The Human Operating Manual

Microbiome Basics

Microbiome Basics

Microbiome – The Key to a Healthy Stomach (Boundless and Biohacker)

The microbiome refers to colonies of symbiotic, commensal, and pathogenic micro-organisms. They exist on the skin’s surface, the mucous membrane of the mouth, the conjunctiva, and the intestine. It is estimated that there are 500-1000 distinct bacterial species living in the intestine. The most common are Bacteroides, Clostridium, Fusobacterium, and Bifidobacterium. Other known strains are Escherichia and Lactobacillus. 50-60% of your body is made up of bacteria, fungi, and micro-organisms. For each human gene there are 100 micro-organism genes.

Their functions include fermenting carbohydrates (fiber) that the body otherwise cannot digest, creating short chain fatty acids. The intestinal bacterial strain also contributes to the absorption of K vitamins, B vitamins, some minerals (Mg, Ca, Fe) and the production of bile acids, as well as improving the health of the immune system.

A single course of antibiotics can affect as much as 30% of the entire bacterial flora of the intestine and can throw off the balance from six months to two years. However, as bad as antibiotics can be, they are necessary when Salmonella, Shigella, Campylobacter, or Yersinia have entered the intestine. The liberal use of antibiotics may cause predisposition to diarrhea, Clostridium difficile infection, and overgrowth of other harmful bacteria.

Antibiotic resistant bacteria may arise due to: antibiotics given to farm animals, mutated forms of bacteria resisting antibiotics and contaminating the meat, humans eating it and becoming infected by mutated bacteria, and some antibiotics having no effect as they are already immune.

Choose whole, raw, organic, non-GMO foods that are friendly to the gut lining, such as bone broth, sprouted seeds, and cultured dairy products, along with fermented and cultured foods, like sauerkraut, kimchi, and kombucha, and fiber-rich prebiotic foods, like jicama, Jerusalem artichokes, garlic, and dandelion greens. Remember that pasteurized fermented foods often no longer contain living bacteria. If you have a histamine intolerance, you should limit your fermented foods and stick to low-histamine probiotics. Also, don’t forget to get a probiotic that is enteric coated so that the bacteria actually make it to the small intestine. 

A low-fiber diet can deprive your gut bacteria of prebiotics. Not to mention a lack of foods high in probiotics. Most commercial food is pasteurized, packaged improperly, or have lots of sugar added. The opportunistic fungi, Candida albicans, is notorious for multiplying like crazy during periods of high stress, low microbiome competition, and high simple sugar consumption. 

Diversity In the Gut

Some parasites and bacteria may actually improve immune function even though they may be considered “bad” (within reason). There has even been a study suggesting that helminth therapy (parasite supplementation) may help enhance the function of Treg cells and prevent autoimmune disease (MS, IBD, etc.). Rather than using immunosuppressing drugs it is possible to reverse autoimmunity by reducing inflammation and healing the gut instead.

Maternal Bugs

Babies born vaginally have a similar microbiome to their mother’s gut biome. Children born via C-section have a similar gut biome to the mother’s skin biome. Breast milk contains up to 600 different species of bacteria that help promote bacterial diversity in a child’s gut.

During the first few years of a baby’s life, their microbiome adjusts from bacteria that can utilize/digest milk to bacteria that can metabolize energy from solid foods. By age 3, their microbiome is similar to an adult’s. The makeup of their microbiome has a huge impact on how their immune system develops. Some gut bacteria species produce short-chain fatty acids which play a role in the proliferation and differentiation of immune cells, including T and B cells, which produce antibodies. A surplus of bad bacteria and/or lack of diversity between birth and age 3 may result in autoimmunity, allergies, and asthma.

Antibiotics wipe out both dangerous and beneficial bacteria, causing a reduction in diversity. Increasing the child’s lifetime risk of developing asthma, eczema, and type 1 diabetes.

  • Infants who develop asthma often have low abundance of Bifidobacterium, Akkermansia, and Faecalibacterium and a high relative abundance of fungi like Candida and harmful bacteria that release inflammatory metabolites.

Gut-Brain Axis

Good bacteria in the gut help to control harmful colonies of bad bacteria, fight pathogens by producing antimicrobial substances, and affect the pH of the gut environment to provide a chemical barrier against harmful microbes. Gut flora also regulates inflammation and activates immune function. 60% of the immune system is found in gut-associated lymphoid tissue (GALT), which is located just outside the intestinal lining. The intestines are also lined with mast cells, which coordinate the immune system and nervous system’s response to toxins and infectious agents.

