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Mood-Related Gut Microbiome – The Role the Gut Plays in Mood

Most people know that maintaining a healthy gut microbiome plays a key role in promoting optimal digestive function and immune responses. Microbiome refers to an internal ecosystem made up of different microorganisms (e.g., bacteria, viruses, fungi) that naturally live in the gut. The body’s natural microbiome is typically kept in balance by specific components such as immune-influencing cells, proteins, and enzymes that support the growth of good microorganisms and disrupt the growth of harmful ones [1]. Diet, age, and the use of certain medications also influence microbiome diversity.

What some individuals may not realize is that while the gut microbiome directly contributes to digestive health, it also has a strong impact on mood [2]. This means that unexplained mood fluctuations, anxiousness, poorly controlled stress, feelings of hopelessness, and other emotional issues may be linked to gut problems.

For people with chronic mental health or mood-related difficulties, gastrointestinal distress and abnormal immune responses are common problems that often develop due to an issue called dysbiosis—better known as gut microbiome imbalance [3]. Research even indicates that the gut microbiome influences mental development, emotion control, behavior, and performance in individuals with neurodevelopmental problems [4, 5].

How Does the Gut Influence the Brain?

Gut health is linked to mental health because the GI tract promotes the transfer of essential nutrients throughout the entire body, including the brain. This includes vitamins, minerals, and proteins the brain uses as a source of energy as well as antioxidants that heighten its natural defenses [6]. However, the gut does more than just absorb, digest, and transfer nutrients—it also impacts the body’s ability to regulate mood and behavior through an intricate system called the gut-brain axis.

What Is the Gut-Brain Axis?

The gut-brain axis is an elaborate connection between the GI environment and the brain [7]. This includes about 70 to 80 percent of the body’s immune cells along with a highly complex network of nerves that are located exclusively in the GI tract [8, 9]. This complex system allows the transfer of important signals between the brain and the gut [9].

More specifically, this network of structures supports communication between the brain and the gut that reinforces proper digestive function as well as optimal mood, emotions (e.g., motivation), and higher cognitive processes (e.g., memory, thought processing) [6]. Research indicates that the gut-brain axis achieves these benefits by monitoring numerous processes that include [8, 9]:

  • The activation of intestinal immune system responses
  • The intestinal transfer of food particles, cells, and other molecules
  • The production of GI hormones involved with digestion, absorption, and nutrient use

The gut-brain axis responds to these types of biological changes by linking the central nervous system (CNS)—which refers to the cognitive, emotional, and physical control centers of the brain—with intestinal functions that work toward sustaining balance. When this system works properly, the digestive pathway and CNS engage in continuous crosstalk that helps sustain good overall health. Unfortunately, there are several factors that may cause or worsen GI issues and mental health problems (e.g., mood fluctuations) by disrupting the gut-brain axis.

Factors That Disrupt Gut-Brain Axis Function

Factors such as an unhealthy diet (e.g., fast food or processed products), the overgrowth of harmful microorganisms in the gut, and taking certain types of medication may cause tissue damage that alters the structural integrity of the intestinal lining. This issue may cause gut-brain axis dysfunction due to leaky gut, which refers to digestive problems that develop when specialized structures in the intestines called tight junctions begin to loosen. When this occurs, undigested food particles, toxins, or foreign invaders start to leak through the wall of the intestine [10].

Tight junctions are small gaps in the intestinal lining that allow nutrient transfer but prevent undesirable particles from passing through the GI tract into the bloodstream. Complications that cause junctions to loosen allow harmful substances to pass into the bloodstream, where they can quickly accumulate and lead to different types of inflammatory problems [11].

In addition to inflammation, complications such as food sensitivities, gas, bloating, cramps, diarrhea, and constipation may develop due to leaky gut. Over time, this type of gut dysfunction can also contribute to the absence of healthy bacteria that would otherwise boost digestion and enhance defenses against invaders [11]. The loss of essential gut bacteria is also linked to frequent antibiotic use as research shows that antibiotics destroy certain forms of beneficial bacteria [12].

