Monday, June 24, 2024


“You may choose to look the other way, but you can never say again that you did not know.”

— William Wilberforce


Modern Life Depletes Your Gut Microbes

Your intestinal microflora—aka your microbiome—is an integral part of your immune system, and over the past several years, research has revealed that microbes of all kinds—bacteria, fungi, and even viruses—play instrumental roles in the functioning of your body. For example, beneficial bacteria, also known as probiotics, have been shown to:

• Counteract inflammation and control the growth of disease-causing bacteria
• Produce vitamins, amino acids (protein precursors), absorb minerals, and eliminate toxins
• Control asthma and reduce risk of allergies
• Benefit your mood and mental health
• Impact your weight, for better or worse

The composition of the microbiome varies from person to person based on factors such as diet, health history, antibiotic exposures, geographic location, and even ancestry, and it’s readily influenced by diet, chemical exposures, hygiene, and other environmental factors.

In fact, it’s become increasingly clear that destroying your gut flora with antibiotics and pharmaceutical drugs, harsh environmental chemicals, and toxic foods is a primary factor in rising disease rates.

For all of these reasons, and more, I recommend a diet rich in whole organic, unprocessed foods along with traditionally cultured or fermented foods and plenty of fiber.

A high-quality probiotic supplement can also be a helpful ally to restore a healthy balance to your gut flora—especially when taking antibiotics, and/or when eating processed foods, as both of these tend to decimate the colonies of beneficial microbes in your gut.

Modern Lifestyle Depletes Beneficial Microbes

A study1 2 comparing the microbiome of the Yanomami—an indigenous tribe living in remote areas of the Amazon jungle—against those of Americans; a group of Venezuelan Amazonian indigenous people called the Guahibo; and people in Malawi in southern Africa, reveals that the modern lifestyle has dramatically altered people’s microbiome.

For all its conveniences, it takes a considerable toll on the microbes in your gut, which in turn can have far-reaching health consequences. For example, recent research3 4 suggests that repeated use of antibiotics may raise your risk for type 2 diabetes by altering the composition of your gut bacteria.

After analyzing health data from one million Britons, strong dose-dependent correlations were found between the use of certain antibiotics—penicillins, cephalosporins, quinolones, and/or macrolides specifically—and diabetes incidence. The correlation held even when other contributing factors were taken into account.

• Two to five courses of penicillin increased diabetes risk by 8%
• More than five courses of penicillin increased the risk by 23%
• Two to five courses of quinolones increased the diabetes risk by 15%
• More than five courses of quinolones increased the risk by 37%

Interestingly, even the hunter-gatherer Yanomami tribe—which had never come in contact with outsiders prior to the researchers’ arrival, and have never been exposed to antibiotics—were found to harbor microbes with antibiotic-resistant genes.

According to The Star:5

This adds persuasive evidence that bacteria already have the ability to resist antibiotics, even prior to being attacked by pharmaceutical drugs—a finding that underscores the urgency of the antibiotic crisis, where pathogenic bacteria are developing strategies for defeating even the most powerful drugs on the market.

Americans Have Lost a Wide Variety of Health Protective Gut Microbes

In all, the Yanomami had about 50% greater microbial diversity than American subjects, and 30-40% more diversity than the Guahibo and the Malawians, the latter two of which have adopted some Western lifestyle components, such as living indoors and using antibiotics.

According to one of the authors:6

As cultures around the world become more ‘Western,’ they lose bacteria species in their guts… At the same time, they start having higher incidences of chronic illnesses connected to the immune system, such as allergies, Crohn’s disease, autoimmune disorders, and multiple sclerosis.

So the big question is: Are these two facts related? It’s not clear if more diversity in the microbiome is healthier. But maybe we have lost species with important functions.

Sophisticated Sanitation May Be More Detrimental to Your Microbiome Than Previously Thought

While antibiotics are indeed potent adversaries when it comes to maintaining a healthy diversity of microbes in your gut, other factors also play a significant role.

Pesticides, processed food, Caesarean sections, and an over-reliance on antimicrobial products have also contributed to the dramatic decline in the range of microbes occupying people’s guts.

In fact, another recent study7 suggests that sophisticated sanitation may be a greater factor than antibiotics when it comes to destroying microbial diversity.

Here, researchers looked at the microbiome of two indigenous populations in Papua New Guinea who, unlike the Yanomami tribe, regularly use antibiotics, yet still have significant microbial diversity in their guts. These two groups were found to have about 47 different species that Americans don’t have.

The data collected in this study suggests that lack of sanitation may be the reason for the Papua New Guineans’ microbial diversity. NPR reports:8

Sophisticated sanitation and hygiene in Western society might be limiting the species that end up in our guts… Bacteria spread more easily from person to person in Papua New Guinea because the communities don’t have sewage systems and clean drinking water. ‘Clean drinking water is one of the most important achievements of Western culture,’ [lead author Jens] Walter says. ‘It prevents the spread of infections, but it also prevents the easy exchange of our microbiomes.’

