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  • Microbiome Info

    Posted at 11:50 am
    Feb 19th

    What is The Microbiome Diet?

    This is the first diet of it’s kind, based upon cutting edge scientific breakthroughs to heal and replenish the microbiome.  When the microbiome flourishes so do we, however when it’s out of balance, a state called dysbiosis, our health begins to falter. The Microbiome Diet was created with the specific focus of nourishing friendly, protective bacteria, while pruning species that have overgrown healthy limits. This approach not only improves function through the entire body, it raises the bar on what it means to actually be healthy. Patients frequently report benefits in systems and areas that seem completely disconnected from gut health.  All roads lead to the microbiome and all health stems from a vibrant, thriving ecosystem.

    Microbiome Basics

    1) As much as 90% of the cells in your body are actually bacterial, not human!

    2) The vast majority of species are helpful and necessary for both life and health, including those that may become pathogenic when overgrown.  In the right balance, most strains contribute to the health of the whole. (So let’s maintain balance!)

    3) The microbiome produces Short Chain Fatty Acids (SCFA) which are used as a fuel source by cells of the intestine, promote the growth of healthful strains of bacteria, decrease inflammation, improve the immune system, boost brain function, balance mood, and even alleviate anxiety.

    4) Neurotransmitters are chemical messengers transmitting information through the brain and body, influencing the way we think and feel, plus they’re made by bacteria!

    5) They produce natural antibiotics and vitamins to protect and nourish us.

    6) Microbes regulate metabolism.  

    7) The immune system and microbiome live together in the intestine and are inextricably intertwined.  The health of one depends on the health of the other.

    Microbiome Diet Basics

    While we’ll go much deeper into the specifics of The Microbiome Diet in part two, here are some of the basic principles of eating for the overall health of your microbiome.

    1) Load up on plant foods that heal your gut and support the microbiome.

    2) Avoid foods that are inflammatory and trigger imbalances in the gut microbiome.

    3) Consume foods loaded with natural probiotics, which replenish the microbiome.

    4) Consume foods containing prebiotic fibers to nourish healing bacteria. Certain herbs, spices, and compounds are beneficial and can improve the overall health of both your intestine and bacteria.

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  • More About Microbiome Diet

    Posted at 12:02 pm
    Feb 17th

    The Microbiome and Our Genes

    Researchers often speak about the microbiota as the full collection of genes and microbes living within a community, in this case the community that inhabits our guts. According to the University of Utah Genetic Science Learning Center, “the human microbiome (all of our microbes’ genes) can be considered a counterpart to the human genome (all of our genes). The genes in our microbiome outnumber the genes in our genome by about 100 to 1.” (14)

    You might have learned in school when you were younger that all human beings actually have very closely related genetic codes, even though we are all so different-looking as a species. What’s amazing is that each of our gut microbiomes is vastly different. One of the most amazing things about the microbiome is how different it can be from one person to another.

    Estimates of the human gene catalog show that we have about 22,000 “genes” (as we normally think of them) but a staggering 3.3 million “non-redundant genes” in the human gut microbiome! The diversity among the microbiome of individuals is phenomenal: Individual humans are about 99.9 percent identical to one another in terms of their host genome but usually 80 percent to 90 percent different from one another in terms of the microbiome.

    Today, researchers are rapidly working on better understanding the microbiome in order to help prevent, cure or treat symptoms of all sorts of diseases that might stem back to the community living within each of us. DNA-sequencing tools are helping us uncover various bacterial strains and how they might hinder or help the immune system. This effort is part of the Human Microbiome Project, done by the Data Analysis and Coordination Center for the National Institutes of Health. The goal is to “characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health.” (15)

    While some bacteria contribute to diseases, many do not. In fact, there are lots of bacterial strains we could benefit from having more of. At the same time, having certain diseases can negatively impact the microbiome, although we still have a lot to learn about how this happens exactly. The more we can come to understand how bacteria in the microbiome affect our genes and predispose us to diseases, the better we can personalize treatment approaches and prevent and manage diseases before they’re life-threatening.

