Dr. Mercola
Waking Times

Fifteen years ago, it was anticipated the Human Genome Project (HGP) would allow modern medicine to leapfrog into groundbreaking gene-based therapies for virtually every disease known to man—experts were that sure health and disease was governed by genetic predisposition.

Much to everyone’s surprise, the HGP discovered genetics are only responsible for about 10 percent of human disease.¹ The remaining 90 percent are induced by environmental factors, be they nutrients, toxins, or thoughts and emotions.

In more recent years, we’ve come to realize that your microbiome is one of the environmental factors that drive genetic expression, turning genes on and off depending on which microbes are present.

Your body’s microbiome—colonies of various microbes that reside in your gut and elsewhere in and on your body—is as unique to you as your fingerprint, and can be rapidly altered based on factors such as diet, lifestyle, and exposure to toxins and antibiotics.

You have approximately 1,000 different species of bacteria living in your body, and these bacteria actually outnumber your body’s cells by 10 to 1. But that’s not all. You also harbor viruses (bacteriophages), and they in turn outnumber bacteria 10 to 1.

So not only is your body the home of 100 trillion bacteria, you also house about one quadrillion viruses. All of these organisms perform a multitude of functions, and need to be properly balanced and cared for in order to maintain good health.

There are no good or bad bacteria per se. Potentially harmful microbes only become dangerous once they start to take up too much real estate, outnumbering the more beneficial ones.

This also means that living in a sterile environment is by no means ideal, as health-promoting microbes are adversely affected along with potentially harmful bacteria when we wage war against bacteria with hand sanitizers and antibiotics as our prime weapons.

Your Microbiome Appears to Dictate Health and Disease Onset

Research shows that some microbes specifically help prevent certain disease states. For example, simply by eradicating four species of bacteria (Lactobacillus, Allobaculum, Rikenelleceae, and Candidatus arthromitus), researchers were able to trigger metabolic changes in lab animals that led to obesity.²

Studies^3,4 have also found that autistic children have distinctly different microbiome compared to healthy children. Notably, they tend to have fewer beneficial bacteria such as Bifidobacterium.

Importantly, your gut bacteria influence your immune responses.⁵ The inflammatory response starts in your gut and then travels to your brain, which subsequently sends signals to the rest of your body in a complex feedback loop.

Mounting research suggests your microbiome may actually be one of the preeminent factors determining your overall longevity.

Recent findings even make us reevaluate our view of a “healthy diet,” as one of the primary mechanisms of action that explains how a healthy diet “works” is that it upregulates and improves the quality of your gut microbiome.

So it’s not just about getting specific nutrients from your food; your food also needs to support a healthy microbiome—as it turns out though, foods known for their value to health also tend to promote beneficial gut bacteria.

Examples include traditionally fermented foods and raw foods, especially those high in fiber. Certain gut microbes actually specialize in fermenting soluble fiber found in legumes, fruits, and vegetables, and the byproducts of this fermenting activity help nourish the cells lining your colon.

Some of these fermentation byproducts also help calibrate your immune system to prevent inflammatory disorders. Sugar, on the other hand, is a preferred food source for fungi that produce yeast infections and sinusitis.

Diseases Linked to Your Microbiome

So far, a number of health conditions and chronic diseases have been linked to the makeup of your microbiome, as has several specific benefits, including the following:

Elimination of chemical toxins	Production of vitamins and amino acids (protein precursors), and the absorption of minerals
Behavior, mood control, and mental health: Beneficial bacteria may serve the same role as antidepressants and anti-anxiety drugs. In one study,6 people who took a multi-strain probiotic for at least four weeks reported a lessening of rumination—recurring, persistent thoughts about something distressing that has or may happen, which tends to create anxiety.Insufficient amounts of gut bacteria has been linked to “high-risk behavior,” and 90 percent of the neurotransmitter serotonin is also manufactured in your gut, which is thought to play an important role in mood control and depression	Obesity: Infants exposed to antibiotics within the first three years of life may be predisposed to obesity. Mice given antibiotics during infancy grew up to be 25 percent heavier, and had 60 percent more body fat than the controls.7,8,9Four species of gut bacteria in mice found to be of particular importance with regards to metabolism areLactobacillus, Allobaculum,Rikenelleceae, and Candidatus arthromitus—the first three of which are also found in the human gut
Crohn’s disease. Patients with Crohn’s have been found to have lower than normal levels of Faecalibacterium prausnitzii in their guts10	Type 1 diabetes (an autoimmune disease) in young children tends to be preceded by a change in gut bacteria. Research has also found that certain microbes can helpprevent type 1 diabetes, suggesting your gut flora may indeed be an epigenetic factor that plays a significant role in this condition
Type 2 diabetes: Certain types of bacteria and body fat produce a heightened inflammatory response that contributes to the metabolic dysfunction associated with type 2 diabetes11	Autism may be exacerbated or even caused by certain bacteria. Autistic children have distinctly different microbiome compared to healthy children, with notably fewer healthy bacteria such asBifidobacterium. Autistic children also have markedly higher levels of toxic volatile organic compounds (VOCs)12,13
Brain diseases. Dr. David Perlmutter explores the compelling connection between the microbiome and brain health in his book, Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain for Life,connecting it to a number of neurological diseases, including Alzheimer’s	Food allergies. Clostridia helps prevent sensitization to food allergens, recent research14,15shows. Immune responses to food allergens were reversed onceClostridia bacteria were recolonized.Using genetic analysis, it was determined that Clostridia instructs immune cells to produce a signaling molecule called interleukin-22 (IL-22), which reduces the permeability of the intestinal lining, thereby preventing leaky gut syndrome—a condition that allows allergens to enter your bloodstream, thereby producing an immune response

