Bacteria and the Gut: Can They Affect The Brain?

Gut Bacteria

Many people may consider bacteria a bad thing.  However, you may be surprised to know that we contain 10 times more bacterial cells than human cells within the average human body [1].  In fact, a healthy individual can occupy 10,000 different species and carry 360 times more bacterial genes than our own genes [2].  One could argue that we’re less than 10% human! 

The term ‘human microbiome’ refers to all the microorganisms (and their genes) living within the human body. In 2007, the Human Microbiome Project (HMP) was funded $173 million dollars by the National Institute of Health to study how these little organisms interact with the body. The researchers of this project have reported that these bacterial genes might contribute more to human survival than our own genes [2].  However, it’s incredibly complicated and there are still many questions to be answered. 

HMP researchers report that most of these bacteria live “in harmony” with us, and that everyone contains the pathogenic (disease causing) bacteria.  However, in healthy individuals, these pathogenic bacteria cause no problems.  Most of human microbes have beneficial impacts, whose functions are being studied intensively.  This article will summarize a few of the exciting, yet bizarre findings in microbiome research.



Ever had a “gut feeling” or an emotion you felt in your gut?  Our brain is connected to the gut by what’s called the enteric nervous system.  It’s been shown that gut inflammation can induce anxiety-like behavior, and change the biochemistry of the central nervous system [3].  Similarly, it’s known that patients with IBS have significantly higher levels of both anxiety and depression [4].  One could argue whether IBS causes anxiety, or that anxiety causes IBS.  Considering the emerging evidence, both arguments may be valid.  This gut-brain communication is bidirectional, with change in behavior overlapping change in the microbiome (gut bacteria) [5].

Serotonin is a popular neurotransmitter that makes us feel positive and euphoric.  It’s a chemical physicians increase in the body to treat anxiety or depressive disorders.  Interestingly, it’s estimated that 90% of serotonin is made in the gut [6]. What’s fascinating is that scientists have shown metabolites produced by gut bacteria signal to what are called ‘enterochromaffin cells’ (EC) in the gut.  These signals tell the EC cells to synthesize serotonin, increasing levels in the gut and blood [7].  This could partly explain why certain probiotic supplements have shown to improve mood and behavior in both humans and animals.  In fact, researchers have found that certain types of bacteria could decrease anxiety in mice more than drugs commonly used for general anxiety disorder, such as Lexapro [8].

In another study, human volunteers given a formulation of Lactobacillus helveticus and Bifidobacterium longum had significantly reduced depression and anxiety [9].

While possible mechanisms for this were earlier discussed (i.e. serotonin), there may be many other mechanisms at play.  For example, researchers gave the probiotic Lactobacillus rhamnosus to a specific breed of anxious mice, used to study anxiety.  These mice often hide, display low activity and are less motivated when forced to swim.  After receiving L. rhamnosus, these mice improved in all anxious parameters. 

These animals had an increased production of GABA receptors in relevant areas of the brain.  GABA receptors are what anti-anxiety drugs (e.g. Xanax) bind to.  Interestingly enough, this anti-anxiety effect wasn’t seen with mice that had undergone a vagotomy, indicating this bacterium was sending chemicals messages to the brain via the vagus nerve [10].  The mechanisms by which gut bacteria communicate through vagal nerves is much more complicated than the purposes of this article!

Probiotic supplements aren’t the only way to reap these benefits.  Fermented foods such as sauerkraut, kimchi, tempeh or yogurt (if you eat dairy), are good sources of probiotics.  In fact, a group of UCLA researchers were the first ones to show that eating probiotic foods can change connectivity between certain areas of the brain by using functional MRI scans [11].  It’s important to note that some probiotic foods, however, have been pasteurized or preserved.  When purchasing these foods, be sure the item states “live” or “active cultures”.

Another way our gut microbiome likely impacts mood is based on inflammation.  When we eat processed foods, it not only feeds the bad bacteria in the body, but it also increases inflammation in the body. The link between inflammation and mental disorders, such as anxiety and depression, is well known [12]. In fact, a study in JAMA Psychiatry found brain inflammation was 30% higher in clinically depressed individuals than controls [13]. Fortunately, it’s known that eating fiber-rich foods can favor the growth of beneficial bacteria, while reducing inflammation.  This could lower the risk of mental dysfunction and reduce the risk of cancer [14].


What Foods Improve Gut Health and Our Microbiome?

What’s good for us is also good for our microbiome:  vegetables, nuts, seeds, fruits and legumes.  These foods have thousands of diverse fibers/complex carbohydrates that have beneficial effects.  It’s estimated that our hunter-gatherer ancestors consumed on average 86 grams of fiber per day [15], while the average American currently consumes about 8 grams per day.

Foods abundant in fiber/complex carbohydrates can increase the growth of beneficial bacteria [16], which maintain gut integrity, protect us from pathogens, modulate immunity and even increase the nutritional value of food.  In fact, it’s known that animals with a healthy microbiome require 30% less caloric intake than germ-free animals (i.e. absent microbiome) [17].

What’s empowering is that eating fiber-rich foods can actually decrease the amount of bad bacteria within us [18].  Conversely, diets high in refined carbohydrates (flour, sugar, syrups, etc.) are found to increase the growth of pathogenic bacteria, such as Clostridium difficile and Clostridium perfringens [19].  These bacteria can provoke inflammation, which was earlier mentioned to negatively affect mental health.

A diet-dependent microbiome is an important concept to grasp, because bacteria like C. difficile can cause a long list of health issues.  C. difficile forms various toxic compounds, such as p-cresol [20]. P-cresol is a human carcinogen (cancer-causing agent), which can also affect the central nervous system, cardiovascular system, lungs, kidney and liver [21].

Autistic and schizophrenic individuals are known to have increased colonization of C. difficile in the gut, and its toxic metabolites are found at concentrations 300 times higher in the urine of autistic and schizophrenic individuals [22].  These metabolites can deplete what are called brain ‘catecholamines’ and cause autistic-like behavior in animals.

Keep in mind that many things can impact mental status.  However, gut health is a big piece of the puzzle that many physicians are missing.  With each meal we should be conscious of how it may impact our mood or behavior.  Not only because of the impact food has on gut bacteria, but because there are many reports of diet affecting various psychiatric disorders, including schizophrenia, bipolar depression [23] ADHD [24,25] and autism [26,27].


Coauthor and researched by:

James Spurgeon

Naturopathic Medical Student

Bachelors of Science in Biology


Coauthor and edited by:

Angie Sadeghi, MD


Internal Medicine

Health Coach





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