Belly Blues and Mind-Altering Microbes

Depression and anxiety are leading causes of disability and impact millions of people worldwide.  Research continues to validate that our mood and brain function are primarily determined by the health of our gut and the balance of microbes that inhabit our gut. 

The connection between the gut and the human emotional state is so profound that the gut is often referred to as the second brain.   In fact, we should consider the gut and the brain as two parts of the same system. If you look at the communication pathways between the gut and the brain, there are almost two times more communication pathways going from the gut to the brain than from the brain to the gut. 

There is no other part of the body where this exists. The gut and the brain are connected in a bidirectional, autonomous communication system. The gut and the brain are in a very dynamic bidirectional relationship and Functional Medicine with its emphasis on “systems-based biology” has recognized this connection for years. 

Conventional Medicine

Conventional Medicine often views various body systems in terms of silos and continues to see depression and anxiety as imbalances in brain chemistry, not looking at connecting other potential root causes.  Depression and Anxiety are not solely chemical or brain-based disorders, and that isolated focus is the reason why so many people do not get better with conventional interventions and medications.

The mechanisms by which gut health and the microbes that inhabit our gut (microbiome) shape our mood and behavior are far too numerous to contemplate, let alone sufficiently cover in one article.  The foundational basis for their impact on the health and function of our brain is related to inflammation, as are most disease states. 


Depression is known to involve an inflammatory response and many beneficial bacteria in the gut produce short-chain-fatty acids like butyrate, which help to feed the cells lining the gut to reduce “leaky gut” and thereby inflammation. 

Butyrate is essential in maintaining and promoting healthy intestinal integrity and thereby decreasing various toxins and inflammatory compounds from entering our system and inducing inflammation.  

So, an imbalance of gut bacteria (dysbiosis) and a damaged gut can often lead to increased intestinal barrier permeability (leaky gut).  Once the gut becomes permeable, unwanted compounds can cross the intestinal barrier, enter the bloodstream, and can trigger problems systemically. Once these compounds reach the brain, they may affect brain function and balance. 

Intact healthy protective membranes are a foundation of health: leaky gut = leaky Blood Brain Barrier.  Gut dysfunction negatively impacts brain function and our mood. 

In addition to maintaining a protective barrier, the microflora in the gut also produce various signaling molecules (neurotransmitters) that affect the brain’s neurons, supporting better mental health. 

Many neurotransmitters are synthesized in the gut as well as the brain, including dopamine, GABA, serotonin, and norepinephrine. In fact, roughly 95% of the serotonin in the body comes from the gut.  The brain is dependent upon the gut for our “feel good” neurotransmitters and “happy hormones.” 

Keep in mind that the gut microbiome is highly malleable and can be altered throughout our lifespan for good or bad.  Various environmental and lifestyle factors influence the composition and balance of our microbiome and integrity of our gut lining in a positive functional capacity or a dysfunctional, inflammatory, disease provoking manner. 

Microflora in the Gut – Beneficial Microbes

A balanced, healthy, diverse microbiome adequately nourished by a biodiverse primarily plant-based diet, containing a large variety of fibers and polyphenols can improve our mood and support our stress response.  Studies have shown that fermented foods that contain the beneficial microbes and specific prebiotic fibers and polyphenols that feed these beneficial microbes can lower cortisol levels.  

The beneficial microbes in our gut ferment the prebiotic fibers and polyphenols to produce a plethora of vital compounds such as butyrate, neurotransmitters, vitamins and support healthy function of our hormones and blood sugar regulation. 

As we progress in our understanding of the critical gut brain connection, it would be advantageous to prescribe Kimchi for example, as a “calming medication” along with other gut friendly foods, fibers, and polyphenols. 

Standard American Diet (SAD)

Conversely, the Standard American Diet (SAD) and its very appropriate acronym the SAD diet, literally starves our microbial friends with its emphasis on refined carbohydrate sources and a lack of colorful plants. 

