Potential of the Human Microbiome

In previous articles, we have investigated the gut microbiome and how it is affected by a diet high in processed foods and the synthetic sweetener sucralose. However, these two articles do not even begin to scratch the surface of the microbiome.

Here are some facts about the microbiome [2]:

  • Humans are mostly microbes
  • The microbiome is the genetic material of all the microbes, including bacteria, fungi, protozoa, and viruses, that live inside the body
  • Microbes outnumber human cells ten to one, totaling 100 trillion
  • Bacteria in the microbiome help digest food, regulate the immune system, protect against other bacteria that cause disease, and produce vitamins, including B1, B2, B12, and vitamin K, which is needed for blood coagulation.
  • The microbiome was not known about until the late 1990s


I am sure most of you have heard about probiotics, which are a part of the microbiome.

When researchers discovered the microbiome and its essentialness for human development, strong immunity, and healthful nutrition, they were determined to investigate how it regulated human health.

Washington State University claims, “Autoimmune diseases such as diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, and fibromyalgia are associated with dysfunction in the microbiome. Disease-causing microbes accumulate over time, changing gene activity and metabolic processes and resulting in an abnormal immune response against substances and tissues normally present in the body. Autoimmune diseases appear to be passed in families not by DNA inheritance but by inheriting the family’s microbiome” [2].

These findings have warranted further investigation into the unfathomable potential of the microbiome.

Not that we have a base-level understanding of the microbiome, for the remainder of this article, we will inspect newer research about the microbiome as it pertains to inflammatory bowel diseases (IBD) and the possibility of a microbiome in the brain.

Inflammatory Bowel Diseases

Researchers at Harvard and the Massachusetts Institute of Technology led a study which investigated the chemical and molecular events that disrupt the microbiome and trigger immune response during flair-ups of IBD, such as Crohn’s disease and ulcerative colitis [3].

This was part of the second phase of the Human Microbiome Project (HMP); the first phase of the HMP launched in 2007 by the National Institute of Health (NIH) Common Fund, intended to characterize the microbiome in healthy adults and people with specific microbiome-associated diseases.

In this Harvard-MIT study, researchers conducted the most comprehensive analysis to date of human microbiome interactions during IBD. Researchers examined and followed 132 patients for one year and compared Crohn’s disease and ulcerative colitis patients to a control group of patients who did not have IBD. During this time, researchers collected stool samples every two weeks, blood samples every four months, and a set of colon biopsies at the beginning of the study [3].

Researchers evaluated the samples they collected through unparalleled [never used before] molecular, cellular, and clinical tools so that they can understand the biochemistry behind IBS.

These thorough measurements helped scientists be able to observe and verify previously known information, such as the information provided above by Washington State University. They confirmed that during certain diseases, there was a loss or gain of specific “pro” and “anti-inflammatory” microbes during various diseases.

Further, the new tools used in the study helped researchers to understand the reasons for these changes. The study results show that during different periods and stages of the disease, patients with IBD had fewer microbially-derived chemicals, which be a consequence of a variety of factors, including diminished favorable microbial activity, decreased nutrient absorption, more fluids in the bowels (water or blood), and more acute bowel movements [3].

Either a combination of these factors or these factors individually destabilize the overall microbiome in the gut, which can lead to inappropriate immune responses or an overreaction to healthy gut microbiome in IBD patients.

More interesting, though, was that the researchers noticed that during specific periods of disease activity in IBD patients, there were higher levels of polyunsaturated fats, such as arachidonate and adrenate. Further, nicotinuric acid, a metabolite of nicotinate, was found solely in the stool of IBD patients. Nicotinuric acid is a product of the metabolism of niacin (vitamin B3) and fatty acids [4] [5]. Moreover, the researchers noted that the stool of patients with IBD had depleted levels of vitamin B3 and B5.

The researchers also found that bile acids, a set of compounds produced by humans but altered by the microbiome, were depleted in IBD patients, as well as specific bacteria in the genus Subdoligranulum during inflammatory periods.

Overall, this study helps to add to the newly developed pile of evidence supporting the beneficial role the microbiome plays in human health. Further, this information has allowed the possibility for natural health physicians to help patients with IBD.

Evidence of a Brain Microbiome

Although the gut microbiome was unknown until the late 1990s, since then, research has been able to paint a rather colorful picture of its benefits, so we have a competent understanding of it.

However, there is newer research that suggests there might be a previously unknown microbiome in the human brain. Previously, the human brain was generally regarded to be the most sterile part of the human body. After all, it was believed any bacteria in the brain could lead to inflammation, and an inflamed brain is not a good thing. Yet, a 2014 study found that the placenta harbors a unique microbiome [6], and a 2017 study found that even the eye has a microbiome [7]. Like the brain, the placenta and eye have been regarded as sterile, but research now calls that belief into question.

A study posted at the November 2018 Society for Neuroscience scientific conference has challenged the assumption that the brain is a sterile environment [8].

Researchers at the University of Alabama in Birmingham showed high-resolution microscope images of bacteria ebulliently occupying astrocytes, which are star-shaped brain cells that interface between and support neurons.

Researchers were not looking for bacteria but discovered it fortuitously.

An undergraduate researcher named Courtney Walker was comparing brains of healthy people to brains of people with schizophrenia to see the structural differences underlying the disease, and Walker noticed rod-like structures in the brain samples. She told her professor, Dr. Rosalinda Roberts, and after consulting with some colleagues, they learned the structures were bacteria. Upon examining the other brain samples, each of the thirty-four samples had that bacteria.

Being incredulous, Roberts thought perhaps the brain samples were contaminated during transport, so Roberts and her team decided to examine mice brains immediately after death.

Still bewildered, the team found bacteria in the mouse brains as well. They took it further and raised new mice in a clean, bacteria-free environment, and decided to examine the brains once more. This time, however, they found no bacteria in the mice brains that were raised in a sterile environment. This finding indicated that the bacteria in the brain either came from inside the body or from the external environment.

Still intrigued, Roberts and her team examined which type of bacteria the bacteria in the brain was. After the long process of RNA sequencing, they noted that most of the bacteria in the brain were Firmicutes, Proteobacteria, and Bacteroidetes, which are commonly found in the gut.

This has opened many new questions: How did the bacteria get into the brain? Did they climb nerves or traverse blood vessels? How does the brain microbiome differ in people with cognitive dysfunction diseases?

Most of these questions will have to be answered in the new, emerging scientific field that investigated the brain’s immune system, psychoneuroimmunology, but for now, the discovery offers tantalizing evidence of a brain microbiome.


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[1] https://www.nature.com/articles/s41586-019-1237-9

[2] https://depts.washington.edu/ceeh/downloads/FF_Microbiome.pdf

[3] https://www.nature.com/articles/s41586-019-1237-9

[4] https://www.merriam-webster.com/medical/nicotinuric%20acid

[5] http://foodb.ca/compounds/FDB023135

[6] https://www.ncbi.nlm.nih.gov/pubmed/24848255

[7] https://jamanetwork.com/journals/jama/article-abstract/2649167

[8] https://www.abstractsonline.com/pp8/#!/4649/presentation/32057