The neurological and biochemical connection between the enteric nervous system of the intestine and the central nervous system (CNS). The microbiome is known to affect the function of the immune system, nervous system, behavior, stress tolerance, mood, and issues such as anxiety and depression.

Researchers in the University of Alabama (2018) found living bacteria in the brain. Most were Firmicutes, Proteobacteria, and Bacteroidetes.

The brain communicates with the intestine via the autonomic branches of the nervous system: the HPA axis (hypothalamus – pituitary gland – adrenal gland) and the sympathetic nervous system (SNS) – adrenal gland axis which regulates the lymphatic system of the intestine. The first signs of brain dysfunction may be detected in digestion – impaired secretion of pancreatic enzymes, weak gallbladder activity, and the general impairment of intestinal balance and function.

Continuous inflammatory conditions or imbalance of the intestine may cause deterioration of the links between the enterocytes on the surface of the intestine, causing gut permeability. Similarly, impaired brain function or stress-related hyperactivity of the SNS undermines the function of the vagus nerve. This impairs the function of the immune system and reduces blood circulation in the intestine, which increases growth of harmful fungi and bacteria. They can damage the surface tissue and aggravate gut permeability. Continuous low-grade inflammation may also aggravate gut permeability, resulting in production of cytokines. Due to gut permeability, the messenger substances are able to enter the circulation and the brain via the blood-brain-barrier (BBB), causing the BBB to be permeable, activating the connective tissue cells of the brain (microglial cells). The result is chronic inflammatory condition of the brain, which may lead to anxiety and depression.

Intestinal Bacteria Strain and How to Support the Digestive Function

The bacterial strain of the microbiome can change with dietary adjustments. Meaning dietary choices can influence chronic inflammation and gut permeability. Gut permeability relates to the epithelial cells on the surface of the intestine allowing tight junctions to “leak” when nutrients should be absorbed through the epithelial cells. Celiac disease is an example of an autoimmune disease involving gut permeability. Leaky gut is one of the key factors in the development of autoimmunity diseases. Cause or effect is not known though.

To Support the Microbiome:

  • Fermentable fibers, i.e. prebiotics like inulin, pectin, and oligofructose
  • Fermented foods
  • Resistant starch, i.e. green bananas, cooked and subsequently refrigerated rice and potatoes as well as cereals
  • Polyphenols
  • Dark chocolate (polyphenols and fermentable fibers)
  • Pistachios
  • Probiotics (particularly soil-based strains)

Avoid These to Protect the Microbiome:

  • Antibiotics (unless necessary)
  • Pesticides containing glyphosate (including Roundup). Used as a pesticide on cereals, GMO soybeans and corn. Meat from animals that have fed on the plants mentioned above. May be one of the factors contributing to celiac disease
  • Smoking
  • Alcohol
  • Chronic stress
  • Continuous negative thoughts and feelings


Probiotics Can Make Your Gut Worse

Most probiotics on the market contain histamines. Certain bacteria produce histamine through a fermentation process, e.g., Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus delbrueckii subsp. bulgaricus. We need histamine as a neurotransmitter too, but excess may lead to histamine intolerance (migraines, sinus issues, premature aging, etc.). Too much histamine producing bacteria and not enough diamine oxide (DAO) to break it down. More histamine neutral ones are Streptococcus thermophilus and Lactobacillus rhamnosus.

Avoid the histamine producing bacteria by not eating yogurts and fermented foods like sauerkraut, some kombucha, pickles, fermented soy products, soy sauce, fish sauce, buttermilk, kefir, mature cheese, red wine, breads made with yeast, and processed, smoked, and fermented meat. Eat prebiotic fiber and resistant starch to support healthy bacteria without buying probiotics.

It’s possible to take supplements that contain histamine-degrading bacteria such as Bifidobacterium infantis, Bifidobacterium longum, and Lactobacillus plantarum.

Candida can live on sugar or ketones, so it can’t be starved by going into ketosis. You need an antifungal protocol.

