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How the Microbiome Affects Your Overall Health

One of the hottest fields of research in medicine is something called the microbiome.

The microbiology refers to the trillions of organisms which live inside and on your body that are not human cells. These foreign cells have developed side-by-side with human cells over millions of years. They serve several essential functions in our body including:

  • Being the first line of defense for your immune system, including against viruses like COVID-19

  • Creating signals to your brain about the environment in which we live

  • Playing a key role in producing essential nutrients, including short chain fatty acids which nourish the cells lining your gut as well as vitamin K necessary for clotting

  • Balancing your hormone levels

  • Influencing your body in losing and gaining weight

  • Shielding women from vaginal infections through the production of lactobacillus

Resolving Abdominal Discomfort via the Microbiome

One of my patients was recently diagnosed with celiac disease after having several months of abdominal discomfort and episodes of passing out. After being placed on a gluten-free diet she continued to experience symptoms from abdominal discomfort to generalized weakness.

After a stool test demonstrated a high level of a particular bacteria seen in small intestinal bacterial overgrowth she was treated with herbal anti-microbial and limitations of her carbohydrate intake. She had near complete resolution of her symptoms in both in her gut and those impacting her generalized health.

In this case, a disrupted microbiome, a condition called dysbiosis, resulted in multiple symptoms. Abdominal discomfort, generalized weakness, fatigue and passing out. This patient demonstrates the wide ranging impact that imbalances in the gut can cause in one particular individual.

The Brain-Gut Connection

The "second brain" is a term coined for your gut due to the biochemical signals it transmits to the rest of your body, including your brain.

The microbiome as we currently understand are a collection of bacteria, archae (ancient organisms), viruses and other microbes which have lived symbiotically within the human body for millions of years. The microbiome lives in relative safety within our bodies while helping to break down and provide nutrients which human cells are unable to create on their own.

Curiously, when we are born our intestinal track is sterile, meaning there are no bacteria or other organisms residing in us. The colonization begins as we pass through the birth canal and get exposed to the millions of bacteria which reside there. It is why children born via C-section have much less diversity of bacteria. Current studies are investigating supplementation in the first six months of life, especially for those born via C-section. Some studies which have shown an improvement overall health and decrease infections .

One thing is clear: the overall variety and abundance of our microbes is decreasing overtime. When compared to aboriginal cultures around the world, the difference is marked. The loss of diversity may be a contributing reason for the rise of chronic disease in the US and worldwide.

The major thing which impacts of microbiome is the use of broad-spectrum antibiotics. Drugs such as Augmentin, ciprofloxacin and many others are indiscriminate killers. They are able to wipe out pathogenic organisms which cause disease. They also decimate normal bacteria found in our microbiome. There are increasing recommendations for people taking antibiotics to take probiotics during the course of the antibiotic as well as several months after to help protect and re-populate those good bacteria.

One of the most feared infections is something called clostridium difficile colitis or C Diff. It is an infection which causes profound diarrhea, in many cases bloody diarrhea, which is a direct result of the overgrowth of C Diff bacteria. C Diff is usually kept in check in a healthy microbiome. If given broad-spectrum antibiotics for an infection, or sometimes the overuse for a questionable infection, C Diff is allowed to overgrow and take over your gastrointestinal tract.

While other antibiotics can be used to treat it, one of the most effective treatments, with a 90% cure rate, is use of a fecal transplant of stool from healthy people. This is versus a 30% cure rate using antibiotics. As gross as that sounds it allows the repopulation of your GI tract with good bacteria stopping C Diff in its tracks. It is now recommended as first line therapy.

How do you maintain a healthy microbiome?

Start with clean whole foods to nourish both yourself and your microbiome. Processed foods cause both inflammation and damage to your microbiome and should be avoided as much as possible. Similarly high doses of sugar laden foods can also cause damage. Avoid all sugar sweetened beverages.

Avoid the use of unnecessary antibiotics. According to many studies the overuse of antibiotics in the US is at least 30%. In our world order the attractiveness of a pill for every ill is a mindset that predominates. Each person must ask for themselves and for their children, "Is this antibiotic truly necessary?" What are the long term risks we face by taking a 10 day course of Augmentin for a questionable sinus infection or bronchitis. It is always higher than you think.

Feed your microbiome good prebiotics. These are foods that typically travel to the large intestine mostly undigested where the majority of our microbiome reside. It is here where these foods are broken down and transformed into vitamins like vitamin K as well as short chain fatty acids which feed the lining of your intestinal track.

Typical prebiotics include:

  • Chicory root

  • Dandelion greens

  • Jerusalem artichoke

  • Garlic

  • Onions

  • Leaks

  • Asparagus

  • Plantains

  • Whole oats

  • Flaxseeds

  • Jicama root

  • Seaweed

Consider using probiotics. Natural sources of probiotics including yogurts, kombucha, kimchi, and other fermented foods. You can also take supplemental probiotics using 30 to 50 Billion colony forming units (CFUs) per dose. There are various probiotic preparation’s available and an excellent website for review of these is It is worth being a member if you are interested in objective information on supplements.

Your microbiome is increasingly recognized as an important part of your immune system, hormonal regulation, nutrient absorption and positive (or negative) impact on overall health. Further research will continue in this area and the simple steps above can help to improve the diversity and functioning of your own microbiome leading to better health and longevity.

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