Feed Your Gut Microbes Well, Lest They Feed on You

feeding gut microbes

Story at-a-glance

  • Researchers have found a functional link between certain gut bacteria and the onset of Parkinson’s disease — further evidence suggesting the disease may originate in your gut, not your brain
  • One mechanism by which your microbiome can make you more or less prone to disease is by regulating gene expression, and this mechanism is primarily driven by dietary influences
  • An unbalanced microbiome predisposes you to bowel diseases. Research shows dietary fiber helps fight mucus-devouring bacteria in your gut, thereby preventing many gut problems and bowel diseases


This is an older article that may not reflect Dr. Mercola’s current view on this topic. Use our search engine to find Dr. Mercola’s latest position on any health topic.

By Dr. Mercola

The truth of the old adage that "you are what you eat" is becoming increasingly clear, the more we learn about the microbiome — the colonies of microorganisms, including bacteria, viruses and fungi that live in your gut.1

It's been well-established that your gut acts as a second brain, providing all sorts of input to your brain. This input not only affects your mood and general well-being, but also your immune responses and nervous system functioning.

Your microbiome is individual to you, much like your fingerprints, and is a reflection of who your parents were, where you've been, who you spend intimate time with, what you eat, how you live, whether or not you're interacting with the earth (gardening, for example) and much more.

Research shows that your gut microbiome plays a role in the development of many diseases and health conditions, including obesity and difficulty maintaining weight loss after dieting,2,3 depression and multiple sclerosis (MS), just to name a few.4

Parkinson's Disease May Originate in Your Gut

Most recently, researchers say they've found a "functional link" between certain gut bacteria and the onset of Parkinson's disease.5,6 In short, specific chemicals produced by certain gut bacteria worsen the accumulation of proteins in the brain associated with the disease.

The link is so intriguing; they suggest the best treatment strategy may be to address the gut rather than the brain using specific probiotics rather than drugs. Indeed, mounting research suggests we may have had the wrong idea about Parkinson's all along.

Parkinson's patients have been known to struggle with constipation for as long as a decade before neurological symptoms appear, and another recent study found that proteins implicated in the disease actually travel from the gut into the brain.7

Once clumped together in the brain, these proteins, called alpha-synclein, form fibers that damage the nerves in your brain, resulting in the tell-tale tremors and movement problems exhibited by Parkinson's patients.

In fact, the researchers believe alpha-synclein producing gut bacteria not only regulate, but are actually required in order for Parkinson's symptoms to occur.

Protein Clumps Implicated in Parkinson's Originate in the Gut

In this study, synthetic alpha-synuclein was injected into mice's stomachs and intestines. After seven days, clumps of alpha-synuclein were observed in the animals' guts. Clumping peaked after 21 days.

By then, clumps of alpha-synuclein were also observed in the vagus nerve, which connects the gut and brain. As noted by Science News:8

"Sixty days after the injections, alpha-synuclein had accumulated in the midbrain, a region packed with nerve cells that make the chemical messenger dopamine. These are the nerve cells that die in people with Parkinson's, a progressive brain disorder that affects movement.

After reaching the brain, alpha-synuclein spreads thanks in part to brain cells called astrocytes, a second study suggests. Experiments with cells in dishes showed that astrocytes can store up and spread alpha-synuclein among cells …"

Over time, as these clumps of alpha-synuclein started migrating toward the brain, the animals began exhibiting movement problems resembling those in Parkinson's patients.

Findings such as these suggest that, at least in some patients, the disease may actually originate in the gut, and chronic constipation could be an important early warning sign. Pesticides have also been linked to Parkinson's and the authors suggest the chemicals may produce this effect by affecting gut bacteria.

The good news is constipation can be remedied through diet (a listing of recommendations is provided at the end of this article), exercise and squatting.

Gut Microbes Influence Your Genetic Expression

Gut bacteria influence your health through a variety of different ways. One mechanism by which your microbiome can make you more or less prone to disease is by regulating gene expression, and this mechanism is primarily driven by dietary influences.

Research shows that eating a plant-rich diet nourishes bacteria that turn "on" certain host genes that help protect against disease.9 As described by Medical News Today:10

"Interactions with the environment do not change the genes, but they alter their expression by switching them on and off through chemical tags on the DNA.

The complete set of genetic material contained in our genes is called the genome, and the multitude of molecules that tell the genome what to do is called the epigenome …

For their study, the researchers used mice raised on two different diets: one rich in plant carbohydrates (mimicking a human diet rich in fruits and vegetables) and the other high in simple sugars and fats (mimicking a Western diet).

The researchers found that a small group of short-chain fatty acids — metabolites produced when gut bacteria ferment nutrients from plants — were communicating with the cells of the host animals through the epigenome …

[T]he Western-style diet prevents many of the epigenetic changes that occur in the plant-rich diet."

