The nearly 100 trillion bacteria living on and in your body perform a wide variety of functions. We have only now come to realize the bacteria must be properly balanced and nourished to maintain good physical and mental health.
Although the Human Genome Project was expected to demonstrate gene-based therapies could rid us of disease, it actually revealed genetic makeup plays a much smaller role than previously imagined. Emerging science also shows your microbiome may be rapidly altered, for better or worse, based on factors such as your diet, lifestyle and chemical exposure.
While this is a double-edged sword, since many modern conveniences are extremely detrimental to gut flora, your diet is likely one of the easiest, fastest and most effective ways to optimize your microbiome. The importance of the bacteria growing in your gut is become increasingly clear as we learn these colonies of microorganisms lend truth to the old adage, 1 “you are what you eat.”
Research has demonstrated your gut microbiome plays a significant role in your immune system and in the development of many diseases and health conditions, including obesity and difficulty maintaining weight loss after dieting, depression and multiple sclerosis, just to name a few.
Most recently, a study from National Institutes of Health (NIH) scientists and colleagues have demonstrated a balance of beneficial bacteria in your digestive tract may help protect you against antibiotic-resistant Staphylococcus. 2
Staphylococcus Infections Deadly Worldwide
Staphylococcus aureus (S. aureus) is a bacterium commonly found on the skin and nose, even in healthy people. Although it normally doesn't cause infections or problems, if it invades your body or colonizes your gut, it can create significant problems. S. aureus has also become antibiotic-resistant, and is a common cause of sepsis.
Staph infections can range from skin infections to endocarditis, a potentially deadly infection attacking your heart muscle. As a result, the symptoms of a staph infection are varied, depending upon the system the bacteria is attacking in your body. 3
The emergence of methicillin-resistant S. aureus (MRSA) began in the 1960s and disseminated globally, quickly becoming a leading cause of bacterial infections, both within the health care system and community settings. 4 MRSA is resistant to several antibiotics, including methicillin, penicillin and amoxicillin.
The resistance makes the infection challenging to treat and increases the risk of death when it triggers sepsis. In the U.S., S. aureus is one of the most common triggers for skin infections, including boils, impetigo, abscesses and wound infections. 5
Over 95,000 MRSA infections are diagnosed annually, approximately 18,000 of which result in death. 6 Nearly 86 percent of all invasive MRSA infections occur in the health care setting. 7 Staphylococcus bacteria are also a common trigger for food poisoning. 8 Symptoms usually happen within hours of eating the contaminated food, but often disappear quickly after lasting just 12 hours.
However, when S. aureus enters your blood it may trigger septicemia, including fever, low blood pressure and infections in internal organs, bones, muscles and around surgically implanted devices.
Between 2009 and 2014, the average percentage of S. aureus isolates found to be antibiotic-resistant was nearly 20 percent in the U.S. 9 In response, the National Institute of Allergy and Infectious Diseases, sponsored by NIH, investigated the potential of Bacillus (beneficial bacteria used in probiotic supplements) protecting against S. aureus. 10
Probiotic Kills Antibiotic-Resistant Bacteria
Bacteria are microscopic, single-celled organisms existing in every environment, both inside and outside of other organisms. Some, like S. aureus, are harmful, but others serve a useful purpose. 11 However the proliferation of S. aureus increases your risk of becoming infected with a serious antibiotic-resistant infection.
Unexpectedly, they found Bacillus bacteria prevented S. aureus from growing in the gut and nose of healthy individuals. Bacillus is commonly found in probiotic supplements and may eliminate these bacteria by secreting a compound that blocks a key signaling system known as quorum sensing. 12 This signaling mechanism controls the cell's adaptation to the population density of bacteria.
Different species of bacteria have different signals and sensors, making it possible a substance inhibiting quorum sensing in S. aureus may not affect another bacteria. The bacteria were able to inhibit the specialized system producing molecules known as fengycins.
Using chromatography and mass spectrometry, the scientists identified the fengycins, a class of lipopeptides, as the specific substance inhibiting the sensing system. Fengycins inhibited the growth of S. aureus, including USA300 MRSA, the superbug responsible for most of the life-threatening, community-associated infections in the U.S. 13
Bacillus and S. Aureus Were Not Present in the Same Subjects
Researchers first collected and analyzed stool samples from nearly 200 participants in rural areas of Thailand. They hypothesized those living in rural areas would be less exposed to antibiotics or food sterilization than individuals in Western countries. 14
An analysis of the samples found 12.5 percent of the subjects had S. aureus in their intestines and 13 percent had the bacteria in their nasal passages. This was striking as it was far lower than the colonization commonly recorded in adults in urban areas, which is 20 percent in the gut and 40 percent in the nose. 15
The fecal samples also demonstrated those containing Bacillus did not contain S. aureus and vice versa. The scientists then conducted tests on mice, demonstrating S. aureus bacteria have a specialized system allowing them to colonize within the body. In further experiments using mice, S. aureus was introduced and allowed to colonize in the guts of the rodents. 16
They then fed the mice Bacillus subtilis spores once every other day. These rodents were soon free of S. aureus in their gut. The hope is to find a strategy preventing S. aureus from colonizing and thus reducing the potential for staph infections. Some of the current methods for decolonization are controversial as they require considerable amounts of antibiotics and have had limited success.