Some healthcare professionals do not recognize leaky gut as an actual medical diagnosis, but mounting clinical research demonstrating the influence that leaky gut has on the gut-brain axis indicates that this is a true condition [11]. Furthermore, gut-brain axis dysfunction caused by leaky gut is associated with the development of various health problems, such as asthma, allergies, skin disorders, and chronic fatigue syndrome (CFS) [10, 13, 14]. In addition, many people with persistent mood fluctuations, mental difficulties, or neurodevelopmental problems tend to suffer from digestive issues including leaky gut [2, 12, 15].

Why Do Digestive Problems Disrupt Mood and Mental Health?

One of the main reasons mood control and mental performance are linked to digestive function is because continuous communication between the structures that comprise the gut-brain axis (e.g., GI nerves, immune cells, and microbiome) supports optimal cognitive function [12, 15]. In order to maintain proper communication, the intestinal environment must remain healthy, but a poor diet, medications (e.g., antibiotics), or a leaky gut may cause harmful substances to damage the intestinal lining.

If this happens, the damage may interrupt the digestion, absorption, and transfer of vital nutrients the brain needs. Similarly, if the nerves that line the gut become injured or inflamed due to gut-brain axis problems (e.g., leaky gut), the transfer of important signals that influence mental performance will be hindered as well. This means that persistent digestive issues can initiate or worsen mood disturbances or mental health problems [12, 15].

Another major issue involves changes that occur in the gut microbiome. More specifically, eating unhealthy foods, frequently taking antibiotics, or experiencing microorganism overgrowth can lead to dysbiosis—microbiome imbalance. Probiotics, which are also known as good bacteria, make up a large portion of the microbiome. These beneficial bacteria interact with the nervous system through their influence on immune responses, hormone signaling, and GI nerves that play a role in emotion control, learning, and memory [16]. Healthy levels of probiotics also enhance the absorption of nutrients in the gut and help stabilize the intestinal wall [16, 17]. These processes heighten the body’s ability to regulate mood and behavior.

Unfortunately, problems may arise due to a sluggish digestive system, nutritional deficiencies, or intestinal inflammation (e.g., leaky gut, invader overgrowth) that hinder the growth and activity of probiotics—making it hard for the gut-brain axis to support good mental health [16, 17]. This is because inflamed nerves along the gut-brain axis or low levels of probiotics create the optimal environment for harmful invader growth to impair the intestinal lining, decrease nutrient absorption, and disrupt the transfer of signals that regulate cognitive processes [18]. Reduced probiotic activity also interrupts the activity of chemical messengers in the brain called neurotransmitters.

A key neurotransmitter that influences digestion and mental function is serotonin [19, 20]. In particular, serotonin helps control stress responses, sleep patterns, emotion regulation, and appetite. It also reinforces key processes in the gut such as stomach acid production and proper GI movement. However, research shows that low levels of this vital neurotransmitter may contribute to feelings of despair, anxiety, and altered digestive function [19, 20]. Fortunately, in addition to protecting the lining of the intestines, probiotics also support optimal serotonin levels by targeting inflammatory particles that can negatively affect neurotransmitter activity.

Furthermore, the body uses the essential amino acid tryptophan to produce serotonin, but poor probiotic levels are linked to decreased tryptophan production [21]. Interestingly, probiotic supplementation boosts tryptophan levels and this supports heightened serotonin production [19, 21]. Enhanced serotonin release helps minimize anxiousness and stress while bolstering mood [21].

Therefore, healthy bacteria are a vital part of the gut microbiome that encourage a more pleasant mood by reinforcing healthy levels of important neurotransmitters, including serotonin, which is associated with less stress, nervous tension, and restlessness.  

Now that several possible explanations regarding how digestive problems may alter mood have been described, the next question is, what strategies target and reduce the risk of gut issues? 

