Your Microbiome May Be Key Factor Determining Your Health and Longevity

Healthy Diet

Story at-a-glance -

  • Your microbiome may be a primary factor determining your health and longevity
  • Specific species of bacteria appear to have specialized functions and abilities to prevent disease; Faecalibacterium prausnitzii appear to play an important anti-inflammatory role in the human microbiota
  • While genetic factors can predispose you to inflammatory bowel diseases like Crohn’s, research shows it’s actually the loss of specific anti-inflammatory microbes that ultimately allow the disease to blossom

By Dr. Mercola

Mounting research suggests that your microbiome—colonies of bacteria, viruses, and other microbes living in your gut—may be one of the preeminent factors determining your health and longevity. 

Feeding health-promoting gut bacteria with a healthy diet, avoiding hospitals (which are hotbeds for drug-resistant bacteria), and boycotting processed foods and animal foods raised in confined animal feeding operations (CAFOs)—both of which tend to have an adverse effect on your microbiome—may be keystone strategies for longevity.

Beneficial Microbes Prevent Disease

A number of studies have begun to identify specific species of bacteria that appear to have specialized functions and abilities to prevent disease.

For example, in one study, DNA analysis of diseased sections of intestine removed from patients suffering from Crohn's disease revealed that one particular bacterium, Faecalibacterium prausnitzii, was lower than normal.

While researchers have linked the presence of specific bacteria to various diseases, this finding suggests certain species may be actively involved in preventing certain disease states.

When Faecalibacterium prausnitzii was transferred into mice, it protected them against induced intestinal inflammation, suggesting this particular species may play an important anti-inflammatory role in the human microbiota. As reported by Scientific American:1

"Each of us harbors a teeming ecosystem of microbes that outnumbers the total number of cells in the human body by a factor of 10 to one and whose collective genome is at least 150 times larger than our own.

In 2012 the National Institutes of Health completed the first phase of the Human Microbiome Project, a multimillion-dollar effort to catalogue and understand the microbes that inhabit our bodies. The microbiome varies dramatically from one individual to the next and can change quickly over time in a single individual...

[A] burgeoning body of research suggests that the makeup of this complex microbial ecosystem is closely linked with our immune function. Some researchers now suspect that, aside from protecting us from infection, one of the immune system's jobs is to cultivate, or 'farm,' the friendly microbes that we rely on to keep us healthy."

Specific Microbes with Health-Promoting Functions

One group of microbes that appear important for maintaining healthy immune function is the clostridial group of microbes—ironically enough, this group is related to Clostridium difficile, which can cause severe and life-threatening intestinal infections.

But whereas C. difficile prompts chronic inflammation, the clostridial clusters help maintain a healthy and well-functioning gut barrier, preventing inflammatory agents from entering your bloodstream.

The featured research suggests that while certain genetic factors can predispose you to inflammatory bowel diseases like Crohn's, it's actually the loss of anti-inflammatory microbes that ultimately allow the disease to blossom. As noted by Scientific American:2

"[A]lthough... other good bacteria besides F. prausnitzii exist, this similarity hinted at a potential one-size-fits-all remedy for Crohn's and possibly other inflammatory disorders: restoration of peacekeeping microbes...

The tremendous microbial variation now evident among people has forced scientists to rethink how these communities work. Whereas a few years ago they imagined a core set of human-adapted microbes common to us all, they are now more likely to discuss core functions—specific jobs fulfilled by any number of microbes."

Inflammatory bowel diseases are not the only health problems affected alterations in your microbiome. Other research has found that onset of type 1 diabetes (an autoimmune disease) in young children tends to be preceded by a change in gut bacteria.

Previous research has also found that certain microbes can help prevent type 1 diabetes, suggesting your gut flora may indeed be an epigenetic factor that plays a significant role in this condition.

Research also suggests there's a connection between certain types of bacteria and body fat that produces a heightened inflammatory response that contributes to the metabolic dysfunction associated with type 2 diabetes.

In addition, preliminary research3  presented in 2010 revealed that transplanting fecal matter from healthy thin people into obese people with metabolic syndrome led to an improvement in insulin sensitivity, again suggesting that such conditions can be effectively addressed by correcting the microbial composition of your gut.    

Antibiotic Overuse Has Fueled More Deadly Infections

Just as some bacteria help prevent disease, others promote it. One such bacterium is Clostridium difficile,4 the prevalence of which has steadily risen as a result of massive antibiotic overuse, especially in farm animals.

According to the latest statistics released by the Centers for Disease Control and Prevention (CDC), half a million Americans were infected with Clostridium difficile in 2011, and 29,000 of them died within a month of diagnosis.5,6 ,7 Besides the human death toll, fighting C. difficile costs hospitals a staggering $4.8 billion per year.8

Hospitals are the number one location where you're apt to contract this type of infection, but the CDC also notes that many appear to have contracted it during visits to doctor's and dental offices.9 Nursing homes are also hotbeds for this hard-to-treat infection. As reported by Reuters:10

"The study11 by the US Centers for Disease Control and Prevention focused on the Clostridium difficile bacterium, which can cause deadly diarrhea. The findings... highlight how overprescription of antibiotics has fueled a rise in bacteria that are resistant to treatment.

People who take antibiotics are most at risk of acquiring C. difficile because these medications also wipe out 'good' bacteria that protect a healthy person against the infection.

'Antibiotics are clearly driving this whole problem,' Clifford McDonald, CDC senior advisor for science and integrity, said... One in every three infections occurred in patients 65 and older, the study found, with more than 100,000 C. difficile cases found in US nursing homes."

Fecal Transplants Found Effective Against C. Difficile Infections

One novel treatment that has been shown to be quite effective against C. difficile infections is the fecal transplant.12 Fecal microbiota transplant (FMT) is a relatively simple procedure that involves taking feces from a healthy donor and transferring it to the patient during a colonoscopy.

