Magic In Your Microbiome

The Magic in Your Microbiome 


Dr. Grace Liu, PharmD is a trained functional medicine practitioner and founder of The Gut Institute. She is a clinical pharmacist with a doctorate in practice for 19+ years and specializes in complex disease management. 

Dr. Grace PharmD consults and helps clients gain optimal performance through rebuilding the microbiome after damage from modern living. She uses nutrigenomic tools and other advanced functional lab testing. 

Currently she is training functional medicine leaders to approach gut protocols with her expertise.

Clients include paleo movement leaders and a UFC MMA fighter in the top 10.

She has been invited to speak at Ancestral Health Symposium, including 2016 in Boulder, CO, Paleo Convention Berlin, PaleoFx for two years in a row, interviewed for a documentary (by ‘Microbirth’ producers) and Women’s Health UK magazine on the skin-gut microbiome. Recently she shared the stage with Dr. David Perlmutter (author Grain Brain) on the Expert Microbiome Panel at Paleof(x)16 in Austin, Texas. Dr. Grace PharmD has also been interviewed for the Keto Summit, Detox Summit, Supercharge Your Gut Summit with Lee Holmes, Robb Wolf podcast, Sigma Nutrition, Endurance Planet, and Bulletproof Radio with Dave Asprey. She is currently finishing a book on the topic, “The Amazing Gut: The Magic and Madness of the Microbiome”, scheduled to be released in October 2016. The Gut Institute will be hosting Microbiome Medicine, live training on December 3-4th, 2016 in Oakland California. Dr. Grace is co-teaching with 2 other doctorate trained Functional Pharmacists Dr. Anh Nguyen, PharmD BCACP and Dr. Erika Gray, PharmD.

Your Gut Is an Ecosystem

Believe it or not, your gut is an ecosystem - and a complex one, at that. Like any other ecosystem, the microbes in our guts have layers and layers of relationship with each other, and with us (see below). There are apex species at the top,primary producers at the bottom, and even invasive species that can threaten the harmony of the entire system. The presence (or absence) of some of these species are key determinants of our health, and a strong and robust microbial community lays the foundation for longevity and leanness. In every society, ‘Blue Zone’ or civilization that exhibits happiness and vitality, excellent gut health is a hallmark.


Finding a Core Microbiota

It will probably come as no surprise that our modern lifestyles have had a dramatic - and negative - impact on our microbial ecosystems. One of the clearest signs of a modern gut is the increased presence of harmful gut bacteria compared to traditional (and healthy!) hunter-gatherers. A 2010 study that compared the microbiota of children in Burkina Faso, in rural Africa, to those in urban Italy found that there were 10x as many opportunistic pathogens (harmful gut bacteria) in the Italian children than in their African counterparts. Why the stark difference? A few things stand out: the children of Burkino Faso regularly snack on termites that carry soil-based organisms (beneficial bacteria found in the soil) in their bellies, allowing them to digest the complex plant fibers found in millet, which is a staple of their diet. Millet is used to make a fermented gruel known as ben-saalga, which is full of beneficial lactobacilli bacteria, and withstands spoilage despite a lack of refrigeration. Their diets also include tasty fermented vegetables, aged legumes, and pickled boabab leaves as condiments for traditional stews and porridges - there is a constant stream of beneficial bacteria and plant fibers for them to eat.

The Italian children, on the other hand, ate a diet rich with sugar, baked goods, refined grains, few legumes and high-fiber vegetables, and few fermented foods beyond yogurt, as is common in industrialized countries. You can probably see where this is going: unsurprisingly, populations in Burkino Faso have little to no obesity, autism, allergies, diabetes, depression, cancer, or digestive disorders. Most of the chronic ailments we suffer from in industrialized countries are almost completely absent! By studying the microbiomes of these and other hunter-gatherers from around the world, it becomes clear that there is a core microbiota in healthy people that defies gender, geography, and age. This core microbiota, as we will see, is marked by high numbers of beneficial, peacekeeping protectors, and low numbers of opportunistic pathogens.

What Is a Healthy Microbial Signature?