Health Benefits of Beneficial Living Microbes:

  • Alleviating constipation
  • May help acute diarrhea
  • Preventing traveler’s diarrhea (particularly Saccharomyces boulardii)
  • Facilitating the treatment of IBS
  • Stopping the progress of inflammatory intestinal diseases, may help recovery (particularly Lactobacillus acidophilus and Bifidobacterium lactis)
  • Facilitating recovery from non-alcoholic fatty liver disease
  • Preventing and treating diarrhea caused by antibiotics

Foods That Provide Probiotics:

  • Sauerkraut and other fermented vegetables
  • Fermented vegetable juices
  • Kefir
  • Kombucha
  • Kimchi
  • Natto
  • Tempeh
  • Jun tea

Postbiotics are the by-products of probiotics after they have fermented and metabolized prebiotics. Key factors in maintaining long-term digestive health.


Prebiotics are water-soluble fiber and include oligosaccharides, arabinogalactans, fructo-oligosaccharides, and inulin, which are found in vegetables, grains, and roots. Insoluble fiber promotes healthy bowel movements but does not selectively fuel growth of beneficial bacteria like soluble fiber, and is found in legumes, oats, rice bran, barley, citrus, and potatoes. Insoluble fiber may have a positive effect on the absorption of trace elements, the immune system, blood pressure, and reduced risk of colon cancer.

Prebiotic Fiber:

  • Vegetables that are rich in soluble fiber like sweet potatoes, Brussels sprouts, and asparagus. Bacteria use the fiber to produce short chain fatty acids like butyrate.
  • Grains, legumes, and beans have plenty of fiber but they also contain lectins, which damage your gut lining and cause inflammation, and autoimmune conditions. Agglutinins, or WGA, impair the integrity of your intestinal lining, allowing small molecules to pass through.
  • Essentially just eat a lot of green vegetables unless you have SIBO. Go a short period without fiber to kill the bacteria off and then get back to eating the good fiber.
  • Shown to: reduce risk of the four killers. 15-30% decreased risk of cardiac-related death and all-cause mortality, 16-24% reduction in stroke, and 19% reduction in type 2 diabetes and colorectal and breast cancer. Reduces intestinal and brain inflammation, reducing dementia. Less insulin resistance, waist/hip ratio measurements, LDL cholesterol, and glycated albumin.

Resistant starch, found in potato starch, is beneficial for the microbiome, insulin sensitivity and obesity as well as hunger regulation in rodents and humans. Inulin and oligo-fructose are prebiotics that promote the wellbeing of the intestine as well as health benefits from dietary fiber.

Resistant Starch:

  • Stays undigested until it enters the colon and acts as a prebiotic there to be used to produce more butyrate.
  • RS1 is embedded in the coating of seeds, nuts, grains, and legumes, which means it is packaged with lectins that harm your gut even though bacteria like to eat it.
  • RS2 is the resistant granules in green bananas and raw potatoes.
  • RS3 is the type of resistant starch formed when certain starchy foods, like white potatoes (nightshade) and white rice are cooked and cooled.
  • RS4 is the man-made resistant starch. Polydextrin or modified starch. One study found that it improved insulin resistance and reduced inflammation in women with type 2 diabetes. Just make sure it is a non-GMO source, otherwise you’ll also get glyphosate.
  • Resistant starch helped to kill precancerous cells in mice prostate cancer studies and reduced inflammation caused by the cancer. Blood sugar and insulin levels don’t rise as it is not digested.
  • Obese people tend to have more firmicute bacteria and less Bacteroidetes. Eat more spice and vegetables that contain polyphenols, the preferred food source. The more color the more polyphenols typically. Your gut bacteria also affect weight by producing a hormone called fasting-induced adipose factor (FIAF), which tells the body to stop storing fat and to start burning it instead. Starve the bacteria of starch and sugar and they’ll produce FIAF.

Modbiotics are compounds that influence the growth of gut microbiota through their antibacterial, antifungal, and anti-parasitic properties. They can reduce excessive firmicutes (sugar-eating bacteria that drive inflammation, oxidative stress, and metabolic acidosis) and increase gut Bacteroidetes. Usually found in natural foods that also contain the sugars, such as pomegranate seeds, fruit peels, pulp, and skin.

If You Have Insufficient Levels of Gut Bacteria, You Are Likely to Experience the Following:

  • The complete absence of gas
  • Undigested fiber in your stool, which appears as white or dark specks
  • Constipation, with occasional diarrhea or IBS
  • Frequent sickness and allergies
  • Blood-clotting problems
  • Neurological problems and brain fog
  • Decreased physical performance

Microbiome Analysis:

  • Balance of the microbial bacteria.
  • Helpful bacterial strain.
  • Harmful bacterial strain.
  • Yeast fungi.
  • Amoebas and other parasites.

