May 15, 2018

The Bugs that Live With Us: Gut Microbiome and Dysbiosis

Ozark Holistic Center

Many of my patients complain of stomach problems. Some of had chronic diarrhea others have had chronic constipation. All of them have had an upset stomach of sorts. They have tried many different avenues to figure out why and I am here to rely some information on that. How many of you know that there are microorganisms on and in your body right now? That not only are a few but trillions of bacteria that live with us.  This is called the microbiome. I will talk specifically about the gut microbiome or gut normal flora. I will also talk about some of the negative effects of an imbalanced microbiome or dysbiosis.

Essential to understanding what happens with an imbalanced microbiome or dysbiosis is understanding the complex system of the gut. Our gut is made up of everything from our mouth to our anus which includes esophagus, stomach, small intestine, and large intestine. There are other organs often included in this because of their role in digestion such as the pancreas and liver. Our gut is very unique and not many know that it has its own functioning nervous system that works in conjunction with our central nervous system. It is called the enteric nervous system. Enteric means “pertaining to the intestines”. Some have dubbed it the “second brain”.  There is continual communication between this second brain and our brain. Furthermore, around 80% of immune system is contained within the gut. This is due to the gut being open to the external environment. I know what you are thinking, how is it external but yet it is inside me? Just think about eating. You put food from the outside world into your body. The tube that starts at your mouth and ends at your anus is essentially open to the world in this regard. That is why it has contains so much of our immune system. In fact it “contains on the order of ten to the eighth neurons, the gastroenteropancreatic endocrine system uses more than 20 identified hormones, and the gut immune system has 70-80% of the body’s immune cells. When this response is maladjusted or is overwhelmed, the consequences can be severe or debilitating as in irritable bowel syndrome.” (1) That is why gut health is so important! That is why I harp on it all the time.

Now that we understand a little bit more about the gut let’s talk about the flora or microbiome. There are trillions of bacteria that live as normal flora in the gut. That means they are supposed to be there, it is by design! They are immunoprotective as well. They add to your defense but they do much more! This is a hot topic right now and is being researched heavily.  

Here is list of the benefits:

  • Help with our immune system protecting us from pathogens (2)
  • Create serotonin, an essential neurotransmitter often associated with anxiety and depression. In fact almost 90% of serotonin is made in the gut. (3)
  • Protection from tuberculosis (4)
  • Lower risk for type 1 diabetes (5)
  • Regulation of our nerve insulation (6)
  • Production of short-chain fatty acids, B vitamins, and Vitamin K (7)
  • Intestinal motility (8)
  • Metabolism of nutrients, lipids, bile acids, and dietary fiber. (9)

That is a mere sample of all the benefits our little friends provide. We have a tremendous symbiotic relationship.

Many people including many of my patients have abnormal bowel movements. Yes, I am talking about poop. It is an important indicator of gut health. This is a good indicator of a gut flora imbalance or dysbiosis. Dysbiosis causes many problems and it can be caused by many things as well.

First some of the associated health conditions and increased risks with dysbiosis:

  • Anxiety and Depression (10,11,12)
  • Parkinson’s disease (13,14)
  • Irritable bowel syndrome (15)
  • Diabetes (16)
  • Juvenile idiopathic arthritis and other systemic inflammatory diseases (17)
  • Multiple Sclerosis (18)
  • Autoimmune disease (19)
  • Hyperthyroidism (20)
  • Hashimoto’s (21)
  • Autism (22,23,24)

And the list goes on and on. We are finding more

This can be caused by many things. One is cesarean birth or a c-section. When a baby is delivered vaginally the baby is able to get a healthy dose of the mother’s flora. In c-section babies this does not happen, however there are interventions that are now being done to combat this issue. (25) This gives credence to the increased risk for asthma, gut infections, and allergies later in life for babies born via c-section. (26,27,28) Another issue is babies being fed formula versus breastfeeding. Babies that breastfeeding get more of the mother’s flora further strengthening the baby. 30% of a baby’s beneficial bacteria comes from mother’s milk. And an additional 10% comes from the skin on the mother’s breast. (29) There is a caveat to this. If the mother has a disrupted flora this will likely result in the baby having issues as well. These are simply suggestions from studies that have been done.

Another common thing we do that tends to disrupt the microbiome is our frequent use of anti-bacterial soaps and cleaners. We have become germ freaks. We worry about them constantly when in reality we want a balance. Some of the bacteria we worry about most actually lives on us or in us and is beneficial when properly balanced.