Gut Microbes May Influence Your Immune Response to Vaccines

The influence of your microbiome doesn’t end there. In an effort to tease out the reason why there are so many “non-responders” to the rotavirus vaccine in Asia and Africa, a research team in Amsterdam devised a study to find out whether gut microbes might play a role in how people respond to vaccines. As reported by Scientific American:¹⁶

“Harris and her colleagues, including collaborators in South Asia, studied 66 Pakistani infants and 66 matched Dutch control subjects, all of whom received the oral rotavirus vaccine. Most of the children in the Netherlands mounted the expected immune response, but only 10 of those in Pakistan did the same.

A genetic scan of fecal samples taken from each infant before the vaccine revealed that the responders harbored a higher diversity of microbes in their intestinal tract. They also carried more organisms from the group Proteobacteria.”

Interestingly, many Proteobacteria have a tail that helps propel them forward, and this tail, called a flagella, contains flagellin—a protein that heightens the activity of immune cells. Thus a preponderance of these bacteria may act as a natural vaccine booster.

In a previous study,¹⁷ mice without any intestinal bacteria, and mice inoculated with nonflagellated bacteria only, both failed to raise antibodies in response to the influenza vaccine, rendering the vaccine completely useless. Mice with normal gut flora and those inoculated with nothing but flagellated bacteria all responded to the vaccine with robust immune activity. A small-scale human follow-up study is planned to see whether the same pattern can be found in humans. Research also suggests there may be a link between the microbiome and adverse vaccine reactions. As noted by Scientific American:¹⁸

“Research published in 2014 in Pediatrics showed that varying compositions of gut bacteria in Bangladeshi infants correlated with reactions to the tetanus, tuberculosis and oral polio vaccines. Taken together, these lines of research indicate that our body’s native bacteria may help determine our individual immune response to vaccines.”

Contact Lenses Found to Change Your Eyes’ Microbiome

Another surprise was recently delivered by researchers claiming you may alter the microbiome of your eyes by wearing contact lenses. This may explain why contact lens wearers are more prone to certain kinds of eye infections. The study, which has not yet been accepted for publication, was presented at the 2015 American Society for Microbiology’s meeting. Bacteria collected from the eyeball and the skin below the eye was analyzed and compared, and in people who wore contacts, the two areas were more similar in their bacterial makeup than in those who did not wear contacts, in whom the two areas showed a greater diversity of bacteria.

As reported by The Atlantic:¹⁹

“Specifically, contact-wearers had higher numbers of four species: Lactobacillus, Acinetobacter, Methylobacterium, andPseudomonas. This microbiome disruption could explain why people who wear contacts are more likely to get some kinds of eye infections, including corneal ulcers, which, incidentally, have been linked to Pseudomonas bacteria…Infections often come when people don’t take proper care of their lenses—sleeping in them overnight, or not cleaning them well or often enough.”

The researchers suggest using daily wear contact lenses rather than bi-weekly or monthly lenses, as there could potentially be bacteria lurking in the cleaning solution. Also carefully wash your hands before handling your contacts to avoid transferring bacteria from your fingers to your eyeball.

