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 Diseases and the Importance of Bacteria Balance in the Gut.

By Dr. Ashraf Girgis N.D.
Published First 10/19/2017

updated 05/10/2019

In the last decade, there has been a lot of buzz about the microbiota and microbiome, or ecology, of our gut. Scientists are finding out that we have a universe of our own within our body. It reminds of me of the saying from the Persian poet, Rumi, about humans, “You are not a drop in a ocean, but an ocean in a drop”.

These scientists are demonstrating that we are indeed a universe of our own, living within a much bigger universe. We are a universe made of bacteria, fungi, viruses, and many other microbes that are make up who we are and influence how we behave.

Some may object by saying, “But we are made of billions of human cells, not all are bacteria!” Yes, that is very true; however, we have about 100 trillion bacteria.  They overpower our cells 10 to 1.

It is becoming quite clear that keeping these bacteria in harmony and balance in our ecosystem, in our little universe within, is very important.  It plays a very fundamental role in our overall health. In fact, scientists are finding out that the more we harm and destroy this harmonious ecosystem by ingesting harmful food and beverages and conducting an unhealthy lifestyle, the further we damage our overall health.

We now know about the importance of food and mood; this is the fact that what we eat can impact and change our mood. Now, thanks to these findings, we are learning to some degree the mechanism in which these effects take place. Such as how what we eat impacts the level of good bacteria in our gut and in turn affects our mood.

For example, GABA(gamma-aminobutyric acid), a neurotransmitter,  levels can be increased by increased level of good bacteria such as Lactobacillus and Bifidobacterium found in yogurt or other probiotics in food. I published an article in June 2014 at about probiotic and prebiotic foods. You can read it here.

Although the research in this field is still very much young and ongoing, it will not be surprising to see more in the near future. We have procedures such as fecal transplant (Yeek!!) or other ways of transporting good bacteria into our system. We do this to treat various diseases by adjusting the balance of bacteria in our gut.  

Unfortunately, we inadvertently have detrimental effects on our children's early developmental health and bacteria balance due to our current lifestyle.


 By having C- sections for reasons other than absolute necessity or creating a very clean, sterile environment for our children with all these anti-bacterial wipes, we upset the level of much needed good bacteria and the balance of the ecosystem in babies guts. This balance is vital at these early developmental stages, especially between the ages of 1-3. Adding salt to the wound, the high level of antibiotic prescriptions, in addition to using cow milk rather than breast milk, play a very important and significant role in the balance of gut bacteria.

In a study published in Journal of Gut in 2007 by Gareau MG et & al, they separated rats from their mothers and measured the level of stress hormone. They found out that the rats who received a probiotic during this time had a lower level of stress hormone as opposed to those who did not. This is the summary of their conclusion:

“The results indicate that altered enteric flora are responsible for colonic pathophysiology. Probiotics improve gut dysfunction induced by MS(maternal separation), at least in part by normalization of HPA axis activity”.

We know also that these helpful bacteria perform certain tasks in our gut such as:

1.    Modulates the immune system in our gut. We know that 70-75% of immune system activity takes place in the gut.
2.     Promotes new blood vessel regeneration and impact the nerve function in the gut
3.     Acts to normalize the gut flora, getting rid of the bad bacteria, viruses, fungi and others
4.     Assists in making Vitamin K and Vitamin B.
5.     Has the ability to change/affect our genes. Therefore, affecting diseases.
6.  Enhances the GI mobility
7. Helps with food digestion and absorption of nutrients, and prevents abdominal distension due to gas.
8.  Helps with energy levels due to nutrients obtained from gut

Since good bacteria in the gut is seen regulating many important functions, they are considered vital to overall good health.

Relating to good health, it is also important to note that according to NIH there are about 23.5 million Americans who suffer from autoimmune diseases. American autoimmune disease associations believe the number might actually be about 50 million. I have previously written about autoimmune diseases, you can read my article here.

