Mental Health May Depend on the Health of Your Gut Flora

Mental Health

Story at-a-glance -

  • Mice without microbes in their intestines are unable to recognize other mice around them
  • When the intestines of germ-free mice were colonized with bacteria from other mice, they took on aspects of the donor’s personality
  • Probiotics alter brain function in adults in regions linked to emotion and sensation
  • Nourishing your gut health with fermented foods is vital to nourishing your mental and emotional health

By Dr. Mercola

When it comes to your mental health, your behavior, and even your mood, we tend to think that the brain is in charge. In reality, your gut may be calling the shots. In the 1800s and early 1900s, it was thought that wastes in your colon could produce infections that lead to depression and psychosis.

Widely accepted for a time, mental-health patients were often treated with colonic purges and bowel surgeries, but eventually this was regarded as quackery.

Today, research is bearing out what the scientists of yesteryear were already privy to – that your mental health is very much dependent on the microbes in your gut. As Scientific American reported:1

"Scientists are increasingly convinced that the vast assemblage of microfauna in our intestines may have a major impact on our state of mind."

Your Gut Is Intricately Connected to Your Brain

In addition to the brain in your head, embedded in the wall of your gut is your enteric nervous system (ENS), which works both independently of and in conjunction with the brain in your head.

Your ENS contains 500 million neurons and is thought to be largely responsible for your "gut instincts," responding to environmental threats and sending information to your brain that affects your well-being.

This communication between your "two brains" runs both ways and is the pathway for how foods affect your mood.

For example, fatty foods make you feel good because fatty acids are detected by cell receptors in the lining of your gut, which then send warm and fuzzy nerve signals to your brain.

However, this gut-brain connection is far more than just comfort food or butterflies in your stomach. According to Scientific American:2

"The gut-brain axis seems to be bidirectional—the brain acts on gastrointestinal and immune functions that help to shape the gut's microbial makeup, and gut microbes make neuroactive compounds, including neurotransmitters and metabolites that also act on the brain.

These interactions could occur in various ways: microbial compounds communicate via the vagus nerve, which connects the brain and the digestive tract, and microbially derived metabolites interact with the immune system, which maintains its own communication with the brain."

Germ-Free Mice Show the Importance of a Microbiome

So-called germ-free mice, which have no microbiome to speak of, have altered behavior and brain function. In a study by John Cryan from the University College Cork in Ireland, mice without microbes in their intestines are unable to recognize other mice around them.

He believes that microbes may communicate with the brain and help us be social, which in turn allows the microbes to spread to others.3 In addition, mice lacking gut bacteria have been found to engage in "high-risk behavior," and this altered behavior was accompanied by neurochemical changes in the mouse brain.4

When examining the animals' brains, the researchers discovered a number of genetic alterations in the germ-free mice. According to The Guardian:5

"Brain-derived neurotrophic factor (BDNF) was significantly up-regulated, and the 5HT1A serotonin receptor sub-type down-regulated, in the dentate gyrus of the hippocampus.

The gene encoding the NR2B subunit of the NMDA receptor was also down-regulated in the amygdala. All three genes have previously been implicated in emotion and anxiety-like behaviors.

BDNF is a growth factor that is essential for proper brain development, and a recent study showed that deleting the BDNF receptor TrkB alters the way in which newborn neurons integrate into hippocampal circuitry and increases anxiety-like behaviors in mice.

Serotonin receptors, which are distributed widely throughout the brain, are well known to be involved in mood, and compounds that activate the 5HT1A subtype also produce anxiety-like behaviors."

Further, researchers have discovered that the absence or presence of gut microorganisms during infancy permanently alters gene expression. Through gene profiling, they were able to discern that absence of gut bacteria altered genes and signaling pathways involved in learning, memory, and motor control.

This suggests that gut bacteria are closely tied to early brain development and subsequent behavior.

These behavioral changes could be reversed as long as the mice were exposed to normal microorganisms early in life. But once the germ-free mice had reached adulthood, colonizing them with bacteria did not influence their behavior.6

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Psychobiotics: A New Treatment for Mental Health

Cryan believes beneficial microbes could one day be used to treat mental health problems in humans. He dubbed the compounds "psychobiotics." He told Scientific American:7

"That dietary treatments could be used as either adjunct or sole therapy for mood disorders is not beyond the realm of possibility."

Interesting research led by microbiologist Premsyl Bercik and gastroenterologist Stephen Collins also found that when the intestines of germ-free mice were colonized with bacteria from other mice, they took on aspects of the donor's personality.8

Other research shows that women who had high prolonged fevers during pregnancy are more likely to have children with autism.

The finding held up in mice, too, and the MIA (maternal immune activation) mice were also found to have leaky intestines and abnormal microbiomes – a common occurrence in children with autism as well.9

Of particular importance, when the MIA mice were treated with a microbe called bacteroides fragilis, their gut permeability was corrected and many of their behavioral symptoms went away. According to the researchers:10

"…these findings support a gut-microbiome-brain connection in a mouse model of ASD [autism spectrum disorder] and identify a potential probiotic therapy for GI and particular behavioral symptoms in human neurodevelopmental disorders."

