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How the Gut Controls the Mind and Heals the Brain

gut health affects brain health

Believe it or not, many ancient people thought that most of our thinking and what we consider to be our ‘mind’ was centered in the heart. That’s where the sayings “follow your heart”, “heartbreak”, “follow your heart’s passion” and many others came from.

This was fairly rational for the time given that not much was known about human anatomy, but now we know definitively that our consciousness and control center is solely located in the brain, right? Well, not completely.

In our bodies, bacterial cells outnumber human cells and research is showing that they have a say in how the body operates and possibly how the brain functions as well. Bacteria are becoming known as ‘the forgotten organ’ for the role they play.

It has also been shown that when our body gets harmed, and more specifically our brains, the microbiome may be harmed and play an important role in the healing process.

The Role Bacteria Play In General Health

Given the importance, it’s startling how recent the discovery was of the true role bacteria play in our bodies. They are crucial for digestion, development and maintenance of the immune system, defense against infection, formation of blood vessels as well as acting as a wall of defense that sifts through what goes in and out of our body through the digestive tract [1].

Depending on the health of the microbiome (the community of bacteria whose home is the body), inflammation can either be boosted or suppressed. This is important because an unhealthy microbiome has been associated with conditions such as rheumatoid arthritis, inflammatory bowel disease and psoriasis in addition to others such as obesity, heart disease and non-alcoholic fatty liver disease [1].

So, the point is that the microbiome is very important for general health, but back to the original topic, what about the brain?

The Gut-Brain Connection

I once thought that all of our neurons were kept in the brain, and I was wrong. It’s an interesting fact that there are many neurons in the gastrointestinal tract (the gut) and they form a large network called the enteric nervous system (ENS) [2].

The ENS is deeply connected to the Central Nervous System (CNS) and the brain through the Vagus Nerve. This connection is called the gut-brain axis. The microbiome plays a role by sending signals that influence the ENS which then directly influences the CNS [3].

While we are still in the early stages of the gut bacteria story, you can see how the little bacteria in our bodies may have more control over us than we think. Furthermore, researchers have found that modifications to the microbiome can affect the immune system responses in the CNS [4] and may be crucial to CNS function [5].

This back and forth communication is important for the proper function of our gut and possibly mental health, given that 90% of our serotonin is stored in our gastrointestinal tract [1].

The link between the microbiome and the brain doesn’t stop there. The gut can influence the brain through many other pathways as well including hormonal production, upkeep of the blood-brain barrier, and metabolism (gut bacteria break down a lot of what we eat) [6].

How the Gut Affects Brain Health

Because of the massive amount of input the brain and CNS receive from the microbiome, you can probably predict that there will be health implications.

Right off the bat, there have been a few studies that have linked the gut-brain axis to many CNS and brain malfunctions. Conditions such as autism, anxiety, depression, chronic pain, stress, Alzheimer’s and Parkinson’s among others have been associated with an unhealthy gut microbiome [7].

“The gut microbiota likely plays a role in a wide range of neurological conditions, including autism spectrum disorder, anxiety, depression, chronic pain, stress, Alzheimer’s disease, and Parkinson’s disease”

It is well known that patients who suffer from irritable bowel syndrome (IBS) are also highly likely to develop depression as well. One study found that administering probiotics to patients with IBS not only alleviated gastrointestinal problems, but their depression was significantly improved as well [8].

In another study, patients lacking healthy diversity in their microbiome were more likely to suffer from anxiety and depression [9]. This is especially interesting given that most of our serotonin is held in the gut.

These recent studies are causing the entire medical field to reconsider how we determine causes for brain diseases and the significance placed on the health of the gut.

How Brain Health Affects the Gut

The gut-brain axis isn’t a one-way street. The health of the brain also can have effects on the microbiome as well. One big area of focus among researchers is how the microbiome changes after traumatic brain injuries (TBI). If you’ve ever had a brain injury, this is important.

Studies show that there are specific alterations to gut bacteria following traumatic brain injuries [1]. In mice, TBI made changes to microbiome composition just two hours after the event [1]. The changes were harmful because they decreased the diversity in the gut, most of which came from decreasing the ‘good’ bacteria and increasing ‘bad’ bacteria [3].

One study among stroke patients had similar findings as the mouse study. After having a stroke, the diversity of organisms in the gut drastically decreased and digestive problems and bad bacteria increased [10]. All of this was accompanied by an increase in inflammation.

“A decrease in relative abundance in traditionally beneficial bacteria was observed, specifically in the families Lachnospiraceae, Mogibacteriaceae, and Ruminococcaceae.”

