Is An Imbalanced Gut Microbiome Affecting Your Mental Well-Being?

Published on: Mar 3, 2024

How Dysbiosis Impacts Mental Health: Part Three in the Series

In Part Three of my Digestion and Mental Health Series, we’ll explore the powerful connection between gut dysbiosis and mental health. 

The trillions of tiny microbes living in our digestive tract make up the human gut microbiome: the diverse community of bacteria, viruses, fungi, and other organisms that play a role in digesting the food we eat, fighting infection, and ultimately, keeping us physically and mentally healthy. In fact, because of its profound impact on our mental health and well-being, the gut microbiome is commonly known as our second brain! We have our vagal nerves to thank for this connection between the gut and brain (i.e. the gut-brain axis). 

When there’s a disruption in the gut-brain axis; however, it has the potential to affect us both physically and mentally. Chronic stress, trauma, leaky gut, and dysbiosis are just a few of the factors that affect the gut-brain crosstalk — impairing our digestion and increasing our susceptibility to mental health concerns such as major depression, anxiety, attention-deficit/hyperactivity disorder (ADHD), and others. 

Let’s take a closer look at how dysbiosis may affect your mental well-being so you can take steps to boost gut health, treat depression and anxiety, and reduce neuroinflammation.  

What is Dysbiosis?

As I mentioned above, the human gut microbiome consists of trillions of microbes. Most of them are protective (like Lactobacillus, Bacillus, and Bifidobacterium), but others (such as Escherichia coli, Clostridium difficile, and Helicobacter pylori) are potentially harmful. Especially when more harmful microbes live in our bodies than beneficial ones. 

While the “good” and “bad” microbes in our guts can usually coexist without issue, certain disturbances (like physical and psychological stress, trauma, and gut inflammation) may alter the composition and function of our microbiome. This creates an imbalance of “helpful” and “harmful” bacteria in our guts, which we call dysbiosis. Characteristics of gut dysbiosis include:

  • Decreased microbial diversity in the microbiome.
  • A loss or deficit of protective microbes in the gut. 
  • An overgrowth of harmful microbes in the gut. 

Other disturbances that may trigger gut dysbiosis include infections such as COVID-19; high-sugar/low-fiber diets; and exposure to xenobiotics (e.g. antibiotics, food additives, artificial sweeteners, and preservatives). Genetic factors also come into play, as certain genetic variants are associated with alterations in microbiome composition. 

Genetic Variations Associated with Gut Dysbiosis

Having one or more genetic variations associated with alterations in microbiome composition doesn’t necessarily mean we’ll go on to develop dysbiosis of the gut, as our genes are just one piece of the puzzle. However, knowing our genes can help us gain clarity into how our unique bodies work, guiding us in choosing the best foods, probiotics, supplements, and well-being practices for optimal health and wellness. This is why nutrigenomics is such an integral part of my approach to holistic mental wellness!

Several genes associated with alternations in microbiome composition include the following:


According to an article in Gastroenterology that explores the link between genetics, intestinal dysbiosis, and inflammatory bowel disease (IBD), variations in the NOD2 gene are associated with lower amounts of Faecalibacterium in the gut and higher amounts of Escherichia and Bacteroides vulgatus. Variants in the NOD2 gene are also known to increase one’s risk of developing Crohn’s disease.


In the same article referenced above, variations in genes CLEC7A and CARD9 were associated with lower amounts of Lactobacillus in the gut — a beneficial type of lactic acid bacteria. Homozygous variations in the CARD9 gene have also been linked to increased susceptibility to chronic mucocutaneous candidiasis, a type of fungal infection affecting the skin or mucosa. We’ll talk a bit more about candida — a member of the gut mycobiome — later on in this blog post. 


According to an article published in Gut Microbes, “genetic manipulations in animals induce both behavioral changes and gut microbiome remodeling”. (Cheng, et. al, 2023). In mice, for instance, variants in the genes SHANK3, SHANK3B, CHD8, CNTNAP2, EPHB6, NLRP3, EPHX2, and CHRNA7 have all been associated with altered gut microbes and behavioral phenotypes related to autism spectrum disorder (ASD), anxiety, and depression. 

Without going into too much detail on this topic, preclinical studies have shown that mice with variations in the CHD8 gene have a lower abundance of Bacteroides uniformis in their gut microbiome — while those with variations in SHANK3, SHANK3B, and CNTNAP2 have lower amounts of Lactobacillus reuteri. Genetic variations in these genes (along with EPHB6 — which is linked to low abundance of Mucispirillum in mice) are all associated with ASD-like behaviors.

