Dr. Mercola
Your body houses some 100 trillion bacteria. In essence, we’re little more than walking microbe colonies.
These organisms perform a wide variety of functions, and we’ve now come to realize that they need to be properly balanced and nourished if we want to maintain good physical and mental health.
While the Human Genome Project (HGP) was expected to result in gene-based therapies to more or less rid us of disease, it actually revealed that your genetic makeup plays a much smaller role than anyone imagined. Your genes, as it turns out, are only responsible for about 10 percent of diseases.1
The remaining 90 percent are induced by environmental factors, and researchers are now realizing that your microbiome may be among the most important factors, as genes are turned on and off depending on which microbes are present!
Emerging science also shows that your microbiome can be rapidly altered, for better or worse, based on factors such as diet, lifestyle, and chemical exposures.
This is a double-edged sword, no doubt, considering how many of our modern conveniences (such as processed foods, antibiotics, and pesticides) turn out to be extremely detrimental to our gut flora.
On the other hand, your diet is one of the easiest, fastest, and most effective ways to improve and optimize your microbiome. So the good news is that you have a great degree of control over your health destiny.
How Gut Bacteria Influence Your Weight
The foods known to produce metabolic dysfunction and insulin resistance (such as processed foods, fructose/sugar, and artificial sweeteners) also decimate beneficial gut bacteria, and it may well be that this is a key mechanism by which these foods promote obesity.
Chemicals may also contribute to your weight problem by way of your gut microbiome.
A study found that one microbe called Akkermansia muciniphila helps ward off obesity, diabetes, and heart disease by lowering blood sugar, improving insulin resistance, and promoting a healthier distribution of body fat.
Fiber-Digesting Bacteria Also Influence Your Immune Function

Previous research has also shown that gut microbes specializing in fermenting soluble fiber play an important role in preventing inflammatory disorders, as they help calibrate your immune system. Specifically, the byproducts of this fermenting activity help nourish the cells lining your colon, thereby preventing leaky gut — a condition in which toxins are allowed to migrate from your gut into your blood stream.

The inflammatory response actually 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. So in order to address chronic inflammation and inflammatory diseases, it’s important to nourish your gut flora with the right foods. Examples include traditionally fermented foods and raw foods, and especially those high in fiber.
Sugar, on the other hand, feeds fungi that produce yeast infections and sinusitis. Researchers have also linked high-sugar diets to memory – and learning impairments, courtesy of altered gut bacteria. According to lead author Dr. Kathy Magnusson:
“We’ve known for a while that too much fat and sugar are not good for you. This work suggests that fat and sugar are altering your healthy bacterial systems, and that’s one of the reasons those foods aren’t good for you. It’s not just the food that could be influencing your brain, but an interaction between the food and microbial changes.”

Fiber and Fermented Foods Are Key Components of a Healthy Diet

While it’s virtually impossible to determine the composition of an ideal microbiome, seeing how our gut flora is as individual as our finger print, what we do know is that a healthy diet is key for optimizing your individual microbiome. We’ve also come to realize that fermented foods and foods high in fiber are very important components of a healthy diet, as these foods help nourish a wide variety of beneficial bacteria.
Such foods have been part of the human diet since ancient times, and replacing them with chemically altered and “sterilized” processed foods has led to many of our current health problems. Traditional sauerkraut, for example, has been identified as a heart-healthy superfood.

It helps in the following ways:
• Reduced cholesterol levels
• Reduced triglyceride levels
• Significantly increased levels of two powerful antioxidants known as superoxide disumutase (SOD) and glutathione
• Decreased the degradation of fats in the body (a process known as lipid peroxidation)”

Are You Getting Enough Fiber and Fermented Foods in Your Diet?

Ideally, include a variety of fermented foods and beverages in your diet, because each food will inoculate your gut with a mix of different microorganisms. There are many fermented foods you can easily make at home, including:
• Fermented vegetables
• Chutneys
• Condiments, such as salsa and mayonnaise
• Cultured dairy, such as yogurt, kefir, and sour cream
• Fish, such as mackerel and Swedish gravlax
As for fiber, dietary guidelines call for 20 to 30 grams of fiber per day. I believe an ideal amount for most adults is likely much higher, perhaps twice as much. Many whole foods, especially fruits and vegetables, naturally contain both soluble and insoluble fiber.
This is ideal, as both help feed the microorganisms living in your gut. So to maximize your health benefits, focus on eating more vegetables, nuts, and seeds.