    The Microbiome Key Takeaways

    How Else Can You Establish a Strong Microbiome?

    1. Avoid Antibiotics as Much as Possible

    Antibiotics have been commonly prescribed for over 80 years now, but the problem is that they eliminate good bacteria in addition to cleaning the body of dangerous “germs,” which means they can lower immune function and raise the risk for infections, allergies and diseases. While antibiotics can save lives when they’re truly needed, they’re often overprescribed and misunderstood.

    Over time, dangerous bacteria can become resistant to antibiotics, making serious infections harder to fight. (4) Before taking antibiotics or giving them to your children, talk to your doctor about alternative options and the unintended consequences to our microbiomes that can result from taking antibiotics too often and when they aren’t needed.

    2. Lower Stress and Exercise More

    Stress hinders immune function because your body diverts energy away from fighting off infections and places it on primary concerns that keep your alive — which is one reason why chronic stress can kill your quality of life. When your body thinks it’s facing an immediate danger, you become more susceptible to infections and experience more severe symptoms while also developing higher levels of inflammation.

    Stress causes immune compounds known as cytokines to contribute to the inflammatory response that damages healthy cells. Exercise is a natural stress reliever that can help lower inflammation, balance hormones and strengthen the immune system.

    3. Add Supplements

    Co-enzyme Q10, carotenoids, omega-3 fish oil, selenium and antioxidants (vitamins C, D and E) can help keep free radical damage from disturbing micrbiota gut health.

    What Diseases Are Connected to the Microbiome?

    The microbiome is a lot like Earth’s ecosystems, meaning as its conditions change, so do the organisms that inhabit it. Microbes interact with one another within the community they live in (our gut), plus they change in concentration depending on their surroundings — which means your diet, lifestyle, use of medications/antibiotics and environment really impact your gut health. At the forefront of how your gut microbiome determines whether or not you’ll deal with various illnesses is inflammation.

    Inflammation is the root of most diseases. Studies show that an anti-inflammatory lifestyle is protective over brain neurons, balances hormones, fights the formation of tumors and has mood-enhancing benefits. While you might not think that gut health impacts your mood and energy much, think again. Gut-friendly bacteria can help manage neurotransmitter activity, which makes them natural antidepressants and anti-anxiety organisms. Instead of taking anti-inflammatory medications to manage illnesses like arthritis or heart disease, we’re much better off reducing inflammation in the body.

    Poor gut health is tied to dozens of diseases, especially:

    The microbiome diet - Dr. Axe

    What Is the Human Microbiome?

    Each of us has an internal complex ecosystem of bacteria located within our bodies that we call the microbiome. The microbiome is defined as as “community of microbes.” The vast majority of the bacterial species that make up our microbiome live in our digestive systems.

    According to the Department of Chemistry & Biochemistry at the University of Colorado, “the human microbiota consists of the 10–100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut. The human ‘microbiome’ consists of the genes these cells harbor.” (1)

    Our individual microbiomes are sometimes called our “genetic footprints” since they help determine our unique DNA, hereditary factors, predisposition to diseases, body type or body “set point weight,” and much more. The bacteria that make up our microbiomes can be found everywhere, even outside our own bodies, on nearly every surface we touch and every part of the environment we come into contact with. (2)

    The microbiome can be confusing because it’s different than other organs in that it’s not just located in one location and is not very large in size, plus it has very far-reaching roles that are tied to so many different bodily functions. Even the word “microbiome” tells you a lot about how it works and the importance of its roles, since “micro” means small and “biome” means a habitat of living things.

    It’s been said by some researchers that up to 90 percent of all diseases can be traced in some way back to the gut and health of the microbiome. Believe it or not, your microbiome is home to trillions of microbes, diverse organisms that help govern nearly every function of the human body in some way. The importance of our gut microbiome cannot be overstated: Poor gut health can contribute to leaky gut syndrome and autoimmune diseases and disorders like arthritis, dementia, heart disease, and cancer, while our health, fertility and longevity are also highly reliant on the balance of critters living within our guts.