The patient basically receives a transplanted population of healthy flora that can go to work correcting any number of gastrointestinal problems, including C. difficile infection.

According to Dr. Mark Mellow, medical director of the Digestive Health Center at Integris Baptist Medical Center in Oklahoma City, fecal transplants lead to rapid resolution of symptoms in 98 percent of patients with Clostridium difficile who have not responded to other treatments.

While I believe fecal transplantation can be lifesaving in some circumstances, I want to make it clear that you will likely never have to resort to receiving donated feces if you address your gut health on a daily basis—by avoiding factors that kill off your beneficial gut bacteria, and continuously "reseeding" your gut through a healthy diet and regular use of fermented vegetables. Also, any time you take an antibiotic, it is important to take probiotics and/or fermented vegetables to repopulate the beneficial bacteria in your gut that are killed by the antibiotic, right along with the pathogenic bacteria. If you don't, you're leaving the door wide open for further health problems.

Beware of the Risks of Hospital-Acquired Infections

Hospitals are notorious hotbeds for drug-resistant disease, and hospital-acquired infections now affect one in 25 patients! Some of these infections are resistant to antibiotics, which is why avoiding hospitals, barring an acute, life-threatening condition, is good advice. You could enter with a minor ailment only to come out with one that is much worse...

In an effort to rein in some of these hospital-acquired drug-resistant infections, the US government is now finalizing new cleaning protocols for duodenoscopes13,14—camera-equipped flexible tubes that are threaded through your mouth, down your throat, through your stomach into the top of your small intestine. These reusable medical instruments have been implicated in a number of hospital-acquired drug-resistant outbreaks. In the latest outbreak, two of the seven patients affected died. The family members of one of them recently spoke out,15 chastising the hospital for not disclosing the risks of contracting such lethal infections upon admission.

According to Dr. John Allen, president of the American Gastroenterological Association:16 "This problem has been known since at least 1987. It certainly is disturbing that a fundamental design issue with these scopes would cause problems for this long."

Factory Farming Is a Major Promoter of Antibiotic-Resistant Pathogens

While antibiotics are certainly overprescribed in medicine, the primary driver of deadly "superbugs" is actually factory farming. Animals raised in CAFOs are routinely given low doses of antibiotics to promote growth and prevent diseases resulting from the crowded and unsanitary conditions of these facilities. Eighty percent of all antibiotics sold in the US are fed to livestock, so eating CAFO-raised foods is likely to be the greatest source of antibiotics for many people.

Not only may this low-dose ingestion of antibiotics have an adverse effect on the composition of your microbiome, thereby affecting your health, about half of all meats sold in American grocery stores have also been found to harbor drug-resistant bacteria that can cause severe food-borne illness. This is one of the reasons why I recommend eating only organically-raised, grass-fed or pastured meats and other animal products, such as dairy and eggs, as organic standards do not permit non-medical use of antibiotics.

Processed Food Ingredients That Decimate Your Microbiome

Besides avoiding CAFO-raised animal food products, you'd also be wise to reconsider your consumption of processed foods of all kinds. Not only are processed foods very high in added sugars—high fructose corn syrup in particular—but recent research has also found that emulsifiers found in processed foods have a very detrimental effect on your microbiome. As reported by Time Magazine:17

"Ingredients such as polysorbate 80, lecithin, carrageenan, polyglycerols, and xanthan and other 'gums,' all of which keep ingredients—often oils and fats—from separating. They are also used to improve the texture and shelf-life of many foods found on supermarket shelves, from ice cream and baked goods, to salad dressings, veggie burgers, non-dairy milks, and hamburger patties. Now, a new study18... suggests these ingredients may also be contributing to the rising incidence of obesity, metabolic syndrome, and inflammatory bowel disease by interfering with microbes in the gastrointestinal tract."

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 study19 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...

Optimizing Your Gut Flora May Be One of Your Most Important Disease Prevention Strategies

Overusing antibiotics on humans and animals that do not need them has led to a pandemic of antibiotic-resistant disease, and both medical and agricultural uses are in dire need of serious revisions. Unfortunately, such changes are slow in the making, and I advise you not to wait for the food and medical industry to correct the problem. It seems quite clear that 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 all sorts of disease—including infections. Reseeding your gut with beneficial bacteria is key for preventing pathogenic microbes and fungi from taking over and wreaking havoc with your health. To optimize your microbiome, keep the following recommendations in mind:

  • Eat plenty of fermented foods. Traditionally fermented and cultured foods are one of the best routes to optimal digestive health. Healthy choices include lassi, fermented grass-fed organic milk such as kefir, various pickled fermentations of cabbage, turnips, eggplant, cucumbers, onions, squash and carrots, and natto (fermented soy). Fermented vegetables, are an excellent way to supply beneficial bacteria back into our gut. And, unlike some other fermented foods, they tend to be palatable, if not downright delicious, to most people. As an added bonus, they can also a great source of vitamin K2 if you ferment your own using a starter culture that is optimized with bacterial strains that produce high levels of vitamin K2.
  • 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.

In addition to knowing what to add to your diet and lifestyle, it's equally important to know what to avoid, and these include:

Antibiotics, unless absolutely necessary (and when you do, make sure to reseed your gut with fermented foods and/or a probiotic supplement) Conventionally-raised meats and other animal products, as CAFO animals are routinely fed low-dose antibiotics, plus genetically engineered grains, which have also been implicated in the destruction of gut flora 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.20

Unless 100% organic, they may also contain GMOs that tend to be heavily contaminated with pesticides such as glyphosate
Chlorinated and/or fluoridated water Antibacterial soap Agricultural chemicals, glyphosate (Roundup) in particular