Beneficial Strategies That Support Gut Health

Supplementing the diet with probiotics is one of the easiest strategies that help maintain sufficient levels of beneficial bacteria in the gut. Good bacteria provide natural defenses against bad bacteria by blocking the growth and spread of harmful invaders [17, 21]. Regular probiotic supplementation also enhances the absorption of vital nutrients such as zinc, magnesium, calcium, and iron by preventing them from being rapidly degraded by stomach acid [22, 23, 24]. This bolsters the concentration of nutrients that actually enter the bloodstream to ensure their delivery to vital organs (e.g., brain).

Taking probiotics regularly not only encourages optimal nutrient use but also targets abnormal inflammatory responses in the gut—a process that helps maintain the proper communication of important signals along the gut-brain axis [17, 21]. The loss of good bacteria is associated with poor brain-gut communication that often results in decreased mental performance, mood disturbances, and abnormal neurotransmitter activity [7, 25]. Inadequate communication is also associated with [7, 25]:

  • Social avoidance
  • Increased anxiousness
  • Poor memory function
  • Altered stress responses
  • A loss of desire for pleasurable activities
  • Reduced motivation to engage in social activity

However, these types of behaviors tend to improve if the diet is supplemented with probiotics regularly [17, 21]. This is because reinforcing probiotic activity in the gut enhances microbiome diversity and re-establishes proper gut-brain axis communication [16].

In addition to probiotics, micronutrient supplementation affords similar benefits. More specifically, increased dietary intake of omega-3 fatty acids, B vitamins, and vitamin E, for example, boosts the health of nerves throughout the body, including those along the gut-brain axis [26]. Magnesium also plays a major role in the transfer of signals between the gut and the brain, which means boosting the intake of this essential mineral is particularly important [27, 28]. Increased micronutrient intake may be in the form of dietary supplements or by consuming ample amounts of fruits and vegetables.

Another useful strategy that helps target digestive issues for people who are suffering from mood-related issues involves eliminating foods that irritate the GI tract or cause inflammation. Examples include:

  • Soy, eggs, and corn — These contain common allergens
  • Dairy products — Some people experience casein (milk protein) or lactose intolerance
  • Gluten-containing foods — This protein is another common allergen that is also hard to digest    

Avoiding these types of foods, when possible, helps the gut naturally recover from intestinal irritation or damage [18]. This is especially beneficial for people who have emotional or neurodevelopmental difficulties [15, 16, 17].

It is important to remember that these are just a few of the beneficial strategies that positively impact gut microbiome, mental function, and physical performance [21]. Highly trained health care professionals who specialize in functional medicine and psychiatry can also offer useful guidance that supports optimal health from the inside out. A specialist can even design an individualized program that targets specific needs.


Overall, research has repeatedly demonstrated a link between the gut microbiome and mood due to the strong influence various microorganisms in the GI environment have on the gut-brain axis [2, 7]. Healthy microbiome diversity supports [2, 9]:

  • Optimal nutrient use
  • Heightened physical health
  • Better immune system function
  • Enhanced cognitive performance (e.g., mood control)

Dysbiosis—an imbalance of the gut microbiome—can lead to or worsen mood, emotional, and mental health issues, but several beneficial strategies target this issue in order to promote microbiome balance. These include probiotic and micronutrient supplementation, which, according to research, foster a healthier gut and help boost mood for many people who struggle with emotion regulation [17, 26].

Micronutrient supplementation, in particular, addresses nutritional deficiencies that may contribute to microbiome imbalance, cognitive impairments, and mood-related problems [26]. Similarly, probiotics heighten digestive function by targeting harmful invaders linked to intestinal inflammation [17]. Good bacteria also optimize nutrient absorption as well as neurotransmitter activity, and some probiotics even release enzymes that assist with the digestion of food [17, 29]. This means that the combination of supplements with a healthy diet can shift an imbalanced intestinal environment in the right direction to encourage microbiome diversity that enlivens the body and mind for years to come.


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