If You Have Insufficient Levels, Do the Following

  1. Consume a wide variety of fermented foods, such as kimchi, sauerkraut, and pickled vegetables, along with yogurts, kefirs, miso, natto, and other foods. This provides good bacteria and the fiber to feed them. When repopulating the gut with good bacteria, the pH tends to lower, which is a natural deterrent for pathogens.
  2. Consume a full-spectrum probiotic, such as Seed, Caprobiotics, Throne Floramend, or VSL-3, along with a soil-based probiotic such as Prescript Assist. If you’ve ever been on antibiotics, also take Saccharomyces boulardii. It is also a good idea to swap brands every month or two to change up strains.
  3. Consume plenty of vegetables and moderate amounts of fiber from other sources, such as seeds and nuts. If eating salads, smoothies, and plant matter is logistically tough, consider a greens powder rich in polyphenols, flavonols, and prebiotics derived from organic greens. Organifi Green Juice, Living Fuel SuperGreens, Athletic Greens, and EnerPrime.
  4. Don’t eat grains, legumes, or nightshades to prevent leaky gut syndrome
  5. Quit eating sugar as bad bacteria love to eat it, potentially causing SIBO and Candida
  6. Never eat industrially-raised animals because of the antibiotics they receive and the glyphosate in their food, which will harm your gut bacteria
  7. Eat more prebiotic fiber. Eat a variety of polyphenol rich vegetables, drink coffee and tea, and add 10g of prebiotic fiber like plain acacia fiber
  8. Add MCT oil. Saturated fatty acids found in coconut oil have antifungal, antibacterial, and antiviral properties
  9. Grass-fed collagen protein and bone broth. Collagen helps to maintain the gut lining health

Other Causes of Gut Microbiota Imbalances

Chronic stress, particularly from overtraining, can produce inflammation in the gut, which causes stress that promotes the movement of toxic lipopolysaccharides (LPS) from the gut to the bloodstream, as well as the growth of harmful bacteria in the gut. This is why endurance athletes who don’t consume high-carb foods can still experience gut distress, bloating, constipation, and other GI issues.

Several studies have shown that gut microbiota molecules, including short-chain fatty acids such as butyrate, are essential for controlling mitochondrial oxidative stress, inflammatory response, and pathogen growth, and also improve metabolism and energy expenditure during exercise. Furthermore, short-chain fatty acids and their precursors – such as those found in butter, coconut oil, buckwheat, quinoa, millet, amaranth, cultured vegetables, coconut water, kefir, and probiotic beverages – can induce mitochondrial biogenesis, through a variety of mechanisms such as an increase in the activity of PCG-1alpha (a key regulator of energy metabolism), an increase in redox sensitive energy sensor SIRT1 (a cell-protective and anti-aging pathway), and an increase in the enzyme AMPK (crucial for ATP production), all of which suppress inflammatory responses and enhance the beneficial effects of exercise.

Mitochondria affect gut bacteria too. Mitochondrial ROS production influences the integrity of your intestinal barrier and mucosal immune responses, which regulate the balance and quality of your gut microbiota.

To care for your gut microbiome, eat foods rich in short-chain fatty acids, and support your mitochondria by consuming mineral-rich water and electrolytes, get enough sunlight and infrared light exposure, grounding, using PEMF therapy, cold exposure, and heat therapy.

Too Much Gut Bacteria

Small intestinal bacterial overgrowth (SIBO) can be problematic for people who consume a high-carbohydrate diet (bacteria feed on sugars and starches) and in people with any of the following:

  • Low stomach acid production
  • Celiac or Crohn’s disease
  • IBS
  • Poor liver function
  • A history of heavy alcohol consumption
  • A history of taking oral contraceptives

SIBO is a chronic bacterial infection of the small intestine. These bacteria usually live in other parts of the gastrointestinal tract, but when they expand into the small intestine, they interfere with healthy digestion and absorption of nutrients and are associated with damage to the lining of the small intestine (leaky gut syndrome). This can lead to deficiencies in iron and B12, reducing RBC levels.

With poor nutrient absorption comes undigested material for the bacteria to feed on, creating a cycle. Bacteria can also reduce fat absorption by de-conjugating bile, leading to fat-soluble vitamin deficiencies. Undigested food particles can also enter the body, and your immune system reacts to them, creating food allergies and sensitivities. Bacteria can also enter the bloodstream and lead to an immune response. This can lead to endotoxemia, characterized by chronic fatigue and stress in the liver. The bacteria secrete acids which can cause neurological and cognitive symptoms, such as depression and autism.