As new techniques for identifying and measuring microbes have become available, our understanding of the key players in our microbial ecosystems has advanced quickly. Studies of hunter-gatherers from around the world, like the ones in Burkina Faso, have helped to identify the bacteria that help maintain and promote a healthy gut lining, and those that harm it. When gut ecosystems are rich and full of beneficial bacteria such as Bifidobacteria longum, Akkermansia,Roseburia, Faecalibacterium and Bacteroides, the gut lining naturally maintains balance and effortless functioning. When these microbes are missing, however, havoc ensues, and harmony is disrupted, contributing to many of the chronic diseases that plague us today. Normally these beneficial commensal organisms are ‘gifted’ to us by our mothers, hugs and kisses from our loved ones and healthy, organic dirt - in modern environments, we feel the absence of these connections that we have blindly taken for granted.

Many factors have contributed to the destruction of our guts - widespread antibiotic use, over-sanitation, and a lack of exposure to healthy dirt (and the bacteria that come with it) all work together to eliminate our peacekeepers. With these helpful bacteria depleted, empty niches in our gut’s ecosystem are filled instead by harmful, opportunistic pathogens. Using the analogy of a garden, cultivating beneficial plants, ladybugs, and butterflies and allowing them to flourish crowds out destructive, invasive species - just like in the guts of the children of Burkina Faso.

What to Look for: Genova

Genova GI Effects testing are a great way to get a peak under the hood of your gut. The table below lists examples of both the opportunistic pathogens and the beneficial peacekeepers that may appear in your results. A useful acronym to remember the major beneficial bacteria is ABC: Akkermansia, Bifidobacteria longum, Bacteroidiales, Christensenella, and Clostridiales (Faecalibacterium andRoseburia).
Your Personal and Unique Genova Diagnostic GI Effects Gut Analysis Will List Some of These

Interpreting Your Results

The chart above provides us with a general outline of what should be present (beneficial commensals), and what is hopefully absent (opportunistic commensals) in our guts. Make sure to take a look at the first column too! The diversity present in our gut ecosystem is hugely important as well. Here are some general thoughts about the major players that can be found in our guts:

Beneficial Peacekeepers


Akkermansia: This strain grows from the top of the small intestines to the end of the anus, resting deep in the mucosa layer and providing ultimate barrier protection and security. There are no Akkermansia probiotics currently available, but we can support the growth of Akkermansia with plant polyphenols (green tea, berries) and ‘bionic’ fiber which increases mucus (inulin, oligosaccharides, psyllium, pectin). 

Faecalibacterium, Roseburia, Bacteroides: These are protective, peacekeeping bacteria. Hundreds of studies in humans show that abundance of these genera are associated with healthier and disease-free babies, children and adults. The ancestral microbiome has plenty of these life - giving bacteria! Keep these around!
Bifidobacteria longum: Fortunately, many excellent commercial probiotic formulations exist on the market to replenish this vital fountain of youth, including our proprietary Bifido|MAX product.
Bacillus species: Prescript Assist from Enviromedica contains these soil probiotics (as well as Bacteroides) that are hallmarks of healthy, balanced guts -
such as those found in rural African villages - as well as those who are lean and healthy.

Opportunistic Pathogens


Opportunistic, pathogenic bacteria are normal inhabitants of our guts, but are often associated with the microbial signatures that show up with chronic illness:

Prevotella, P. copri: In healthy individuals without dysbiosis, Prevotella is correlated with good health; however, after antibiotic exposure and in the face of gut imbalance, Prevotella can be highly associated with joint aches, headaches, rheumatoid arthritis, metabolic disorders and autoimmune disorders (!). Prevotella consumes complex starches and fiber, and psyllium may cause it to flare if there are pathogenic overgrowths.
Clostridium clostridioforme: In gut ecosystems with low gut diversity, this strain may be associated with excess alcohol production, inflammation, digestive disorders, insulin resistance and metabolic syndrome. Clostridium consume both sugar and simple starches, as well as complex plant fiber, and are part of a versatile group of microorganisms capable of great health or great disease. Some Clostridium produce butyrate (food for the cells of our intestines), while others produce neurotoxins, including tetanospasmin, which causes tetanus.
Bifidobacterium animalis: Although Bifidobacteria are commonly used as probiotics, high numbers of non-human strains signals dysbiosis. The overabundance of these strains and other starch-eating bifidobacteria (like B. adolescentis) are correlated with gluten and food allergies, celiac disease, autoimmunity, atopic diseases, senile dementia, colorectal cancer, IBD and diverticulitis.
Gammaproteobacteria, Enterobacter cloacae: Lipopolysaccharide (LPS) is part of the cell wall of Gram negative bacteria in the gut. The LPS of Enterobacter has been shown to be 100 to 1000 times more inflammatory than that of normal Gram negative inhabitants. It is associated with inflammation, morbid obesity and insulin resistance. By crowding out Enterobacter cloacae to zero (or undetectable stool levels), one study showed loss of over 100 lbs. weight loss in 6 months by one morbidly obese subject on a high oligosaccharide -fiber diet and oligosaccharide supplements (oligosaccharides are present in whole legumes, and whole gluten-free ancestral grains)
Klebsiella: This strain can be highly associated with joint aches, headaches, obesity, metabolic disorders and autoimmune disorders. Certain prebiotic fibers can worsen these overgrowths, including inulin -FOS and resistant starch. Klebsiella eats sugar, starches, and simple carbohydrates, and produces alcohol and other inflammatory toxins. Streptococcus, Corynebacteria, Staphylococcus: These are all frequent inhabitants of our skin, sinuses, mouth or throat, but do not belong in high concentrations in our gut. Babies born by Caesarean section have higher colonization in the gastrointestinal tract of these skin microorganisms compared to those born via vaginal birth. They are associated with inflammation and disease if present in high amounts.
Desulfovibrio, Bilophila: This group of Deltaproteobacteria blooms with high fat food (red meat, dairy) that is not accompanied by sufficient fiber or in gut dysbiosis. Bilophila loves bile (which is secreted into the gut to aid in digestion of fatty acids). In high abundance, Desulfovibrio and Bilophila is associated with gut inflammation, colitis, adenoma, and colorectal carcinoma. They secrete toxic sulfur gas (H2S), which may be inflammatory in excess quantities. Probiotics and fermented foods, however, such as fermented milk products (like yogurt and kefir) have been shown to lower Bilophila in irritable bowel syndrome (IBS), and improvements in IBS symptoms were observed to occur alongside reductions in Bilophila.

Fertilizing Your Microbial Ecosystem


Your bacterial peacekeepers love to eat complex plant fibers from a variety of sources. These fibers are found all over in roots, stems, leaves, legumes, and soaked, fermented, unrefined ancient grains like millet, brown rice, amaranth, buckwheat, and wild rice. Over 36,000 plants on Earth contain the powerful fibers knows as inulin and oligosaccharides – these “bionic” fibers selectively feed the beneficial, peacekeeping bacteria in our guts, and help crowd out opportunistic pathogens. Below are some whole-food sources of plant fibers and probiotics:
•Wild, white, and yellow yams
•Dandelion leaves, Belgian endive, many vegetable greens, chives, and leeks
•Non-starchy root vegetables, including Jerusalem artichokes (sunchokes), chicory, dandelion, onions, leeks, garlic, scallions, and shallots
•Cruciferous vegetables like broccoli, cauliflower, kale, kale sprouts, cabbage, Napa cabbage, purple cabbage, and Brussel sprouts
•Legumes, lentils, and purple and other heirloom starchy tubers
•Fermented roots, legumes, beet kvass, sauerkraut, kombucha, natto, koji, and miso.

A Note from Dr. Grace
I work with executives, endurance athletes and multitasking moms to rebuild their biome and decrease brain fog, body fat and fatigue in 6 months or less. I use advanced gut microbiome testing to target and customize their regimens to them and their health goals. I hear all the time they are tired of searching google for gut solutions that do not work for them and spending hundreds or even thousands of dollars on supplements that don’t work for them or make them worse. What I find is that people want to be personally guided and educated on how to fix their health. The Gut Institute has solutions for people! To schedule a consult with me, click here.





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Dr. Grace Liu PharmD Founder of