We saw earlier that problems with gut bacteria may be a cause of anxiety and other mental health issues, but it has also been shown that stress can also harm the gut as well, another two-way street [11].

If you’ve ever had a TBI such as a concussion, stroke or other issues, it is very possible that your gut suffered as well without you even knowing about it.

Physiological Problems Caused By An Unhealthy Gut

So, we know that an unhealthy gut microbiome can cause serious problems for brain health along with brain injuries causing disruptions in gut health, but why does this happen?

Unfortunately, other than knowing that the gut and brain are connected through the ENS, CNS and Vagus Nerve, scientists aren’t sure about the exact mechanism through which they affect each other. However, we do know the consequences of this connection.

When the gut microbiome gets harmed, there is an influx of inflammation that wreaks havoc throughout the body and brain, creating a nasty loop that can possibly make the brain injury worse [1].

In addition to this, the defense that is normally provided by healthy bacteria breaks down, allowing mischievous ‘bad’ bacteria to spread to places in the body they normally aren’t allowed [12]. This is the cause of much of the inflammation due to an immune response to fight the misplaced bacteria. The breakdown can also make it harder to digest nutrients required for brain recovery.

When it comes down to it, inflammation is one of the root causes of many chronic diseases especially in the brain, so harming the gut microbiome can be devastating.

In addition to this, when the microbiome isn’t functioning properly, the serotonin in the gut may not be stored properly which might cause some of the mental health problems. There really is a plethora of different explanations for why the two can harm each other.

What You Can Do To Boost Gut Health

In general, gut health is very important if you want to live a long and healthy life. It is especially important if you’ve had or are recovering from a TBI. Luckily, you have quite a bit of control over the health of your microbiome. Those little bacteria that outnumber your own cells rely on you to give them what they need to be successful.

It has been shown that diet plays a large role in microbiome health [13], and likely the largest role. Going a bit deeper, studies show that the diversity of vegetables you eat is correlated with the diversity of bacteria in the gut, which is what we want [14].

It is also well known that processed foods are the arch-nemesis of a healthy microbiome. In general, focusing on eating whole foods is one of the best things you can do for your gut.

As we mentioned earlier, anxiety and stress are also detrimental to the health of the microbiome, so findings ways to de-stress and live more peacefully can help them out. Other healthy lifestyle practices such as taking walks out in nature and getting regular exercise are very beneficial as well.

Another way to replenish gut diversity to eat foods and take supplements that contain healthy bacteria. Probiotics (pills with healthy bacteria) and foods like kombucha, kimchi, kefir, and Greek yogurt are all some ways to eat your way to better gut health.

More specific supplements for gut health include glutamine, arginine, nucleotides, and omega-3 fatty acids [15]. In addition to these, vitamins and minerals such as nicotinamide, zinc, and magnesium have also been shown to yield healthy gut flora [16].

The Take-Away

So, we have seen here that the gut-brain axis deeply connects our microbiome to the brain. The health of one is dependent on the health of the other. While this can harm us if one is unhealthy, it can also help us if we are proactive about our health.

If you do suffer from a TBI, the microbiome takes a hit as well. However, researchers are speculating that we can use this to our advantage. By stabilizing and improving the health of the microbiome, we could possibly speed the brain’s recovery process.

In general, the key is to eat a balanced diet and maintain a healthy lifestyle if we want optimal microbiome health and brain function. This is something that is possible for everyone and based off of the research, might be necessary for everyone.

There was a lot of information here! Here are some quick points to sum it all up:

  • The health of our microbiome (gut bacteria) is crucial for general health.
  • More and more research is showing that the microbiome plays a large role in brain health
    • Sends signals through the enteric nervous system to the central nervous system and the brain.
    • The gut microbiome can either increase or decrease inflammation. More inflammation can be harmful to the brain.
    • An unhealthy microbiome has been associated with various brain conditions.
  • New research also shows that brain health can affect microbiome health.
    • Brain injuries have been shown to decrease microbiome health
    • The harm to the microbiome could possibly cause increased inflammation, making the brain injury worse.
  • The good news is that we have a lot of control over microbiome health which could speed the brain’s recovery process.
    • Some easy steps to a healthier microbiome:
      • Eat a balanced diet with minimally processed foods and a variety of vegetables.
      • Take walks under the sun and in nature.
      • Exercise Regularly
      • Eat foods with good bacteria like yogurt, kombucha, kefir, kimchi, and probiotics.
      • Give your gut the minerals and vitamins it needs


What is your experience with the connection between gut and brain health?

How do you keep your gut healthy?