SIBO can cause nutrient deficiencies, flatulence, bloating, abdominal pain, constipation, diarrhea, and food sensitivities. If you have SIBO, you may also have a negative reaction to fermented foods and IBS from probiotics.

You can test for SIBO with an at-home breath test that measures the amount of gas produced by bacteria. These can produce false negatives though. Try lower carbohydrate intake, juicing, and doing herbal cleanses, as well as an elemental diet.

Basic Protocol for Eliminating SIBO:

  • Eat only nonfermentable carbohydrates, and limit carbohydrates in general.
  • Juice once or twice daily: fresh plantain leaves, one-quarter of a medium sized cabbage, 2 small-to-medium-sized beets, 2 carrots, 2 stalks of celery, and 1-to-2-inch chunk of ginger.
  • Herbal antibiotics and tinctures such as goldenseal extract, phellodendron, coptis, cordyceps, garlic extract, and oil of oregano. People who do not recover after this protocol may benefit from the prokinetic agent such as octreotide or low-dose naltrexone to increase muscular contractions of the bowel. You will also likely find Atrantil to be helpful.
  • Palpate the area about 2 inches to the right of your belly button, or massage it with an iliacus and psoas massage tool like a Pso-Rite. If there’s a problem with the ileocecal valve, you’ll find this area extremely tight and sensitive. This is often correlated to poor vagus nerve tone. Addressing vagal tone can be useful for constipation. Parasym Plus has been successful for eliminating constipation due to poor vagus nerve function.
  • The antimicrobial peptide LL-37 may be effective for autoimmune issues and gut-inflammation conditions, including fungal and bacterial overgrowth. 100mcg per week for about 6 weeks, injected subcutaneously in the abdomen. Probably not worth the pain and could just do the prior instructions.

The Effect of the Microbiome on the Immune System (The Immunity Fix)

Bacteria like Lactobacilli and Bifidobacteria have been shown to improve gut health and immunity. You can get them from fermented foods such as sauerkraut, kimchi, kefir and fermented dairy. Lack of fermented foods in the diet has been shown to cause a fall in innate immune response. Akkermansia has also shown to protect against obesity and type-2 diabetes. You can get them from polyphenol-rich foods.

  • A 2017 systematic review and meta-analysis of randomized controlled trials found that probiotics and prebiotics improve efficacy of influenza vaccination. Experimental studies show that probiotics may have direct antiviral effects through probiotic-virus interaction or by stimulating the immune system.
  • Probiotic supplementation enhances immunity in the elderly. Older people can benefit from long-term use of an oral blend of probiotics including Lactobacillus plantarum, Lactobacillus rhamnosus, and Bifidobacterium lactis, which enhance secretory immunity and increase IgA antibodies. In another study, a probiotic strain Bacillus subtilis was shown to stimulate IgA in the elderly to reduce the frequency of respiratory infections by 45%. Lactobacillus plantarum has been found to enhance human mucosal and systemic immunity as well as prevent NSAID-induced (such as ibuprofen) reduction in T regulatory cells.
  • Prebiotics are foods that the bacteria in our gut will eat. They can improve the integrity of the gut lining and reduce inflammation. Resistant starch, which is a type of prebiotic, improves glucose control and insulin sensitivity, which are risk factors for worse outcomes in viral infections. Cooking and cooling starch like potatoes or rice creates resistant starch. Other prebiotic foods include asparagus, leeks, onions, green bananas, artichoke, dandelion greens and garlic, which have all beneficial effects on the immune system.


Endotoxins, in this case lipopolysaccharides (LPS), are large molecules made of lipids and polysaccharides found in the outer membrane of gram-negative bacteria. The harmful effects of endotoxin are mediated by the release of pro-inflammatory substances such as tumor necrosis factor (TNF) and interleukin-1β. This activates innate immunity, causes a fever and is implicated in sepsis, intra-vascular coagulation and multiple organ failure. Elevations in LPS can also lead to the release of reactive oxygen species like superoxide.