How the GAPS Diet May Help Autism and More

Research by pioneers such as Dr. Natasha Campbell-McBride also shows there's a profound dynamic interaction between your gut, your brain, and your immune system.

She has developed what might be one of the most profoundly important treatment strategies for preventing and treating autism, as well as a wide range of other neurological, psychological, and autoimmune disorders—all of which are heavily influenced by your gut health.

Her findings show that children born with severely damaged gut flora are at a significantly increased risk of vaccine damage, which may help explain why some children develop symptoms of autism after receiving one or more childhood vaccinations while others do not.

Autism isn't the only potential outcome in this case. GAPS may manifest as a conglomerate of symptoms that can fit the diagnosis of either autism, or attention deficit hyperactivity disorder (ADHD), attention deficit disorder (ADD), dyslexia, dyspraxia, or obsessive-compulsive disorder, just to name a few possibilities.

Digestive issues, asthma, allergies, skin problems, and autoimmune disorders are also common outgrowths of GAPS, as it can present itself either psychologically or physiologically. It's critically important here to understand that the gut flora your child acquires during vaginal birth is dependent on your—the mother's—gut flora. So if your microflora is abnormal, your child's will be as well. Hence, addressing your gut health prior to, and during pregnancy, is essential.

The GAPS diet consists of easily-digestible foods that are dense in nutrition, including fermented foods. In general, avoiding processed foods and foods high in sugar/fructose is an essential component of a gut-healthy diet, as sugar feeds harmful bacteria and throws your microflora off kilter. For more information, please see my interview with Dr. Campbell-McBride, below.

Probiotics Alter Brain Function in Adults

Much of the research on the gut-brain connection has been conducted on mice, because we don't have "germ-free" humans around… however, research has been conducted on adults with promising results. For instance, women who regularly ate yogurt containing beneficial bacteria had improved brain function compared to those who did not consume probiotics.11 Specifically, they had decreased activity in two brain regions that control central processing of emotion and sensation:

  • The insular cortex (insula), which plays a role in functions typically linked to emotion (including perception, motor control, self-awareness, cognitive functioning, and interpersonal experience) and the regulation of your body's homeostasis
  • The somatosensory cortex, which plays a role in your body's ability to interpret a wide variety of sensations

The fact that this study showed any improvement at all is remarkable, considering they used commercial yogurt preparations that are notoriously unhealthy -- loaded with artificial sweeteners, colors, flavorings, and sugar. Most importantly, the vast majority of commercial yogurts have clinically insignificant levels of beneficial bacteria. Clearly, you would be far better off making your own yogurt from raw milk—especially if you're seeking to address depression through dietary interventions. Keep in mind that some signs of depression aren't widely known or may even be counterintuitive. Following are some of the more subtle signs of depression to keep an eye out for:12

Aggression or hostility


Withdrawing from those you love

Extreme fatigue (mental and physical)

Seeking out an affair

Lashing out or being very short-tempered


Inability to concentrate

Extreme guilt

Self-medicating with alcohol, cigarettes, food, or other addictions

How to Help Your Gut Flora Flourish

Your gut bacteria are vulnerable to your diet and lifestyle and can be harmed by:

Antibiotics, unless absolutely necessary (and when you do, make sure to reseed your gut with fermented foods and/or a probiotic supplement)

Conventionally raised meats and other animal products, as CAFO animals are routinely fed low-dose antibiotics, plus genetically engineered grains, which have also been implicated in the destruction of gut flora

Processed foods (as the excessive sugars, along with otherwise "dead" nutrients, feed pathogenic bacteria)

Chlorinated and/or fluoridated water, especially in a hot shower, which is worse than drinking it

Antibacterial soap

Agricultural chemicals

In addition to avoiding the harmful aspects above, reseeding your gut with beneficial bacteria is essential for maintaining proper balance and achieving optimal physical and mental health. In light of this, here are my recommendations for optimizing your gut bacteria.

Fermented foods are the best route to optimal digestive health, as long as you eat the traditionally made, unpasteurized versions. Healthy choices include lassi (an Indian yoghurt drink, traditionally enjoyed before dinner), fermented grass-fed organic milk such as kefir, various pickled fermentations of cabbage, turnips, eggplant, cucumbers, onions, squash, and carrots, and natto (fermented soy).

Fermented vegetables, in particular, are an excellent way to supply beneficial bacteria back into our gut. As an added bonus, they can also a great source of vitamin K2 if you ferment your own using the proper starter culture. We had samples of high-quality, fermented organic vegetables made with our specific starter culture tested, and a typical serving (about two to three ounces) contained not only 10 trillion beneficial bacteria, but it also had 500 mcg of vitamin K2, which we now know is a vital co-nutrient to both vitamin D and calcium. Most high-quality probiotic supplements will only supply you with a fraction of the beneficial bacteria found in such homemade fermented veggies, so it's your most economical route to optimal gut

Probiotic supplement. Although I'm not a major proponent of taking many supplements (as I believe the majority of your nutrients need to come from food), probiotics is an exception if you don't eat fermented foods on a regular basis.