Bacteria in our gut is not necessarily a bad thing. As a matter of fact, we have 30-50 trillion cells in our body, but only 1 in 10 is actually “us”—the rest are bacteria, fungi, viruses, and other microorganisms, including your microflora—a.k.a. your microbiome. Our bodies contain anywhere from 2 to 3 pounds of this stuff!

What does gut bacteria do?

Our good bacteria help modulate our neurotransmitters, keeps our gut functioning correctly, helps make vitamins, and can influence genetic expression.

Their presence helps the immune system by stimulating the production of Secretory IGA (SigA) immunity as well as our T killer cells. The majority of our immune system resides in our gut, which makes sense considering our intestines are the wall to the outside world.

Gut bacteria also plays a role in:

  • Absorption of nutrients
  • Manufacture and utilization of vitamins and neurotransmitters
  • Aids in detoxification
  • Aids in bile acid metabolism
  • Help gut integrity by producing short chained fatty acids
  • Mitigates the effects of stress
  • Helps regulate blood sugar via incretin
  • Aids in adipose tissue regulation and weight gain
  • Influences antioxidant load
  • Activates neural pathway between the gut and brain
  • Supports carbohydrate metabolism
  • Helps support the use of omega-3 fatty acids, minerals, and phytochemicals
  • Modulates pain

How does gut bacteria affect my health?

Small Intestine Bacteria Overgrowth

There should be a ratio of 80% of good bacteria to 20% bad bacteria in the body. When the reverse happens, that’s referred to as dysbiosis. For instance, small intestine bacteria overgrowth or SIBO occurs when bacteria from the large intestine migrate in the small intestine–leading to pain, bloating, gas,  malabsorption, etc.

Genetic expression

When we think about the thyroid or brain, we look to Dr. Kharrazian PhD for insight, but when it comes to genetics and the human biome, Dr. Jeffrey Bland, PhD, is the man. In his book Disease Delusion, he discusses the importance of gut bacteria for our microbiome. Why is that so significant? Our microbiome goes on to influence our genes.

“The gut is where 50% of our immune system is localized, and is speaking directly 24/7/365 to the bacteria that live in the intestinal tract, so we might have a good family of what’s called the microbiome, these families of bacteria living in our gut. If you have a good one, then it speaks favorably to our genes; if we have an imbalance with some of these parasitic bacteria, clostridia and various types of the conjugating bacteria that can live in our intestinal tract, now it sends a message of alarm to our genes and we start getting inflammation and increasing risk of all sorts of disease. So, I think we now recognize that food, bacteria, human interaction is much more important and complex than we originally recognized.”


When pathogenic bacteria start to colonize, they start to kill off our friendly bacteria, and when bacteria die, lipopolysaccharides (LPS) from their cell walls are released into the gut. These particles are very small. They’re so small, in fact, that they can pass directly from the GI system into the bloodstream. According to Dr. Bland diet adds to the situation, “When we eat a high fat/high sugar diet, within the next few hours, the LPS creates chronic systemic inflammation throughout the body, increasing the risk of most chronic diseases, including dementia and diabetes.”

LPS is serious stuff. Dr. Kharrazian shared a video showing with LPS activating neuroinflammation in the brain. Those with head trauma and or stroke are most vulnerable as it can lead to priming of microglial cells. This is an irreversible process that not only effect the brain, but function throughout the entire body.


A recent study released by Neuroscience News in 2019 found bacteria in the soil generate a natural fat that may act as natural vaccine to stress.

“It seems that these bacteria we co-evolved with have a trick up their sleeve,” said Lowry. “When they get taken up by immune cells, they release these lipids that bind to this receptor and shut off the inflammatory cascade.” Overall, the study offers further proof that bacteria are important. “This is just one strain of one species of one type of bacterium that is found in the soil but there are millions of other strains in soils,” Lowry said. “We are just beginning to see the tip of the iceberg in terms of identifying the mechanisms through which they have evolved to keep us healthy. It should inspire awe in all of us.”