Lipoolygosaccharides can mimic some of the carbohydrates in human cells and end up causing an autoimmune flare-up like multiple sclerosis or CNS demyelinating disease. In other words, anything that damages the gut and increases LPS in the blood may increase the risk of certain autoimmune conditions. H. pylori can also exploit this molecular mimicry. In those who are genetically susceptible, H. pylori may lead to autoimmune gastritis. Endotoxemia in the intestines contributes to the development of alcoholic hepatitis, which is inflammation of the liver. It’s thought to originate from a combination of alcohol, bacterial overgrowth and increased intestinal permeability.

LPS activates toll-like receptor 4 on Kupffer cells in the liver, which causes the release inflammatory cytokines damaging the liver. When the level of endotoxin surpasses the phagocytic capacity of Kupffer cells, there is then a spillover of endotoxin into the blood. Importantly, Kupffer cells contain a glycine receptor (known as glycine gated chloride channels), that when stimulated reduces LPS-induced inflammatory cytokine release. Thus, supplementing with glycine may be one strategy to potentially reduce the harms of LPS and intestinal endotoxemia.

Endotoxemia typically occurs as a result of poor dietary habits. In other words, it’s the effect but not the cause of many chronic conditions. However, in germ-free mice, injecting purified endotoxin from E. coli induces obesity and insulin resistance. So, there are direct causal roles of LPS but it’s the inappropriate leaking of LPS out of the intestines and into the liver via the portal vein and the ensuing inflammation that’s the issue.

Several Proposed Causes of Endotoxemia:

  • Bacterial Infections – Endotoxins are associated with pathogens like Salmonella, E. coli, Haemophilus influenzae, and Vibrio cholerae. Small intestine bacterial overgrowth or SIBO can also promote LPS growth. Any foreign parasite or pathogen for that matter will do the same to a certain extent because endotoxins are intrinsic to these kinds of bacteria.
  • Smoking Tobacco – Cigarette smoke has been found to contain bacterial LPS. During smoking you’re inhaling LPS and causing a lot of oxidative stress. The same applies to air pollution, dust, and house mold. Endotoxins cause stress and inflammation and inflammation and stress promote endotoxin proliferation.
  • Processed Food and Sugar – Sugar and artificial sweeteners lower the body’s responsiveness to endotoxin and make it more likely to spread it. Raw sugar can contain 100 mg of E. coli endotoxin per gram whereas beet sugar has less than 1 ng/g. All pathogens and bacteria thrive on sugar.
  • Artificial Sweeteners and Flavorings – Artificial sweeteners like saccharin, aspartame, sucralose and stevia may disrupt the microbiome potentially leading to overgrowth of bad bacteria and glucose intolerance. More natural sweeteners like monk fruit seem to be less harmful but may cause problems if consumed in excess.

Things That Can Help to Combat Endotoxin and Pathogenic Bacteria Harm:

  • Raw Carrots – The indigestible fiber and phenolic compounds in carrots, especially purple carrots, may reduce the absorption of endotoxins in the intestine and suppress LPS-induced inflammation. Slicing some carrots into your food or having them as a snack may be a great way to help keep the bad gut bugs at bay.
  • Coconut Oil – Coconut oil has anti-microbial properties that may help lower endotoxin levels. It also has antifungal properties against things like Candida. You can use coconut oil for cooking.
  • Dandelion Root – Dandelion has been found to have antiviral and anti-influenza properties. It inhibits replication of viruses and has other beneficial effects on stimulating liver detox pathways.
  • Garlic and Allicin – The main compound in garlic, allicin, has antibacterial activity against many gram-negative as well as gram-positive bacteria, including multidrug-resistant E. coli. Fresh garlic even enhances the antimicrobial activity of antibiotics on resistant strains.
  • Carrageenan – Carrageenans are extracted from edible red seaweed and used in the food industry as stabilizing or thickening agents. Pretreating mice with carrageenan once a day before injecting them with LPS reduced TNF-alpha inflammation by 2-fold compared to the control. You can get carrageenans from edible seaweed or algae.
  • Short-Chain Fatty Acids – Short chain fatty acids like butyric acid and butyrate have antibacterial properties. Your body creates them from digesting fiber or by eating animal fats.
  • Ginger Extract – Ginger has many anti-inflammatory benefits but it also fights endotoxin. Using ginger extract in root canals has been shown to eliminate microorganisms and endotoxin.
  • Activated Charcoal – Charcoal is a potent chelator that can bind to various compounds and remove them from the body. Taking it on an empty stomach is great for eliminating pathogens and toxins. However, don’t take it with food because it’ll bind to the nutrients as well.
  • Salt Water – Salt is the most ancient and natural antibacterial substance used for thousands of years to preserve food. It kills bacteria through osmosis. If there’s a high concentration of salt outside of a bacterial cell, water inside the bacteria diffuses out of the cell to equalize the reaction. This will lead to dehydration, cellular destruction, malfunction and death of the bacteria.
  • Glycine – Glycine inhibits LPS-induced proinflammatory cytokine release from Kupffer cells in the liver. Taking 5 grams 3-4 times per day has been suggested, as this dosing has shown benefits in patients with metabolic syndrome and in type 2 diabetics.