The SAD diet is devoid of the vital fibers and polyphenols necessary to feed and support the function of health promoting and mood lifting microbes.  In fact, components of the SAD diet such as sugar, refined carbohydrates and saturated fats feeds inflammatory species of gut bugs that make produce inflammatory compounds and disrupt the integrity of our gut lining.  

Certain medications such as antibiotics and acid-blocking medication decimate our gut gardens by decreasing the population of healthy microbes and inhibiting the function of those remaining. 

These two medications are the most prescribed medications in the US and have been show in multiple studies to increase the risk for depression. In fact, studies have shown an incremental increase in depression and anxiety related to each course of antibiotics taken and the time spent on acid-blocking medications. 

Spore-based Probiotics

One of the most potent positive modifiers to our gut microbiome are spore-based probiotics that function in a unique manner to upregulate the communication system between microbes in our gut. 

A foundational concept is that all the microbes in our body and our body systems are in constant communication in a healthy system-this is one of the ways our body maintains balance or homeostasis. 

The use of spore-based probiotics is highly important, as spore-based probiotics are designed to survive through the gastric system and colonize well to produce potent, positive effects on our sensory system in the gastrointestinal tract. 

Spore-based probiotics are important to police and defend the gut from unwanted microbes and to support the growth of the natural beneficial species found in each individual.   

Women and Depression 

Women are more prone to depression, especially when estrogen levels decline and again one of the root causes may be linked to the gut microbiome, as evidenced by a recent study published study in Cell Metabolism.  The researchers demonstrated a connection between depression in premenopausal women and a microorganism in the gut (Klebsiella aerogenes) that can express an enzyme known to degrade estradiol.

Specifically, depression was associated with the degradation of estradiol through this enzyme.  They proposed that future ways to address depression in women may be connected with therapeutically altering certain estradiol-degrading bacteria which express this enzyme so that there isn’t such a rapid breakdown of this hormone in the gut.


Many factors can contribute to depression, but as was mentioned, inflammation and oxidative stress are thought to play significant roles. When it comes to these root causes, food choices may either harm or improve the situation.  For example, a recent meta-analysis of 547,606 study participants demonstrated that sugar intake and inflammatory foods (such as those found in a typical Western or processed foods diet) were highly correlated with depression.

The nutrients in our food provide the building blocks necessary for healthy brain and neurotransmitter processes.  Also, the phytonutrients and fiber found in colorful plants provide the necessary “food” for the mood boosting healthy microbes in our gut.  This is one of the reasons why a diet rich in fruits and vegetables can help to boost a sense of wellbeing.  

It’s important to focus on variety as you are building your mood-boosting diet, as we are discovering that different species of beneficial microbes prefer different fibers and polyphenols from a variety of plants.  Therefore, if we want to “seed and feed” a diverse species rich microbiome, we must incorporate a diversity of plant-based foods. 

Biodiversity in our diet supports biodiversity of our microbiome.  Diversity equals strength and resilience in any community, and it is of utmost importance for the “community” of microbes that inhabit our gut, as each species has its own role to play in our physical and mental health.  When we have a diverse and balanced microbiome, it helps to support gut-brain axis health.  

One study that illustrates the importance of a biodiverse diet followed the dietary habits of 4,105 Australian men and women over the course of 12 years found that consuming 4 to 6 different vegetables per day was associated with a 24-42% lower risk of experiencing symptoms of depression compared to eating only 3 different kinds of vegetables!  

At AustinMD, with our advanced testing and individualized protocols, we provide our clients a unique brain support opportunity with specific targeted protocols- including ZenBiome Cope and ZenBiome Sleep.

These probiotic based products contain specific bacterial cultures called “psychobiotics” that play a role in the gut-brain axis and support brain health in addition to different herbs and vitamins shown to support brain health and reduce anxiety and depression.

Scientific research suggests that consuming psychobiotics could be a viable option to maintain and support mental wellbeing without possible undesired secondary effects from traditional remedies.

Increasing evidence suggests that a brain–gut–microbiome axis exists, which has the potential to play a major role in supporting a healthy mood and modulating behavior.  Therefore, supporting a robust and diverse microbiome is a critical step in supporting mental health.


Share this post
You may also like