Superorganism You: The Role of Gut Bacteria in Health and Disease

Friday Jun 28 | BY |
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Digestive System

Your digestive health, and even your overall health, could be dependent on the bugs in your gut.

Why is it that up until recently, medical theory was based on a time before smart phones, high-speed personal computers, and international research collaboration? For much of the last century, only findings by American scientists were considered important. Your doctor parroted what was taught in medical school, which was often based on incomplete, naïve, and often outright wrong research findings.

That’s why much of medical dogma does not serve post-modern patients with chronic disease. However, medical researchers—those scientists who keep up with technology—are pushing doctors into the 21st Century.

The Human Microbiome Project (HMP), along with other microbiome projects worldwide, has laid an important foundation for understanding the trillions of microbes that inhabit our bodies. HMP scientists are hoping to identify microbial communities found on the human body, including in the nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease. What they are finding is amazing!

Until the HMP and new probiotic research, the ecosystems of the human body were largely unstudied. The influence of microorganisms upon human development, physiology, immunity, and nutrition was almost entirely unknown. Traditional microbiology focused on individual species as isolated units, but only a few hundred of these have been studied out of known thousands of species. The idea of the complexity of human microbial communities was not even considered. But that’s all changing.

The American Gut

The American Gut project provides an opportunity to participate and compare the microbes in your gut to those in the guts of thousands of other people in the U.S. and around the world. This fascinating project is built on open-source, open-access principles. The data collected is for the common good, and understanding gained by the research will be shared with participants and with scientists.

As you might have imagined, your early health starts in the womb and at birth. Your inherited genetics come with you, but your gut’s microbiome starts at birth. As the newborn passes through the birth canal, maternal bacteria catch a ride. Special bacteria inhibit the mother’s nipple and as the infant suckles, these pass into the mouth and down to the gut feeding on milk. By age 3, your microbial community has stabilized into your personal gut ecosystem. That doesn’t mean it can’t change, and it does through out life, but it is never as virgin, nor as robust, and not as nimble.

Early use of antibiotics plays havoc with your gut’s ecosystem and sets the stage for childhood infections and adult disease. Refined foods, too much dairy fat and high protein milk diets, as well as low fiber foods and too much sugar cripples your gut probiotic species.

Our gut bacteria play important roles in manufacturing neurotransmitters, including serotonin, enzymes and vitamins B12 and K, as well as important amino acid and short-chain fatty acids. They compose a suite of signaling molecules that can significantly influence immunity and have effects on the metabolic system.

Bad diet, food additives, and antibiotics disrupt our gut mucosal lining as well as the natural flora. This disruption is linked to inflammation, which if unchecked, can spread through the body like wildfire. Chronic low-grade inflammation is thought to be the common denominator for nearly all modern illness from metabolic syndrome and diabetes to Alzheimer’s and autoimmune diseases.

Your Body Has A Planet Within

Bacteria outnumber us by at least ten to one—not in the world outside, but as the composition of our own bodies. On the planet, the ratio is even higher. Bacteria are everywhere. Microscopic bacteria live on the tongue, teeth, and skin. Each of your finger tips houses more than 150 different species. Your intestines are the mother load with 100 trillion microorganisms. Bacteria make up most of the flora in the colon—60% of the dry mass of feces, with an estimate of between 300 and 1000 different species living in the human gut.

Gut bacteria play crucial roles in digesting food and modulating the immune system. They make specialized molecules needed for enzymes to work properly. They interact with us, altering which of our genes get turned on and off—a process called gene expression—in cells within the intestinal wall.

Some evidence suggests that they are essential for building a normal heart. They also may indirectly cause cardiovascular disease. It seems that too many egg yolks and lots of meat when acted upon by intestinal bacteria raise plasma levels of trimethylamine-N-oxide (TMAO). It is a naturally occurring organic compound, but too much clogs arteries.

Gut bacteria affect appetite, as well as other aspects of our behavior. Often called the “second brain,” the gut is the only organ with an independent nervous system, an intricate web of 100 million neurons embedded in the intestinal wall. Gut bacteria produce hundreds of neurochemicals that the brain uses to regulate how your body functions including mental processes such as learning, memory and mood. Gut bacteria manufacture about 95 percent of the body’s supply of serotonin, a neurotransmitter that influences both mood and GI activity, including appetite.

Where it really gets amazing is in the gene pool. The gut microbiome contains at least 100 times more genes than the human genome’s 23,000. Scientists found that the 3.3 million genes found in the guts of their research subjects represented about 1,000 species of bacterium. They estimate that each person’s gut contains at least 160 species of the collective one thousand, and that about 40% of a person’s gut species are shared by other people. They also found that more than 25% of the genes have never been seen before.

Tending the Garden Within

Because your gut bacteria are important for health, it makes sense to cultivate good ones.
Diet makes a big difference. Eating lot of simple sugars and fats reduces the diversity of gut bacteria sifting healthy bacterial balance towards disease. It seems that getting off refined foods is the second most important step to a healthy gut.

