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2024 Healthier You Series: Your Microbiome – Key to Healthy Immunity and 7 Ways to Nourish It

Do you suffer from food sensitivities, allergies, digestive problems, skin issues, fatigue or mood swings? Issues such as these — and more — just might be traced back to your gut health. And your gut health depends upon the composition of the community of microbes that lives within it, collectively known as part of the microbiome. In recent years, the human microbiome has taken center stage, emerging as one of the most important considerations when it comes to overall health and the health of the immune system.1a,1b

The Harvard Health website likens the microbiome to a bustling city of people going about their business: only its denizens, instead of being human, are bacteria, parasites, yeasts, fungi, and viruses. 2 And these microscopic critters, called microbiota, are everywhere: on your skin, in your nose and mouth, maybe even in your brain3, but mostly in your gut. Their numbers and diversity are impressive. There are about as many microbiota as there are cells of your body, and collectively they may have more genes than there are stars in the observable universe. At least half of the genes in an individual’s microbiome are unique to that person (which means we each have a signature microbiome).4,5 The microbiome plays so many key roles in the daily operations of the body that it has been labeled a separate supporting organ.6 Much of the research so far has centered on the microbiota of the gut. 

The Microbiome and the Immune System

The microbiome and immune systems have a symbiotic relationship and are constantly reshaping one another. The microbiota of our gut program our immune system, help defend against pathogens, help recognize and tolerate harmless microbes, and provide nutrients to the body to help make the mucosal wall strong. From 70 — 80% of the body’s immune cells are found in the gut wall, so when you take care of your gut, you support your immune system.7

Bacteria teach your immune system how to behave.

Our microbes instruct our immune system to react when there is a threat and not to overreact when there isn’t one. When this aspect of the communication goes awry, we may end up with autoimmune issues. As one example, a study at Mayo Clinic discovered that an imbalance in the microbiome is associated with autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and celiac disease. A bacterium native to the microbiome may be the key to treatment.8

The composition of the microbiome may play a significant role in avoiding many diseases, and the good news is that it is very sensitive to dietary changes. The following paragraph is taken from the Journal of Translational Medicine:

Recent studies have suggested that the intestinal microbiome plays an important role in modulating risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. At the same time, it is now understood that diet plays a significant role in shaping the microbiome, with experiments showing that dietary alterations can induce large, temporary microbial shifts within 24 h.9

Your Microbiome is What You Eat

Diet… can be modified and thus provides a strategy to develop a microbiome that promotes healthy living. We suggest that modifying the microbiome through diet may be part of a plan to reduce the risk of chronic diseases. 
       Dr. Li Jiao, Baylor College of Medicine  10   

A more diverse microbiome is the healthiest and diet plays a key role in shaping that diversity.11 The microbiota are made up of both beneficial and potentially harmful organisms. Research is discovering that the foods you eat determine the populations, in both numbers and types, that will flourish in your body. One recent study shows how the quality of diet can affect the ratio of beneficial to harmful bacteria in the gut. The high quality diet in the study — defined as rich in fruits, vegetables, and whole grains while being low in sugar, alcohol and solid fats — resulted in more beneficial bacteria being present. In contrast, a poor diet, as determined by the Healthy Eating Index (HEI)*, resulted in a higher presence of harmful bacteria, one of which is linked to colon cancer.12 

Strategy for a Healthy Microbiome

The following are some of the dietary steps you can take for good gut health.


1. Be Mindful of Refined Sugar and Added (aka Artificial or Nonnutritive) Sweeteners

To best nourish your microbiome, what you do not eat may be as important, if not even more so, than what you eat. There seems to be virtually unanimous agreement among experts that excess added sugar is detrimental to health and that Americans eat too much of it. Excess sugar in the diet is linked to a host of conditions — including metabolic syndrome and obesity, diabetes, cardiovascular disease, liver disease, tooth decay, and cognitive diseases including Alzheimer’s disease. One way excess added sugar may play a role is through chronic inflammation, which harms the diversity and function of gut bacteria.13  A 2018 study at the Yale School of Medicine found that dietary sugar may block the colonization of a key beneficial bacterium.14,15

Experts also seem to agree that the body can safely handle small amounts of added sugar. The American Heart Association recommends women eat no more than 6 teaspoons and men no more than 9 teaspoons of sugar a day. The U.S. dietary guidelines are a bit more liberal —  recommendations are based upon total calories. For example, 2000 calories a day, which is loosely considered to be what an average adult needs, translates into an allowance of 12 teaspoons of sugar. Whichever guideline you consider, Americans on average consume over 17 teaspoons a day, well above the recommended amounts.

How much sugar is in your diet? If you eat processed foods of any kind, drink sodas, munch on energy bars or consume specialty or sports drinks, you may be surprised. For example, a-16 oz hot chocolate (with cream on top, of course) from a popular coffee shop has about 10 teaspoons of sugar.  One small cocoa concoction from a fast food chain has 25 teaspoons of sugar.  

Added sweeteners, while they have no calories, may contribute to weight gain. There is evidence that many of them may alter the gut microbiota to create insulin resistance, which could lead to Type 2 diabetes. One study using mice found that artificial sweeteners increased a bacteria associated with glucose intolerance, no matter what kind of diet they were fed.16  Sweeteners in foods often pass detection. Health-mindful parents who select low or reduced sugar or low calorie products for their children may end up inadvertently feeding them nonnutritive sweeteners. In one study, parents were unable to identify the added sweeteners in 77% of the foods they were shown.17 The eight sweeteners approved by the FDA are aspartame, acesulfame potassium, luo han guo (monk) fruit extract, neotame, saccharin, stevia, sucralose and advantame. The last one on the list, added recently, is 20,000 times sweeter than sugar.