Bacteria Are Important Epigenetic Communicators

In short, these findings suggest that short-chain fatty acids produced by bacteria that feed on plant fiber are major epigenetic communicators. It also confirms that the typical Western diet, high in sugars and low in fiber, is a poor source of nutrients for beneficial gut microbes.

As a result, you end up with fewer bacteria to communicate with your DNA, which makes you more prone to disease. Bacteria are also very competitive, and bacterial proteins kill rival bacteria to maintain the upper hand.11

If pathogenic bacteria gain too much turf, disease becomes more likely, whereas if beneficial bacteria are the ones winning the turf war you end up with greater protection against disease.

Fiber Prevents Mucus-Munching Gut Bacteria From Ravaging Your Intestines

Case in point: An unbalanced microbiome may predispose you to bowel diseases, and recent animal research12,13 highlights this connection by showing how dietary fiber helps fight flesh-eating bacteria in your gut, thereby preventing many gut problems and bowel diseases.

The researchers transplanted 14 well-known human gut bacteria into mice bred to be microbe-free. The mice were then starved of fiber, which resulted in fiber-eating microbes dwindling in numbers, being replaced instead by bacteria that fed on the mucus lining the animals' guts.

When this protective mucus layer is thinned, either through poor diet or as in this case due to mucus-munching bacteria, your gut becomes more susceptible to infections, such as colitis (inflammation of your colon) and leaky gut.

Indeed, when the fiber-starved mice were infected with Citrobacter rodentium — an E. coli-like bacteria — the pathogens flourished and many of the mice became severely ill.

Meanwhile, those whose diet contained 15 percent natural plant fiber had a thick layer of mucus preventing the Citrobacter rodentium infection from taking hold.

Fiber Starvation Is a Major Driver of Gut Problems and Bowel Diseases

In a recent audio interview, Eric Martens, a microbiologist at the University of Michigan, discusses this research and its implications.14

"The lesson we're learning from studying the interaction of fiber, gut microbes and the intestinal barrier system is that if you don't feed them, they can eat you," he says.15 As reported by Newsweek:16

"The team tried to rectify the problem by feeding the mice with prebiotics. They found that while real unprocessed fiber did the trick, when the mice were fed processed, supplement fiber, such as inulin powder, it didn't work nearly as well …

If we ate more fiber and increased the diversity and health of our microbes this could prevent many diseases. It also suggests that real plant food as a source of fiber is better than processed or refined fiber produced industrially. This has implications for the food industry — and as with vitamin supplements reinforces the view that … natural is best.

The new study also helps us understand why people on permanent junk food diets do so badly … This new work confirms that fiber starvation is the major factor affecting the microbes — not just fat and sugar overload."

Nutritional Ketosis: Powerful Solution for Neurodegenerative Diseases

Improving the health of your mitochondria through teaching your body to burn fat as your primary fuel is one of the most effective strategies you can use for diseases like Alzheimer's, Parkinson's and ALS. If you are interested in more details in this application of nutritional ketosis, I suggest you read this recent scientific review, "Ketogenic Diet in Neuromuscular and Neurodegenerative Diseases."17

My new book, "Fat for Fuel," which comes out in May, will teach you in great detail how to do this. In the meantime, you can review previous articles that I have written on this. The goal is to generate large amounts of ketones so your brain can use them and radically reduce the amount of reactive oxygen species.

Once you have achieved nutritional ketosis, then you can start using short-chained MCT oils like caprylic acid, which will help generate even more ketones. While there are a number of ketone salts on the market now, in the near future ketone esters, which are far more potent, will be commercially available. I don't typically recommend them but for those with advanced neurodegenerative diseases, it makes perfect sense.

If you want to learn more from the leading experts in nutritional ketosis you can join me for the best nutritional ketosis event in San Diego in August 2017. There will be around 500 to 1,500 people at this event. You can view the speakers and see that this is an extraordinary panel.

If you want a more intimate setting, there will be a group of 200 that will be attending a smaller event in West Palm Beach, Florida on January 20 to 22, 2017. Escape the cold and spend some time learning this crucial health information.

You can see all the speakers here. Dominic D'Agostino, Ph.D., Dr. Zac Bush and I will be there all three days. Additionally, Miriam Kalamian, who is helping me write my next book on this topic, will be there. She is Thomas Seyfried's nutritionist and has helped over 400 cancer patients implement this program, and for many it would be worth it just to see her.

9 Ways to Improve Your Microbiome

Getting back to gut bacteria, by far the easiest way to optimize your microbiome is through your diet. Following are nine dietary changes that will contribute to a healthier gut by nourishing beneficial bacteria and dissuading the proliferation of health-harming microbes:18

Diversify! Eating a wide range of different foods — especially plant-based ones — will ensure maximum diversification of gut bacteria. Recent estimates suggest 75 percent of the standard Western diet is produced from a mere 12 plants and five animal species.19

This — besides being high in sugar and low in fiber — helps explain why the Western diet makes you more prone to disease.