The first step is to avoid the unnecessary use of antibiotics. It is well know that antibiotics kill bacteria but cause a lot of collateral damage. Bacterial biodiversity in the gut plunge during antibiotic treatment and reach their lowest level 11 days after starting treatment. They repopulate, but many are damaged, demonstrating lower capacity to produce proteins with less capacity to absorb iron, as well as reduced function to digest certain foods that produce essential molecules necessary for health.

Start eating more plants and you shift the balance back. Natural fiber serves as prebiotics—non-digestible food ingredients that stimulate the growth and activity of bacteria. Add fermented foods and you not only feed the bacteria, but add new species. Bifidobacteria species and Lactobacillus plantarum are common in fermented vegetables and can directly enhance the function of the living tissue that composes the gut lining. But you may not be able to restore robust gut health with food alone.

Five Fermented Foods For A Healthy Gut

  1. Miso
  2. Yogurt
  3. Kefir
  4. Kambucha
  5. Sauerkraut

Top 10 Prebiotic Foods

  1. Raw Chicory Root
  2. Raw Jerusalem Artichoke
  3. Raw Dandelion Greens
  4. Raw Garlic
  5. Raw Leek
  6. Raw Onion
  7. Cooked Onion
  8. Raw Asparagus
  9. Raw Wheat bran
  10. Whole Wheat flour, Cooked
  11. Raw Banana

No one knows the ideal daily serving of prebiotics, but recommendations by nutritionists range from 4 to 8 grams (0.14–0.28 oz.) for general digestive health support, and at least 15 grams (0.53 oz.) for those with active digestive disorders.

Probiotics To The Rescue

Probiotics are big business. But it’s not clear what beneficial bacteria actually do for us. Research suggests that certain probiotics may be useful in a number of ways including modulating the immune system, reducing allergic response, shortening the length and severity of colds in children, relieving diarrhea, and quelling irritable bowel symptoms.

Saccharomyces boulardii, a tropical strain of yeast first isolated from lychee and mangosteen, is highly effective is controlling diarrhea caused by Clostridium difficile infection, as well as inflammation of the gut lining caused by antibiotics. The effective dose is 500 mg twice daily for at least one week.

The KK1 strain of S. boulardii may help prevent Celiac Disease. Other strains of probiotic bacteria have been used for inflammatory bowel diseases like Crohn’s including Faecalibacterium prausnitzii and Butyricicoccus pullicaecorum.

The future of your gut looks promising. Scientists are working on “synbiotics,” mixtures of targeted, next-generation probiotics combined with prebiotic nutrients to nourish them. New therapeutic foods or medical beverages will be introduced to the gut community to repair them and supply important missing species or animate weakened functions.

Probiotics are so important for health that I recommend them to my patients as part of their general daily supplement plan. A comprehensive blend seems best with a range of 10-40 billion active organisms daily. They are best taken with meals, or a blended fiber-rich smoothie, or along with yogurt.

Tips For A Healthy Gut

  • Eat more plants
  • Add more fiber and use different types
  • Avoid refined food products, food additives
  • Avoid sugar
  • Avoid dairy fat and don’t over eat meat
  • Eat small amounts of fermented foods
  • Take a probiotic supplement

Learn More

NIH Human Microbiome Project

Gut Flora Wikipedia

Want to sequence your own microbiome?

Dr. J. E. Williams


Dr. Williams is a pioneer in integrative and functional medicine, the author of six books, and a practicing clinician with over 100,000 patient visits. His areas of interest include longevity and viral immunity. Formerly from San Diego, he now resides in Sarasota, Florida and practices at the Florida Integrative Medical Center. He teaches at NOVA Southeastern University and Emperor’s College of Oriental Medicine.

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  1. Paul Weddle says:

    All this is new to me but I am absolutely hooked and have started trying to ferment vegetables.
    The term “gut flora” is used extensively in these circles but I am puzzled. What is meant by “gut”.
    I had my colon removed from my digestive system about 3 years ago and wondered, is all this good bacteria still beneficial to me? I am guessing the answer is “yes”.
    What caught my attention in the article is the reference to the manufacture of Vitamins B12 and K. From what I have gleaned, scouring info on the internet, K has recently been found to be much more than just a blood co-agulant, but is manufactured approximately where the incision would have been made when my colon was removed.
    This has been bugging me for a while. However, my main query here is “Where in the digestive system does ‘gut flora’ do it’s work?

  2. Regina Clay says:

    I find this article very informative and it saddens me that I maybe the first to comment. I do hope many, many folks have read it. I do fear that it maybe too technical and few understood it. Or, read it all the way to the end for the tips on maintaining a healthy gut. Very helpful. My experience is that a healthy gut is the key to good health and aging well.

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