2. Include Probiotics

Probiotics are foods that contain beneficial bacteria for the gut. They are mostly fermented and cultured foods. You are probably familiar with raw sauerkraut — a fermented food which is traditionally made from cabbage, but other vegetables can be used as well; other sources include pickled vegetables, yogurt, kefir, natto, tempeh, miso, kombucha tea, among others. There are recipes online for fermenting your own veggies. When choosing foods for their probiotic value, you need to make sure they contain live cultures: pasteurization kills the beneficial bacteria. 

There is also a wide variety of probiotic supplements available. Food sources are the best first choice, says Dr. Carrie Daniel-MacDougall, a nutritional epidemiologist who studies diet and the microbiome at MD Anderson Clinic.18 She points to the added value of nutrients and fiber from food. Dr. Mercola agrees, saying that food sources can offer a much higher number of bacteria. His website has a video on how to ferment foods and also offers starter cultures.19 Foods also provide a natural buffer from stomach acid, among other benefits to the colonization in the gut . Supplements, on the other hand, may be of value for targeting certain strains of bacteria or offering the benefits of diverse strains.20 If you take probiotic supplements, you might want to make sure that the strains you take can survive stomach acid.


3. Include Prebiotics

Prebiotics are plant fibers that we cannot digest in our stomachs. These are passed into the intestinal tract and nourish beneficial bacteria. The combination of prebiotics with probiotics is referred to as symbiotics: good bacteria and the food to feed them. There are many food sources rich in prebiotics: bananas, Jerusalem artichokes (sunchokes), chicory root, sweet potatoes, garlic, onions, barley, oats, leeks, apples, cocoa (yay!), seaweed, asparagus, leeks, konja root, dandelion greens, jicama, seaweed, among others. You can also buy prebiotic supplements.


4. Take Antibiotics Only When Necessary 

Broad spectrum antibiotics will indiscriminately kill both beneficial and harmful bacteria. The Centers for Disease Control and Prevention estimates that 30% of antibiotic prescriptions from visits to a doctor’s office are unnecessary.21 The microbiome may take quite a while to recover from a round of antibiotics:  in one research study, some beneficial gut bacteria had not yet returned even after six months. There may also be a link between the use of antibiotics, its effects on the microbiome, and obesity in children.22, 23


5. Get Enough Fiber from Plant Foods

Fiber is the part of plants that is not digestible, most often found in the stalks, skins and seeds.  There are two kinds of fiber: soluble and insoluble. Soluble fiber such as that found in beans, peas, oats, barley, and fruits feed bacteria that produce vitamins such as biotin, folate and vitamin K. Insoluble fiber, found in whole grains, nuts, fruits and vegetables, draws water into the intestines, softening stools and helping to prevent constipation.  

More recently, an expanded role of fiber in the health of the microbiome is emerging, in that it increases the number and diversity of gut microbiota and strengthens the mucus wall of the intestines, lowering inflammation.  Americans on average get less than half the recommended daily amount.24,25


6. Eat Polyphenol Rich Foods

Polyphenols are rich in antioxidants and help protect against inflammation and are good for beneficial bacteria. Some polyphenol-rich foods are pomegranates, dark chocolate (yay), red wine, cherries, green tea, and red wine. 


7. View GMO (Genetically Modified Organisms) Foods with Caution

The vast majority of GMO foods are sprayed heavily with the pesticide glyphosate (Roundup): they were genetically modified to survive such an onslaught. Studies on rats found that glyphosate at regulatory acceptable levels changed the composition of the gut microbiome. In one study the glyphosate decreased the abundance of gut bacteria needed to produce the building blocks of proteins.26, 27  There is much debate about the effects of GMO foods on human health at this time.


Heavy Metals in Food- How The IonCleanse by AMD May Help 

While fish is nutritious, many are high in toxic metals. The FDA recommends limiting fish in the diet and also choosing fish that contain lower levels, such as anchovies, herring, and sardines.28 You can also find a low-mercury canned tuna. Mercury may cause inflammation and compromise the gut wall. U.S.-grown rice absorbs high levels of arsenic from the soil, residues from the period when U.S. pesticides contained the heavy metal. A study in 2018 found that the heavy metals cadmium and arsenic can affect the health and balance of the gut microbiome, decreasing its diversity and altering the balance of microbiota.29 

We at AMD enjoy discovering new ways that the IonCleanse may play a role in a healthy life.  Our heavy metal study showed an increase in the excretion of heavy metals for five days after a session.

If there is one big takeaway from all of this, it would seem to be that whatever diet plan works for you, the more you eliminate processed foods, unhealthy beverages, GMO foods, will go a long way toward better health and a stronger immune system. Also, eat your fresh, unprocessed veggies from the produce department!

* The HEI follows US dietary guidelines and is updated regularly by the National Cancer Institute and US Department of Agriculture.

I hope you enjoyed this second installment of AMD’s 2024 Healthier You Series.  As I did the research for this article, I had this eerie feeling that I am not so much “me” but “us,” a sentiment reflected in an article that proposed thinking of the human body as a combined superorganism of human and microbial cells. The microbiome is an intriguing area of investigation for health solutions. As an example, sinusitis, an inflammation of the sinuses, may be due to the lack of a certain bacteria that lives in the nose. Envision a probiotic nose spray!

I would love any comments and thoughts about this second installment. Email them to  Next in the series: The Pillar of Health: Exercise





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