Along with anti-bacterial soaps we need to talk about antibiotics. We have become a society that uses too many antibiotics. It has created antibiotic resistant bacteria or superbugs. MRSA is an example of this that many of you probably have heard of. Often times patients receive antibiotics with viral illnesses such as the cold or flu. Antibiotics kill bacteria not viruses. So it is not doing anything for a virus. This is sometimes down to placate the patient. Furthermore, it has been shown that antibiotics can disrupt the gut microbiome for up to 12 months. One study showed the antibiotic treatment of tuberculosis resulted in a profound dysbiosis. (30) Disruption of serotonin creation due to antibiotics was shown in another study. (31) That is a frightening thought considering all that the microbiome does for us.  

To further illustrate the point here is a quote from the article, Clinical Consequences of Diet-Induced Dysbiosis, “the consequences of dysbiosis are not innocent, but detrimental when pathobionts (any disease-causing microorganism) become prominent in the microbial communities.  It is well documented that antibiotic treatments cause aberrancies in the host microbiota. Though it is generally believed that such changes are normalized within weeks of cessation of antibiotics, recent evidence challenges this notion.  In a clinical setting, this raises important concern regarding the appropriate use or avoidance of antibiotics.” (32)

Lastly let’s talk about diet. Our diet is one of the biggest contributors to dysbiosis. The Standard American Diet consists largely of processed foods, simple sugars, and nutrient poor foods. The processed foods contain chemicals that can kill and disrupt the gut bacteria. Some of them contain molecules that when the gut barrier is broken down can cause an enormous increase in inflammation which can become cyclical. This leads to dysbiosis. The simple sugars often feed bacteria you do not want a plethora of creating dysbiosis and possibly a very bad infection. Splenda and other sugar free sweeteners can do the same thing. (33) These “bad” bacteria can overgrow in the small intestine creating a terrible environment. This is called Small Intestine Bacterial Overgrowth or SIBO. A difficult thing to deal with and resolve. (34)

Nutrient poor foods limit our body’s ability to fight off infections, heal, and maintain barriers by building and creating new cells. This is an oversimplification of what is going on but I hope you can see the importance of gut health and creating an environment that allows for a healthy balanced microbiome. This is why I recommend a nutrient dense diet to all my patients and it is the first step to healing from dysbiosis. Lay off inflammatory foods such as processed foods, simple sugars, reduce the consumption of grains, in fact, it may be good to go off grains for a short period of time. Include plenty of fruits and vegetables. Include plenty of good quality protein from pasture-raised sources. Don’t forget about the organ meat, liver is one of the most beneficial foods.

What else can be done? You need to get evaluated for SIBO or a large intestine dysbiosis. Figuring out what is overgrowing or what type of imbalance it is is needed for effective treatments to be administered. We use herbal remedies to treat these issues. Which has been shown to be equivalent to antibiotic therapy in SIBO patients. (35) I will list some of the treatments we use below. Food sensitivities should also be investigated. Gluten has been shown to trigger dysbiosis. (36) Milk, eggs, soy, and nightshades are some other common food sensitivities that can trigger dysbiosis. (37) Trying an elimination diet or getting evaluated for specific sensitivities, which we do in house, is a must for stopping dysbiosis. Some of other things to consider are heavy metal toxicity and environmental toxin exposure. Environmental toxins include pesticides and we are exposed to a lot of pesticides. It is in our food and in our water supply. Glyphosate or Roundup is singled out in many studies showing its effect on the gut microbiome. (38,39,40) Unfortunately this is not the only negative effect of glyphosate but that will be for another article. Suffice it to say there is a very good reason to be eating non-GMO, organic foods.


Herbal Remedies

Two herbal remedies that I commonly use to help with SIBO and dysbiosis are neem and noni. Both have great broad-spectrum antimicrobial properties and are very effective helping patients. (41,42)

Supportive Nutrition

In addition to herbal remedies, I also evaluate for nutrition that supports the healing process. I find people often need Vitamin A. One reason might be we are often deficient in this nutrient because we do not eat enough liver and other high vitamin A foods. Many still think you can get vitamin A from carrots. It is true that carrots contain beta carotene, a precursor to vitamin A, but it is not the same. Furthermore, we only absorb about 3% of the beta carotene we eat. Nevertheless, Vitamin A is incredibly useful in healing the gut.

I also evaluate for nutrients you may be in need of. Dysbiosis makes it difficult to absorb nutrients. In addition to this, our good bacteria create vital nutrients as mentioned above. I often find the need to supplement patients with B vitamins and other nutrients due to this. All these nutrients are crucial to healing and supporting a healthy immune system and gut.


Dysbiosis is very common and often an underlying factor in chronic disease. Getting properly evaluated for it and receiving an effective treatment is a must in overcoming many chronic health conditions. If you are dealing with any of the above symptoms or if you have been dealing with a chronic health condition I highly encourage you to seek out a holistic practitioner.

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