Most herbs and spices have antibacterial and antimicrobial properties. The most common ones are rosemary, thyme, clove, oregano, licorice, turmeric, astragalus, elderberry and algae.

There is a direct connection between systemic inflammation throughout the body and the gut microbiome.

The microbiome is a big contributor to innate and adaptive immunity, helping to recognize pathogens and differentiate them from the host. Early-life nutrition and microbiota maturation have been found to shape life-long immunity and reduce the risk of chronic diseases.

Type-1 diabetes (T1D) is associated with low microbiota diversity.

Dysbiosis, or an imbalance in the micro-fauna, controls inflammatory bowel disease. Low amounts of Faecalibacterium prausnitzii have been linked with diseases like Crohn’s. A lower prevalence of bacteria like Akkermansia, Faecalibacterium, and Bifidobacterium may increase the susceptibility to allergies by modulating T cells.

Children with T1D have higher levels of Globicatella sanguinis, Dialister invisus and Bifidobacterium longum and reduced Bifidobacterium pseudocatenulatum and Bifidobacterium adolescentis, unlike healthy controls.

There is a correlation between rheumatoid arthritis and Prevotella copri.

The Most Known Beneficial Strains Include Enterococcus spp., Lactobacillus spp., Bifidobacterium spp., Bacillus spp. and Streptococcus spp.

  • Lactobacillus rhamnosus GG is used to treat pseudomembranous colitis and antibiotic-associated diarrhea. Probiotics like Lactobacillus modulate pro-inflammatory signaling factors like TNF-alpha. Foods with Lactobacillus include sauerkraut, yogurt, tempeh, miso, natto, kimchi, and other fermented foods. These foods have other benefits like antioxidants, vitamins, especially B12, which is important for the nervous system. Consumption of fermented soybeans is associated with reduced osteoporosis in Japanese women.
  • Dairy propionic bacteria like Propionibacterium freudenreichii can improve the microbiota by promoting the growth of beneficial strains like Bifidobacteria, while inhibiting pathogens like H. pylori, Salmonella enterica and enteropathogenic Esherichia coli. You can get propionic bacteria from cultured dairy foods like kefir, cheeses, yogurt, etc. Pasteurized milk is devoid of these bacteria because of the high heat manufacturing process. That is why food industries are considering adding supplemental Lactobacillus and Bacillus into their products to obtain their health benefits. Eating raw cheese and kefir, which contain live probiotics, are a great way to support the gut microbiome.
  • Bifidobacteria can help to alleviate IBS, according to a 2011 randomized control trial. In newborn infants, a probiotic mix of Bifidobacterium bifidum, Bifidobacterium lactis, and Lactobacillus acidophilus reduced incidence of eczema. Bifidobacterium bifidum PRL2010 modulates the host innate immune response, by regulating the production of interleukins and cytokines.
  • Bacillus coagulans is a gram-positive, spore-based bacteria that produces lactic acid. It has been shown to improve symptoms of gut problems, by raising beneficial bacteria and butyrate production. In rheumatoid arthritis, B. coagulans reduces inflammatory markers and pain. Probiotic metabolites of B. coagulans enhance the maturation of antigen-presenting cells in vitro. In healthy adults, B. coagulans promotes TNF-alpha in response to influenza A and adenovirus.

Huberman Lab Notes

#1 Eat Fermented Foods

Dr. Sonnenburg and Dr. Chris Gardner investigated whether diets high in plant-based fiber or fermented foods would influence the health of the gut microbiome. Their results show that fermented foods increased overall gut microbiota diversity, as well as reduced key markers of inflammation (aka ‘inflammatome’).

Participants ate six servings per day of fermented foods; however, higher total amounts of ingested fermented foods did not lead to further benefits. Instead, consistently incorporate fermented foods into your daily diet to achieve better outcomes for gut microbiome health and inflammation reduction.