    Throughout our lives, we help shape our own microbiomes — plus they adapt to changes in our environment. For example, the foods you eat, how you sleep, the amount of bacteria you’re exposed to on a daily basis and the level of stress you live with all help establish the state of your microbiota.

    The Microbiome Diet: Eating to Support Immunity and Lower Inflammation

    Your diet plays a big part in establishing gut health and supporting your microbiome’s good bacteria. Research over the past several decades has revealed evidence that there’s an inextricable link between a person’s microbiota, digestion, body weight and metabolism. In an analysis of humans and 59 additional mammalian species, microbiome environments were shown to differ dramatically depending on the specie’s diet.

    The flip side is also true: Your gut health can impact how your body extracts nutrients from your diet and stores fat. Gut microbiota seem to play an important role in obesity, and changes in bacterial strains in the gut have been shown to lead to significant changes in health and body weight after only a few days. For example, when lean germ-free mice receive a transplant of gut microbiota from conventional/fat mice, they acquire more body fat quickly without even increasing food intake, because their gut bugs influence hormone production (like insulin), nutrient extraction and fat (adipose tissue) storage. (3)

    Now that you can see why it’s critical to lower inflammation and support gut health, lets’s take a look at how you can go about this.

    Foods that promote inflammation include:

    On the other hand, many natural foods can lower inflammation and help increase good bacteria in the gut. High-antioxidant foods help reduce gut damage caused by oxidative stress and turn down an overactive immune system while safeguarding healthy cells. Anti-inflammatory foods that should be the base of your diet include:

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  • Microbiome Diet, Did You Know

    Posted at 11:48 am
    Feb 8th

    Synopsis of Diet Plan. This diet involves three phrases, and, throughout all phases, dieters are encouraged to take “microbiome supersupplements” (ingredients such as garlic, berberine, wormwood and grapefruit seed extract), digestive enzymes, prebiotics and probiotics. Kellman also suggests apple cider vinegar supplementation.

    Plate Diagram of acceptable foods


    Synopsis of Diet Plan

    The first phase is devoted to the removal of unhealthy bacteria, replacement of digestive enzymes, reinoculation with pre- and probiotics and repair of the intestinal wall. Dieters follow Phase 1 for three weeks by removing processed or packaged foods, juices, some fruits, gluten, all grains, sugars and sweeteners, dairy products, eggs, soy, processed or deli meats, peanuts, potatoes and most legumes, among other foods. The second phase lasts four weeks, and dairy, eggs, fruits, gluten-free grains, legumes and sweet potatoes are added back in. Dieters are asked to follow the diet with 90-percent compliance. The final phase, which lasts in perpetuity, promotes all foods allowed in Phase 2 with 70-percent compliance.


    Nutritional Pros and Cons.

    Kellman urges readers to eat foods that feed healthy gut bacteria and avoid foods that nourish harmful gut bacteria, a commendable dietary approach. He also encourages readers to change their relationship with food and describes the perils of stress eating. By Phase 3, the Microbiome Diet calls for a generally healthy diet with 70-percent compliance, allowing for more flexibility and the occasional indulgence.

    Bottom Line.

    Kellman believes all health begins in the gut and he thoroughly explains the relationship between gut bacteria and health, as well as the value of mindful eating and creating a healthy relationship with food. Unfortunately, the benefits of healthy gut bacteria are often overlooked – or perhaps poorly understood or publicized – as is the potential risk of harmful gut bacteria on obesity and chronic disease.

    The Microbiome Diet centers around the idea that the key to optimal body function—and in turn, high metabolism and weight loss—is a thriving internal ecosystem of bacteria. “Research reveals that when the microbiome goes out of balance, people often gain weight, even when they haven’t changed their diet or exercise,” Kellman writes. “An imbalanced microbiome often dooms just about any diet to failure. When the microbiome is balanced, however, people often lose weight, even when they don’t make any other changes.”