Chronic disease

Gut bacteria have been linked to many chronic diseases. You only need to type “gut bacteria and chronic health” into Google or PubMed to see links to diabetes, obesity, autism, Parkinson’s, macular degeneration, anxiety, depression, and more. The research showing the connection between the human biome to our physical and mental health can no longer be ignored.

Mental health

The Human Microbiome Project, launched in 2008, is creating a paradigm shift in world of neuroscience. Research indicates that gut issues such as infections and inflammation, may alter the species and population density of our resident microbiota. This means that our unique biome could influence our brain activity and emotions.

Studies have shown that sensory neurons are less active in germ-free mice, and, when the mice are given probiotics to restore their microbiome, the activity levels of the neurons return to normal. A metadata study published in the 2016 Journal of Neurogastroenterology and Motility, concluded that “probiotics showed efficacy in improving psychiatric disorder-related behaviors including anxiety, depression, autism spectrum disorder, obsessive-compulsive disorder, and memory abilities, including spatial and non-spatial memory.”

Another example of a bacterial connection is the link between antibiotic exposure and altered brain function. Per the 1997 article “Antibiotics: Neuropsychiatric Effects and Psychotropic Interactions”, documented side effects from these drugs ranged from anxiety to major depression, psychosis and delirium. It may even be that Pediatric Autoimmune Neuropsychiatric Disorders or PANDAS, which links streptococcus bacteria to OCD could be attributed to antibiotic use rather than to the bacteria itself.

Can eating fermented food help my microbiome?

Fermented foods have been around since ancient times and are found in cultures around the world, from Roman sauerkraut to India lassi to Korean kimchi. Just as fermented yeasts are used to make wine, sugars and starches are fermented with lactic acid to produce bacteria such as lactobacillus and bifidobacteria. This process is called lacto-fermentation. Learn more here.

If eating these foods make your symptoms worse, you may have issues with yeast, leaky gut, SIBO, etc. Best to heal your gut first or work with a practitioner to  help undercover the cause.

Does taking a probiotic help my gut?

For some taking probiotic supplements may be warranted. But if you have leaky gut, yeast, etc., it is best to heal your gut first before starting to avoid die-off reactions.  

Can prebiotics help my gut?

Why are prebiotics important? There are over 50 different types of bacteria in our colon, and these bacteria ferment soluble fibers such as inulin, fructooligosaccharides (FOS), and resistant starch (RS) to form acids such as butyric acid, propionate acid, and acetate. Because our body is so smart, it designed our gut cells to use these acids as fuel. And happy cells lead to a healthy gut lining. Learn more here.

What can I do to maintain good gut bacteria?

Stress, aging, dietary habits, and other lifestyle issues can contribute to gut dysbiosis. The most important thing you can do is to find and eradicate any underlying infections and sources of inflammation that may affect your flora. In addition, you may want to consider the following:

  • Limit the use of antibiotics—only use them when necessary. (Many people want to treat viruses with antibiotics, but antibiotics work against bacteria, not viruses).
  • Consume a healthy low-sugar diet that contains unpasteurized and fermented foods to help maintain your gut’s ecosystem.
  • Make fermented foods a normal part of you duet. It may be best to start by eating very small servings to avoid die-off and detoxification reactions. You may also want to include a variety of these types of foods in your diet to get the benefits of consuming a mix of microorganisms.
  • Use probiotics and prebiotic foods to maintain and/or re-colonize proper ratios of friendly to unfriendly bacteria in your gut temporarily.  Consider supplementation if necessary.
  • The use of supplemental short chained fatty acids and consumption of lots of fiber help maintain a healthy gut lining.
  • Don’t be afraid of your kids getting dirty. The “hygiene hypothesis” is a theory that says we have been keeping our kids in an environment that’s too sterile, thereby not enabling them to develop a normal flora.

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