Increase consumption of fresh vegetables, legumes, beans and fruits to optimize your fiber intake, and aim for variety to ensure diversification of bacteria. Leafy green vegetables contain a certain kind of sugar that feeds healthy gut bacteria, which in turn help crowd out more harmful microbes.20 The sugar, called sulfoquinovose (SQ), is produced in plants by photosynthesis.

Some of the microbes in your gut 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, thereby preventing health problems associated with leaky gut syndrome. The most important fermentation byproducts are short-chain fatty acids, like butyrate, propionate and acetate.

These short-chain fats help nourish and recalibrate your immune system, thereby helping to prevent inflammatory disorders such as asthma and Crohn's disease.21,22 These fats also increase specialized immune cells called T regulatory cells, which help prevent autoimmune responses.

Eat traditionally fermented and cultured foods such as fermented vegetables, yogurt, kefir, kimchi and kombucha. The fermenting process results in foods that are naturally high in live, beneficial bacteria, and it's easy and inexpensive to do at home.

Eat prebiotic foods such as resistant starches found in unripe bananas, papayas and mangos, as well as white beans, lentils, seeds and products like potato starch, tapioca starch, brown rice flour and Shirataki noodles.

Consider a fiber supplement. I believe 25 to 50 grams of fiber per 1,000 calories consumed is a healthy goal. If you're having trouble getting enough fiber in your diet, consider taking organic psyllium seed husk, flax hemp or chia seeds.

Avoid artificial sweeteners. Research shows aspartame results in higher levels of disease-causing bacteria such as Clostridium and Enterobacteriaceae in your intestines.23

Eat polyphenol-rich foods. Like prebiotics, polyphenols help nourish beneficial gut bacteria. Good sources include raw cacao (dark chocolate), grape skins, Matcha green tea, onions, blueberries and broccoli.

Take a high-quality probiotic supplement. I recommend looking for a probiotic supplement that fulfills the following criteria, to ensure quality and efficacy:

  • The bacteria strains in the product must be able to survive your stomach acid and bile, so they reach your intestines alive in adequate numbers.
  • The bacteria strains must have health-promoting features.
  • The probiotic activity must be guaranteed throughout the entire production process, storage period and shelf life of the product.

Avoid cesarean section and be sure to breastfeed for six months or longer to optimize your baby's microbiome. Human breast milk contains oligosaccharides (unique complex chains of sugars), the primary function of which is to nourish your baby's healthy gut flora.

These are completely absent in commercial infant formulas. When both vaginal birth and breastfeeding are lacking, your child can end up with severely compromised gut flora.

Your Gut Flora Is Perpetually Under Attack

Your microbiome — and therefore your physical and mental health — are continuously affected by your environment, and by your diet and lifestyle choices. If your gut bacteria are harmed and thrown out of balance (dysbiosis), all sorts of illnesses can result, both acute and chronic.

Unfortunately, your fragile internal ecosystem is under nearly constant assault today, making avoidance of certain influences just as important as nourishing your microbiome with a healthy diet. Some of the factors posing the gravest dangers to your microbiome include:

Refined sugar, especially processed high-fructose corn syrup (HFCS)

Genetically engineered (GE) foods (extremely abundant in processed foods and beverages)

Agricultural chemicals, such as herbicides and pesticides. Glyphosate appears to be among the worst

Conventionally raised meats and other animal products; CAFO animals are routinely fed low-dose antibiotics and GE livestock feed


Antibiotics (use only if absolutely necessary, and make sure to reseed your gut with fermented foods and/or a good probiotic supplement)

NSAIDS (Nonsteroidal anti-inflammatory drugs) damage cell membranes and disrupt energy production by mitochondria

Proton pump inhibitors (drugs that block the production of acid in your stomach, typically prescribed for GERD, such as Prilosec, Prevacid and Nexium)

Antibacterial soap

Chlorinated and/or fluoridated water



Exercise Also Helps Promote Bacterial Diversification

Last but not least, research shows that exercise also increases the amount and diversity of gut bacteria, which may have immune boosting effects.24,25,26 Compared to controls, athletes (in this case rugby players) were found to have a "higher diversity of gut micro-organisms ... which in turn positively correlated with protein consumption and creatine kinase," the authors note.

One particular species of bacteria found in greater amounts in the athletes' gut has been linked to reduced risk of obesity and systemic inflammation. The rugby players were chosen specifically because athletes tend to adhere to a more extreme diet than the average person, and they also exercise more intensely — in this case, they trained several hours a day.

This is not necessarily healthy and likely is not for most, nevertheless that is what they studied. The researchers wanted to explore the degree to which exercise and diet in combination might affect the gut microbiota. The controls, meanwhile, consisted of two groups: men with a normal body mass index (BMI) who engaged in occasional light exercise, and sedentary men who were overweight or obese. In conclusion, the researchers stated that:27

"The results provide evidence for a beneficial impact of exercise on gut microbiota diversity but also indicate that the relationship is complex and is related to accompanying dietary extremes."


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