Michael Otto Ph.D., lead investigator of the study commented: 17 “Ultimately, we hope to determine if a simple probiotic regimen can be used to reduce MRSA infection rates in hospitals”
Other Health Benefits of Balanced Gut Microbiome
There are other significant benefits to maintaining a balanced gut microbiome. For instance, scientists in the U.K. took a hard look at the introduction of probiotics to the gut microbiome and found it may help prevent the formation of tumors and even treat existing ones.
In their research, 18 they wrote gut bacterial Lactobacillus has the potential for treating colon cancer, the third most common cancer in the U.S. other than skin cancer. Several studies have found factors increasing the incidence of colorectal cancer include lack of exercise, low vegetable and fruit consumption, being overweight or obese and being diagnosed with inflammatory bowel disease.
In short, your gut microbiome plays an impressive role in your overall health, including the potential development of colorectal cancer. Researchers have also found differences in gut microbiota between those who suffer from nonalcoholic fatty liver disease (NAFLD) and lean individuals. 19
Those with NAFLD are more likely to have bacterial overgrowth in the small intestines along with increased intestinal permeability. Although there is no way to change the fact certain foods increase your risk for packing on pounds, bacteria also play a major role in facilitating the process.
Foods known to produce metabolic dysfunction and insulin resistance, such as processed foods, fructose, sugar and artificial sweeteners, also decimate beneficial gut bacteria. This may in fact be a mechanism by which these foods promote obesity.
Other research has found a functional link between certain gut microbiota and the onset of Parkinson's disease. Their data 20 demonstrate specific chemicals produced by certain bacteria will worsen the accumulation of proteins in the brain associated with Parkinson's disease.
Your Gut Faces Increasing Threats From Environmental Factors Each Year
Your gut microbiome is under continuous attack by environment, diet and lifestyle choices. If gut bacteria become imbalanced, it increases your risk for both chronic and acute illnesses. Some of the factors posing the greatest danger to your gut microbiome include:
Refined sugar, especially processed high-fructose corn syrup
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; factory farmed 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 blocking the production of acid in your stomach, typically prescribed for GERD, such as Prilosec, Prevacid and Nexium)
Chlorinated and/or fluoridated water
Gluten and/or lectins
Fiber and Fermented Foods Are Critical to Your Gut Health
Scientists now understand your gut plays a crucial role in health and disease processes, actually acting as a second brain. Modifying your gut microbiome is an excellent long-term investment in your health and wellness. The consequences of a poorly developed microbiome can affect your mood, emotions, allergies and more. 21
The bacterial diversity in your gut begins at birth (baby is “inoculated” as it moves through the birth canal) and is affected by genetics, whether you’re breast- or bottle-fed, and your immediate environment. Later in life, diversity is affected by your food choices. Nourishing beneficial bacteria is a way to maintain your health and one easy way is by eating traditionally fermented foods.
Ideally, you'll want to include a variety of fermented foods and beverages as each will inoculate your gut with different microorganisms. There are several you can easily make at home, including fermented vegetables, chutneys, condiments, cultured dairy products such as yogurt, kefir and sour cream, as well as fermented fish, such as mackerel and Swedish gravlax.
Foods containing fiber, such as nuts, seeds, fruits and vegetables also help promote better digestive health by feeding your beneficial bacteria. One of the reasons fermented foods are so beneficial is they contain a wide variety of beneficial bacteria.
However, this may not be enough if the rest of your diet is poor. Your gut bacteria are an active and integral part of your body, and as such are vulnerable to your lifestyle choices.
You May Not Be Eating Enough Fiber to Support Your Gut
Eating a lot of processed foods, for instance, compromises your bacteria as processed foods in general destroy healthy microflora and feed harmful bacteria and yeast. Your gut bacteria are also highly sensitive to antibiotics, antibacterial soaps, agricultural chemicals, pollution and chlorinated water.
Since virtually all of us are exposed to these factors, including antibiotics from factory farmed animal products, ensuring your gut bacteria remains balanced must be an ongoing consideration. A high-quality probiotics supplement may be useful in maintaining a well-functioning digestive system if you occasionally stray from your healthy diet or have to take antibiotics.
Gut microbes specializing in fermenting soluble fiber also play an important role in preventing inflammatory disorders as they help to calibrate your immune system. 22 The byproducts of this fermentation activity nourish the cells lining your colon and help prevent leaky gut, a condition in which toxins migrate from your gut into your bloodstream, which triggers an inflammatory response.
Although fiber dietary guidelines call for 20 to 30 grams of fiber per day, I believe the ideal amount is much higher, likely twice as high. Eating whole foods, especially vegetables, also naturally provides you with soluble and insoluble fiber to feed the living microorganisms in your gut.