    It makes plenty of sense: 90% of our cells are bacterial, and there’s strength in numbers. “These intestinal organisms—bacteria—digest your food, govern your appetite, control your metabolism, orchestrate your immune system, influence your mood, and even help determine how your genes are expressed,” Kellman says. “They have a major impact on whether your heart is healthy, whether your bones develop properly, and whether your brain feels sharp and clear or fuzzy and unfocused. They sustain the gastrointestinal tract so your food is properly digested and you get all the nourishment you need. They produce crucial vitamins and other nutrients. They even manufacture natural antibiotics.”


    Processed foods of all kinds are out of the question, as are sugar, eggs, soy, gluten, dairy, yeast, dried fruits, and fungus. Even gluten-free grains like quinoa and brown rice and starchy vegetables and legumes like potatoes, peanuts, and kidney beans are off-limits, as the sugars in those foods can feed bad bacteria. 


    Most non-starchy veggies and fruits are just fine, with a special emphasis on fermented foods like pickles, sauerkraut, and kombucha (which contain digestion-friendly bacteria strains). Chickpeas and lentils are the only legumes permitted, and Kellman advises sticking with coconut oil or ghee. For protein, beef, chicken, low-mercury fish, lamb, and shellfish are all fine (though as low-processed as possible).Kellman also suggests a variety of bacteria-promoting supplements to ingest daily, the most important of which being a probiotic and prebiotic. And here’s where things take a turn for the amazing: A couple cups of coffee per day are allowed, as are wine and beer, since they’re fermented.

    The Microbiome Diet Phase 1-The 4 R’s

    The 4R approach to intestinal health works to rebalance gut flora by:

    1. Removing foods that interfere with a healthy microbiome, disruptive bacteria, pathogens and toxins
    2. Repairing the gut wall
    3. Replacing needed stomach acid and pancreatic enzymes
    4. Reinoculating with large amounts of healing, probiotic bacteria

    Diets high in refined carbohydrates, fat, sugar, processed foods, coloring, and fillers are what creates the perfect storm to allow opportunistic strains of bacteria to overgrow, as well as pathogens to dominate the balance of the ecology. By removing them, the intestine can heal and the composition of the microbiome begins to change for the better. Patients are advised to avoid the following for the first 3 weeks:

    The focus should shift to an organic, plant based diet that includes “Microbiome Superfoods”. These are foods that contain prebiotic fibers necessary to feed and nourish the healthy strains of intestinal bacteria, giving them the energy to grow, multiply and thrive. Since these fibers are indigestible by us humans, they make it into the intestine intact, where they are fermented and broken down by our tiny friends. In the process, compounds called Short Chain Fatty Acids (SCFA) are released, which have many positive effects on our health. It’s a win/win for everyone! Asparagus, garlic, Jerusalem artichoke, Jicama, onion, leek, and radish are all terrific examples of prebiotic foods.

    Probiotic foods are equally as important, as they loaded with huge amounts of healing bacteria. Fermented vegetables, kimchi, sauerkraut, plus sheep, and goat’s milk products like kefir and yogurt, contain exponentially more healing bacteria than supplements do. A true Microbiome Diet includes liberal use of these foods to boost the quantity and types of strains that should be found in great numbers in the ecology.

    Fruits such as apples, berries, cherries, coconut, grapefruit, kiwi, nectarine, orange and rhubarb are also included. To round things out, healthy fats from nuts, seeds (natural nut/seed butters), avocado, fish, and oils from flaxseed, sunflower and olive are all great choices. When it comes to animal proteins, make the healthiest choice possible by focusing on organic, free range and cruelty-free versions.  

    We will explore more on the 4R’s and healing supplements in Part 3.

    Phase 2 – The Metabolic Boost

    After the first 21 days on the diet, the intestine have begun to heal, inflammation is down, and positive shifts are already taking place in the microbiome. In this next phase, we continue to omit damaging foods, while adding in the following for the next four weeks.

    Phase 3 – The Lifetime Tune-Up

    At this point in the process, the intestine is healing or has fully healed and so has the microbiome! A good rule of thumb is to always try to avoid the damaging foods, listen to your body, and follow your inner guide as to what foods work or don’t work for you. By maintaining The Microbiome Diet principles, the health of the bacterial communities is ensured. complete food lists and meal plans please refer to The Microbiome Diet by Raphael Kellman, MD available on

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