The Easiest Way to Decimate Your Microbiome

Your diet can make or break your microbiome, and the easiest way to decimate the health-promoting microbes in your gut is to eat processed foods, and meats from animals raised in confined animal feeding operations (CAFOs), for the reasons discussed in this previous article.²⁰ Processed foods are typically high in added sugars—high fructose corn syrup in particular—which feeds fungi, yeast, and detrimental bacteria. But that’s not all. Recent research^21,22 has also found that emulsifiers found in processed foods have a very detrimental effect on your microbiome, and may contribute to obesity, metabolic syndrome, and inflammatory bowel disease by altering your gut bacteria. This includes ingredients such as:

• Polysorbate 80
• Carrageenan
• Polyglycerols

In this study, widely used food additives caused chronic colitis in mice with already abnormal immune systems. In mice with healthy immune function, they resulted in mild intestinal inflammation and subsequent metabolic dysfunction that led to obesity, hyperglycemia, and insulin resistance. Most notably, the emulsifiers were fed at levels that an average person would be exposed to if eating a lot of processed foods, suggesting these additives may indeed affect the health of many Americans.

Food additives such as these are all approved by the Food and Drug Administration (FDA), again highlighting the severe limitation of our current regulatory system. A 2013 study²³ published in the journal Reproductive Toxicology found that nearly 80 percent of the food additives approved by the FDA lack testing information that would help the agency estimate the amount people can safely consume before suffering health consequences. Processed non-organic foods also tend to containglyphosate residues, which also take a drastic toll on your microbiome, as this commonly used herbicide is also patented as an antibiotic.

Optimizing Your Microbiome Is a Potent Disease Prevention Strategy

I believe optimizing your gut flora may be one of the most important things you can do for your health, and here you can wield your personal power to the fullest by making healthy food and medical choices. Not only can optimizing your gut health help normalize your weight and ward off diabetes, it’s also a critical component for a well-functioning immune system, which is your primary defense against virtually all disease.

The good news is that supporting your microbiome isn’t very complicated. However, you do need to take proactive steps to implement certain key strategies while actively avoiding other factors. To optimize your microbiome both inside and out, consider the following recommendations:

Do:	Avoid:
Eat plenty of fermented foods. Healthy choices include lassi, fermented grass-fed organic milk such as kefir, natto (fermented soy), and fermented vegetables. If you ferment your own, consider using a special starter culture that has been optimized with bacterial strains that produce high levels of vitamin K2. This is an inexpensive way to optimize your K2, which is particularly important if you’re taking a vitamin D3 supplement.	Antibiotics, unless absolutely necessary (and when you do, make sure to reseed your gut with fermented foods and/or a probiotics supplement). And while some researchers are looking into methods that might help ameliorate the destruction of beneficial bacteria by antibiotics,24,25 your best bet is likely always going to be reseeding your gut with probiotics from fermented and cultured foods and/or a high quality probiotic supplement.
Take a probiotic supplement. Although I’m not a major proponent of taking many supplements (as I believe the majority of your nutrients need to come from food), probiotics is an exception if you don’t eat fermented foods on a regular basis	Conventionally-raised meats and other animal products, as CAFO animals are routinely fed low-dose antibiotics, plus genetically engineered grains loaded with glyphosate, which is widely known to kill many bacteria.
Boost your soluble and insoluble fiber intake, focusing on vegetables, nuts, and seeds, including sprouted seeds.	Chlorinated and/or fluoridated water. Especially in your bathing such as showers, which are worse than drinking it.
Get your hands dirty in the garden. Germ-free living may not be in your best interest, as the loss of healthy bacteria can have wide-ranging influence on your mental, emotional, and physical health. Exposure to bacteria and viruses can serve as “natural vaccines” that strengthen your immune system and provide long-lasting immunity against disease. Getting your hands dirty in the garden can help reacquaint your immune system with beneficial microorganisms on the plants and in the soil. According to a recent report,26lack of exposure to the outdoors can in and of itself cause your microbiome to become “deficient.”	Processed foods. Excessive sugars, along with otherwise “dead” nutrients, feed pathogenic bacteria. Food emulsifiers such as polysorbate 80, carrageenan, and polyglycerols also appear to have an adverse effect on your gut flora.27 Unless 100% organic, they may also contain GMOs that tend to be heavily contaminated with pesticides such asglyphosate.
Open your windows. For the vast majority of human history the outside was always part of the inside, and at no moment during our day were we ever really separated from nature. Today, we spend 90 percent of our lives indoors. And, although keeping the outside out does have its advantages it has also changed the microbiome of your home. Research28shows that opening a window and increasing natural airflow can improve the diversity and health of the microbes in your home, which in turn benefit you.	Agricultural chemicals, glyphosate (Roundup) in particular is a known antibiotic and will actively kill many of your beneficial gut microbes if you eat and foods contaminated with Roundup
Wash your dishes by hand instead of in the dishwasher. Recent research has shown thatwashing your dishes by hand leaves more bacteria on the dishes than dishwashers do, and that eating off these less-than-sterile dishes may actually decreaseyour risk of allergies by stimulating your immune system.	Antibacterial soap, as they too kill off both good and bad bacteria, and contribute to the development of antibiotic-resistance.

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