I am a major fan of fiber especially soluble fibers like psyllium as they not only serve as a prebiotic for your microbiome but are also metabolized to short chain fatty acids like butyrate, propionic and acetate that nourish your colonic cells. They are also converted to ketones that nourish your tissues.
I personally consume nearly 100 grams of fiber a day and about 2 tablespoons of organic psyllium three times a day that provides about 25 grams of soluble fiber. The other 75 percent of my fiber comes primarily from vegetables and seeds.

Swapping Gut Bacteria May Help Reverse Type 2 Diabetes

Type 2 diabetes is another common health problem that can be traced back to impaired gut flora. Studies have found that the microbial composition in diabetics differ from non-diabetics. In particular, diabetics tend to have fewer Firmicutes and more plentiful amounts of Bacteroidetes and Proteobacteria, compared to non-diabetics. A positive correlation for the ratios of Bacteroidetes to Firmicutes and reduced glucose tolerance has also been found.
A researcher in Amsterdam, Dr. Max Nieuwdorp, has published a number of studies looking at changes in the microbiome that are characteristic of type 2 diabetes. In one trial, he was able to reverse type 2 diabetes in all of the 250 study participants by doing fecal transplantations on them. Remarkable as it may sound, by changing the makeup of the gut bacteria, the diabetes was resolved.
Even more interesting, type 1 diabetes (insulin dependent) in young children also tends to be preceded by a change in gut bacteria. This makes sense as your gut flora control about 80 percent of your immune response and type 1 diabetes is an autoimmune disease. The good news is that researchers have found that certain microbes can actually help prevent type 1 diabetes, suggesting your gut flora may indeed be an epigenetic factor that plays a significant role in this condition.

Your Gut Is Your Second Brain

The quality, quantity, and composition of the bacteria in your gut have enormous influence on your brain. For example, studies have found that autistic children have distinctly different microbiome compared to healthy children. Notably, they tend to have fewer beneficial bacteria such as Bifidobacterium.
This again goes back to the fact that gut microbes help maintain the integrity of your gut lining. As explained by Dr. Perlmutter, many of the factors that affect permeability of the blood-brain barrier are similar to those that affect the gut, which is why leaky gut can lead to neurological diseases as easily as it can manifest as some other form of autoimmune disorder.

Mood Disorders May Be Rooted in Impaired Microbiome Too

Depression is increasingly starting to be viewed as a symptom of poor gut health, and therein may lie the real cure as well … For example, in one recent study researchers found that fermented foods and drinks helped curb social anxiety disorder in young adults.
Previous trials have also demonstrated that probiotics can help ease both anxiety and depression. In another study, 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. Another recent study found that high-glycemic foods (including those high in refined grains and added sugar) were associated with higher odds of depression.

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.
You will be pleased to know 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:

Eat plenty of fermented foods. Healthy choices include lassi, fermented grass-fed organic milk such as kefir, natto (fermented soy), and fermented vegetables.

Take a probiotic supplement.
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, lack of exposure to the outdoors can in and of itself cause your microbiome to become “deficient.”

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. Research shows 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 that washing your dishes by hand leaves more bacteria on the dishes than dishwashers do, and that eating off these less-than-sterile dishes may actually decrease your risk of allergies by stimulating your immune system.

Avoid:

Antibacterial soap, as they kill off both good and bad bacteria, and contribute to the development of antibiotic-resistance.

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.

Packaged foods, as they can contain emulsifiers such as polysorbate 80, lecithin, carrageenan, polyglycerols, and xanthan gum which appear to have an adverse effect on your gut flora. Unless 100% organic, they may also contain GMO’s that tend to be heavily contaminated with pesticides such as glyphosate.

Processed foods. Excessive sugars, along with otherwise “dead” nutrients, feed pathogenic bacteria.

Artificial sweeteners have also been found to alter gut bacteria in adverse ways.

Be Healthy always.