Try incorporating low-sugar fermented foods into your diet, such as sauerkraut, plain yogurt, kimchi, kombucha, natto, kefir or even drinking brine. Find these products in the refrigerator section to ensure there are live active cultures. (Shelf-stable fermented foods are pasteurized, therefore, will not offer the same boost to the gut microbiome.) 

What About Fiber?

In this study, a high-fiber diet did not lead to an increase in microbiota diversity. However, high-fiber diets did increase the amount of carbohydrate active enzymes which help digest fiber and could further enhance the microbiome’s ability to degrade other complex carbohydrates. Additionally, some participants in the high-fiber group showed a reduction in markers of inflammation. Plant-based, high-fiber foods (i.e., vegetables, legumes, and whole grains) offer significant benefits for overall health and can help provide key nutrients for established microbiota.

#2: Prebiotics and Probiotics

Prebiotics: fermentable dietary fiber or microbiota-accessible carbohydrates; supplements of food for established gut microbiota

Probiotics: live bacteria or yeasts that can colonize in the gut microbiome

Synbiotics: mixtures of prebiotics and probiotics

Augmenting the gut microbiome with low levels of prebiotics and/or probiotics while still focusing on eating whole quality foods leads to improvement in gut microbiome health.

In cases of dysbiosis, such as after taking antibiotics, during high periods of stress, traveling or changing your diet, higher levels of prebiotics and/or probiotics can aid in recovery and replenish your gut microbiome. However, the excessive intake of probiotics has been linked to the induction of brain fog; therefore, if you experience these symptoms, you could try to reduce the level of supplements that you are ingesting.

Since prebiotics and probiotics are considered supplements, they are not FDA-regulated products. When choosing a supplement, look for an independently validated product. Finally, the gut microbiome is uniquely personalized. Therefore, supplementation will impact individuals differently.

#3: Sleep

As the gut microbiome is highly attuned to the amount of stress you experience (through direct links to cells of the immune system), achieving the proper quality (deep) and duration (generally 6-9 hours) of sleep each night is essential to manage stress and, in turn, to ensure gut microbiome health. 

#4: Avoid Processed Foods

Foods additives are ubiquitous in processed foods. Emulsifiers, detergent-like additives, can disrupt the mucus layer of the GI tract. In animal models, emulsifiers reduce microbial diversity, induce low-grade inflammation, and cause an increase in body fat, higher blood sugar levels and insulin resistance – key markers of metabolic syndrome.

The typical Western Diet (i.e., high fat, low fiber, higher in processed foods) does not provide gut microbiota with many of the key essential nutrients. When you eat complex, plant-based fiber, the gut microbiota produces fermentation by-products, such as short-chain fatty acids (e.g., butyrate). These substances reduce inflammation, help maintain the gut’s mucosal barrier, regulate the immune system, and modulate metabolism along the GI tract. To enhance the health of your gut microbiome, prioritize a diet rich in whole foods, plant-based fiber, and fermented foods.

#5: Artificial Sweeteners

Clinical studies have yet to fully tease apart the impact (if any) that artificial sweeteners have on the gut microbiome. However, within animal models, there is evidence that artificial sweeteners can disrupt the gut microbiome. A recent study showed that neuropod cells in the gut can discriminate between natural and artificial sweeteners. Further, these cells send a unique pattern of signals to the brain, depending on whether the sugars they sense are nutritive (i.e., contain calories) or are non-caloric sweeteners.

The Human Microbiome Project found a high degree of individualization of the gut microbiome. Potentially, try removing some artificial sweeteners from your diet to see if you notice an effect and also consider that artificial sweeteners might be capable of influencing your gut microbiome.

*Non-caloric plant-based sweeteners like stevia are probably fine, but there have not been many studies of stevia in regards to the microbiome.

#6: Don’t Over-Sanitize Your Environment

Microbiota are present on any and all surfaces which have come into contact with the environment. Dr. Sonnenburg notes, “Exposure to microbes from the environment is likely an important part of educating our immune systems and keeping everything in the proper balance.” The gut microbiome is also populated from social interactions, including skin contact by shaking hands, hugging, kissing etc. and interactions with pets and dirt, and grass. Over-sanitization of our environments or excessive use of antibiotics can eliminate sources of good gut microbiota. While it is still important to eliminate the introduction of disease-causing pathogens and harmful environmental chemicals (e.g., pesticides), consider that many environmental microbes play an integral role in the establishment and maintenance of a healthy gut microbiome.

JayPT +