome starts establishing at birth. Babies born via caesarean section have a diminished diversity and a different makeup of microbiota than babies delivered vaginally. After that, an infant establishes its microbiome through diet—again, differences take hold depending on whether the child is breastfed or formula fed. Optimizing your kids’ diets can set them up for success. You might be surprised by how much better they behave when they’re sharp and feel good, too.
Besides diet, stress management is one of the most profound ways to heal your gut biome. Studies show that stress affects the brain-gut axis and can lead to decreased nutritional absorption, enzyme production, oxygenation and blood flow to the GI tract.  
Bone broth provides essential amino acids for repairing the digestive tract lining and "leaky gut".