For articles that go more in-depth into the gut-brain axis, here are two good ones:

[1] Zhu, Caroline, et al. “A Review of Traumatic Brain Injury and the Gut Microbiome: Insights into Novel Mechanisms of Secondary Brain Injury and Promising Targets for Neuroprotection.” Brain Sciences, vol. 8, no. 6, 2018, p. 113., doi:10.3390/brainsci8060113.
[2] Leaphart, C.L.; Tepas, J.J., III. The gut is a motor of organ system dysfunction. Surgery 2007, 141, 563–569.
[3] Yoo, B.B.; Mazmanian, S.K. The Enteric Network: Interactions between the Immune and Nervous Systems of the Gut. Immunity 2017, 46, 910–926
[4] Grandhi, R.; Bonfield, C.M.; Newman, W.C.; Okonkwo, D.O. Surgical management of traumatic brain injury: A review of guidelines, pathophysiology, neurophysiology, outcomes, and controversies. J. Neurosurg. Sci. 2014, 58, 249–259
[5] Mu, C.; Yang, Y.; Zhu, W. Gut Microbiota: The Brain Peacekeeper. Front. Microbiol. 2016, 7, 345
[6] Wang, H.X.; Wang, Y.P. Gut Microbiota-brain Axis. Chin. Med. J. 2016, 129, 2373–2380
[7] Mayer, E.A.; Knight, R.; Mazmanian, S.K.; Cryan, J.F.; Tillisch, K. Gut microbes and the brain: Paradigm shift in neuroscience. J. Neurosci. 2014, 34, 15490–15496
[8] Pinto-Sanchez, M.I.; Hall, G.B.; Ghajar, K.; Nardelli, A.; Bolino, C.; Lau, J.T.; Martin, F.P.; Cominetti, O.; Welsh, C.; Rieder, A.; et al. Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: A Pilot Study in Patients with Irritable Bowel Syndrome. Gastroenterology 2017, 153, 448–459
[9] Kleiman, S.C.; Watson, H.J.; Bulik-Sullivan, E.C.; Huh, E.Y.; Tarantino, L.M.; Bulik, C.M.; Carroll, I.M. The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology. Psychosom. Med. 2015, 77, 969–981
[10] Earley, Z.M.; Akhtar, S.; Green, S.J.; Naqib, A.; Khan, O.; Cannon, A.R.; Hammer, A.M.; Morris, N.L.; Li, X.; Eberhardt, J.M.; et al. Burn Injury Alters the Intestinal Microbiome and Increases Gut Permeability and Bacterial Translocation. PLoS ONE 2015, 10, e0129996.
[11] Houlden, A.; Goldrick, M.; Brough, D.; Vizi, E.S.; Lenart, N.; Martinecz, B.; Roberts, I.S.; Denes, A. Brain injury induces specific changes in the caecal microbiota of mice via altered autonomic activity and mucoprotein production. Brain Behav. Immun. 2016, 57, 10–20
[12] Bansal, V.; Costantini, T.; Kroll, L.; Peterson, C.; Loomis, W.; Eliceiri, B.; Baird, A.; Wolf, P.; Coimbra, R. Traumatic brain injury and intestinal dysfunction: Uncovering the neuro-enteric axis. J. Neurotrauma 2009, 26, 1353–1359.
[13] Griffin, N.W.; Ahern, P.P.; Cheng, J.; Heath, A.C.; Ilkayeva, O.; Newgard, C.B.; Fontana, L.; Gordon, J.I. Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions. Cell Host Microbe 2017, 21, 84–96.
[14] McDonald, D.; Hyde, E.; Debelius, J.W.; Morton, J.T.; Gonzalez, A.; Ackermann, G.; Aksenov, A.A.; Behsaz, B.; Brennan, C.; Chen, Y.; et al. American Gut: An Open Platform for Citizen Science Microbiome Research. mSystems 2018, 3.
[15] David, L.A.; Maurice, C.F.; Carmody, R.N.; Gootenberg, D.B.; Button, J.E.; Wolfe, B.E.; Ling, A.V.; Devlin, A.S.; Varma, Y.; Fischbach, M.A.; et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505, 559–563.`
[16] Lucke-Wold, B.P.; Logsdon, A.F.; Nguyen, L.; Eltanahay, A.; Turner, R.C.; Bonasso, P.; Knotts, C.; Moeck, A.; Maroon, J.C.; Bailes, J.E.; et al. Supplements, nutrition, and alternative therapies for the treatment of traumatic brain injury. Nutr. Neurosci. 2018, 21, 79–91