Gut Dysbiosis & Mental Health

While intestinal dysbiosis often causes gut-related symptoms like diarrhea, constipation, and acid reflux, imbalances in the gut microbiome can also affect our psychological health and well-being. Namely our mood, behavior, and cognition. Again, it all boils down to the gut-brain axis!

How Gut Imbalances Affect Mental Wellness

According to a recent article published in Behavioural Brain Research, “gut dysbiosis is associated with the progress or worsening of major depressive disorder (MDD) by involvement with various aspects of gut-brain axis (GBA) such as activation of the immune system or alteration of gut-brain communication.” (Rathour, et. al., 2023). This is because the GBA connects the central nervous system to our gut microbiota, allowing the gut and brain to communicate with one another. Dysbiosis; however, disrupts the gut-brain axis. 

That said, targeting the various pathways involved in the dysregulation of the gut-brain axis is shown to be an effective treatment for depression. Doing so can also help with restoring a dysregulated gut-brain axis and normalizing the composition of the gut microbiome. 

Various pathways involved in the dysregulation of the GBA include:

  • Fatty acid metabolism.
  • Neuropeptide, gut hormone, and neurotransmitter synthesis.
  • Tryptophan metabolism alteration.
  • Immune system activation. 

While there isn’t a one-size-fits-all treatment for gut dysbiosis, GBA dysregulation, or depression, it’s my goal as a registered dietitian nutritionist and holistic mental wellness coach to help you explore the options that will best fit your unique mind-body-soul

For some, this might mean taking probiotic and/or prebiotic supplements — while others may choose to get their probiotics and prebiotics from foods alone. There are plenty of good-mood foods and recipes I can recommend, and I offer customizable personalized meal plans as well. 

The Gut Mycobiome & Mental Well-Being

Now that we’ve explored the link between our gut microbiota and mental health, let’s take a moment to talk about the mycobiome: the fungal community residing within our microbiome. Key members of the mycobiome include yeasts such as Saccharomyces, Candida, and Malassezia. 

While the fungal component of the microbiome is low in diversity, alterations in gut mycobiome composition have been linked to neurological disorders such as Rett syndrome, autism spectrum disorder, and Alzheimer’s disease; bipolar disorder and schizophrenia; and ADHD. Specifically in the case of Candida overgrowth.

Gut Mycobiome Dysbiosis & ADHD

In a recent study published in the Journal of Child Psychology and Psychiatry, for instance, researchers collected the fecal samples of 35 healthy controls and 35 children with attention-deficit/hyperactivity disorder. They found that the ADHD group had lower amounts of Basidiomycota and greater amounts of Ascomycota and Candida, concluding that intestinal permeability and dysbiosis of the gut mycobiome may be associated with increased susceptibility to developing ADHD. 

Candida & Alzheimer’s Disease

There’s even evidence of Candida infections in the brain contributing to the development of Alzheimer’s disease. But fortunately, rebalancing the gut microbiome with probiotics, prebiotics, and synbiotics can have promising effects in those with Alzheimer’s disease and mental health conditions like depression, anxiety, and postpartum depression. 

Gut Dysbiosis & Autoimmunity

Dysbiosis — along with genetic and environmental factors — can also contribute to the development of autoimmune diseases such as Hashimoto’s thyroiditis. This could explain why those with Hashimoto’s disease have an increased risk of developing anxiety and depression. More reasons to rebalance the gut microbiome; prioritize quality sleep; and nourish your mind, body, and soul!

Balanced Gut, Positive Mood

Knowing dysbiosis can affect our mind, mood, health, and overall well-being may seem a bit scary, but the good news is there are evidence-based nutrition and lifestyle practices to treat dysbiosis of the gut — along with the long list of psychological concerns that tend to go along with it. Change is possible and I’m here to guide and empower you on your holistic mental wellness journey!

Ready to nourish your unique body, mind, and soul so you can lead a healthier, happier, and more fulfilling life? Explore my holistic mental wellness coaching and nutrigenomics services or book a Complimentary Support Call to get started! 



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Howdy! I’m Haley. A registered dietitian nutritionist, yoga teacher, personal trainer, and holistic mental wellness coach on a mission to help you transcend the struggle, stress, and suffering that life can bring. I’ve lived through it and discovered a path to feeling amazing in my mind, body, and soul. Now, I want to help you to live your most fulfilled life too through evidence-based nutrition and lifestyle practices!

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