The Importance of Fiber for a Healthy Microbiome

One of the quickest and easiest ways to improve your gut health is via your diet. Beneficial microbes tend to feed on foods that are known to benefit health and vice versa. Sugar, for example, is a preferred food source for fungi that produce yeast infections and sinusitis, whereas healthy probiotic-rich foods like fermented vegetables boost populations of health-promoting bacteria, thereby disallowing potentially pathogenic colonies from taking over.

Fiber is also important for a healthy microbiome. 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. Some of these fermentation byproducts also help calibrate your immune system, thereby preventing inflammatory disorders such as asthma and Crohn’s disease.9 10

As reported by Scientific American,11 recent research shows that simply eating more fiber can shift your microbial profile into one that is correlated with leanness. Fiber has long been considered a factor that promotes weight loss, and its impact on your gut bacteria appears to be one key mechanism responsible for this effect.

Other research has shown that microbes starved of fiber can begin feeding on the mucus lining of your gut, thereby triggering inflammation, which may promote or exacerbate any number of diseases, including ulcerative colitis.12 The study also found that in order to avoid this, you need to eat fiber every single day.

Research published a couple of years ago also showed that common bacterial metabolites—short-chain fatty acids (SCFAs)—selectively expand regulatory T cells called Tregs, which are critical for regulating intestinal inflammation.13 According to one of these studies:14

Treg cells suppress the responses of other immune cells, including those that promote inflammation. This finding provides a new link between bacterial products and a major anti-inflammatory pathway in the gut.” Other research15 16 has linked Tregs—which are fed by dietary fiber—to the prevention and reversal of metabolic syndrome, in part by stimulating oxidative metabolism in your liver and adipose tissue. So, as you can see, fiber appears to nourish microbes that in turn provide a variety of health benefits via a number of different pathways.

Probiotics Again Found Beneficial for Symptoms of Depression

Beneficial microbes also play an important role in your mental health—some researchers have even proposed that probiotics might serve the same role as antidepressants. Most recently, Psychologists Laura Steenbergen and Lorenza Colzato from the Leiden Institute of Brain and Cognition published a paper17 showing that 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.

As explained by Dr. Steenbergen:

Rumination is one of the most predictive vulnerability markers of depression. Persistent ruminative thoughts often precede and predict episodes of depression.

According to Dr. Colzato:

Even if preliminary, these results provide the first evidence that the intake of probiotics may help reduce negative thoughts associated with sad mood. As such, our findings shed an interesting new light on the potential of probiotics to serve as adjuvant or preventive therapy for depression.

Beware: Polysorbate 80 and Other Emulsifiers Can Have Adverse Effect on Your Gut Flora

A processed food diet is anathema to gut health for a number of reasons. First of all, processed foods tend to be loaded with genetically engineered ingredients of questionable safety, including corn-based fructose, which has been repeatedly shown to promote metabolic dysfunction to a greater degree than other sugars. Ingredients may also be contaminated with glyphosate (recently classified as a Class 2 A carcinogen), which can decimate gut health in a number of different ways.

Recent research published in the journal Nature18 also suggests that polysorbate 80, an emulsifier found in many processed foods (as well as vaccines) can alter your intestinal terrain, thereby promoting obesity and inflammatory health conditions. As reported by Prevent Disease:19

“The study used mice to test the effect of two common emulsifiers—carboxymethylcellulose and polysorbate-80—on the microbiome make up and metabolism, finding that relatively low-level concentrations of the emulsifiers resulted in distinct alterations to the gut microbial ecosystem (microbiota) and led to low-grade inflammation and the onset of metabolic syndrome…

The research team reported that the emulsifier-induced metabolic syndrome was associated with microbiota encroachment, altered species composition and increased pro-inflammatory potential. ‘These results support the emerging concept that perturbed host-microbiota interactions resulting in low-grade inflammation can promote adiposity and its associated metabolic effects,’ wrote the team.

Moreover, they suggest that the broad use of emulsifying agents might be contributing to an increased societal incidence of obesity/metabolic syndrome and other chronic inflammatory diseases.

Optimizing Your Microbiome May Be One of Your Most Important Disease Prevention Strategies

Optimizing your gut flora may be one of the most important things you can do for your health, and the good news is that this isn’t very difficult. However, you do need to take proactive steps. To optimize your microbiome both inside and out, consider the following recommendations:

• 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.

• 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

• Boost your soluble and insoluble fiber intake, focusing on vegetables, nuts, and seeds, including sprouted seeds.

• 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. According to the hygiene hypothesis, 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.

• 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. Research23 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.

• 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.


• Antibiotics, unless absolutely necessary (and when you do, make sure to reseed your gut with fermented foods and/or a probiotic supplement). And while some researchers are looking into methods that might help ameliorate the destruction of beneficial bacteria by antibiotics,20 21 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.

• 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.

• Chlorinated and/or fluoridated water.Processed foods. Excessive sugars, along with otherwise “dead” nutrients, feed pathogenic bacteria. Food emulsifiers such as polysorbate 80, lecithin, carrageenan, polyglycerols, and xanthan gum also appear to have an adverse effect on your gut flora.22 Unless 100% organic, they may also contain GMOs that tend to be heavily contaminated with pesticides such as glyphosate.

• Agricultural chemicals, glyphosate (RoundUp) in particular.

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

Note: This article was reprinted with the author’s permission. It was originally published on Dr. Mercola’s website at


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