The reason behind this obvious discrepancy in numbers is that the NIH list of autoimmune diseases includes only 24 diseases, while there are anywhere between 80-100 diseases that are considered autoimmune, and more than 40 diseases seem to be related to autoimmune diseases. So, in reality the numbers are much higher than the 50 million, putting enormous financial burden on American society, and costing billions of dollars as well as an immeasurable amount of suffering and emotional burden.

While scientists and specialists are trying to connect the dots between underlying causes of these diseases, some in alternative medicine, integrative medicine, and the holistic field have done so very effectively. With success using these research findings, they’ve applied it to real patients and situations in order to seek normalization. Many cases have successfully brought an end to their patients’ long suffering simply by using food as their medication, in addition to other approaches such as herbs and homeopathy etc.

Below are few statistics from American association of autoimmune disease web site:

·       Autoimmune disease is one of the top 10 leading causes of death in female children and women in all age groups up to 64 years of age.

·       A close genetic relationship exists among autoimmune disease, explaining clustering in individuals and families as well as a common pathway of disease.

·       Commonly used immunosuppressant treatments lead to devastating long-term side effects.

·       The Institute of Medicine reports that the US is behind other countries in research into immune system self recognition, the process involved in autoimmune disease.

·       Understanding how to modulate immune system activity will benefit transplant recipients, cancer patients, AIDS patients and infectious disease patients.

Thanks to scientists, we now know that the good bacteria in our gut do much more than helping with the absorption of nutrients and vitamin and minerals etc. In fact, an overgrowth of bad bacteria leads to many diseases, including those that are autoimmune.  These can be due to the absence or low level of good bacteria in the gut. This imbalance or dysbiosis can play a leading role in development of autoimmune diseases. The findings are amazing, and it is groundbreaking to know that the microbiome in our guts can have a significant link to autoimmune diseases, from Autism to Alzheimers and Parkinsons to host of other diseases.

 In an article I published in June 2014, I wrote about probiotics and prebiotics, as well as how a Russian scientist, Elli Metchnikoff, brought attention to the role of gut bacteria when he noticed how individuals in Bulgaria who eat yogurt live longer and conduct healthy lives.

In a study by Gabryszewaski SJ, published in the Journal of Immunology in 2011, a group of mice were fed probiotic enriched food containing Lactobacillus. At the end of 13 weeks, scientists concluded:

“In summary, we have identified and characterized an effective Lactobacillus-mediated innate immune shield, which may ultimately serve as critical and long-term protection against infection in the absence of specific antiviral vaccines” showing the effectiveness of bacteria in fighting infections.

In another study conducted in New Zealand, within a group of thirty rugby players, half were given a probiotic and half were not.  Within the group that were not given the probiotic, 83% contracted a cold where in the group that received the probiotic, only 53% got sick(receiving 3 billion CFUs/day). In other words, 30% less people demonstrated cold symptoms when they received the probiotic compared to the group that did not.

Dr. Payami, Ph.D., a professor in the Department of Neurology at the University of Alabama School of Medicine, studies microbiomes. She studied 197 Parkinson patients and 130 control groups and noticed a huge difference in their microbiome. There seemed to be growing evidence that link neurodegenerative disease, such as Parkinson's, to the composition of gut bacteria.

According to her study, Doctor Payami and her team of researchers are not sure at this point what comes first, whether Parkinson's causes changes in the microbiome or vice versa. Regardless of this, it is known that first sign of Parkinson’s often is inflammation, constipation, or other gastrointestinal ailments.

In another important research experiment conducted by the University of Iowa and Mayo Clinic in Rochester, researchers found out P.Histicola, a bacteria that exists in the gut, can not only lower certain types of pro-inflammatory cells in guts but also increase the T cells or killer cells that are very important in fighting bacteria. Dr. Murray, one of the investigators on this study stated: "If we can use the microbes already in the human body to treat human disease beyond the gut itself, we may be onto a new era of medicine. We are talking about bugs as drugs".

Indeed it looks as if we are approaching a new era. After all, putting the old saying in practice, “we are are what we eat”, or shall we say, we are the result of a balance of bacteria in our inner ecosystem?

Thanks for visiting

Ashraf Girgis N.D.


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