5 Ways to Increase Your Good Gut Bacteria For A Healthier Brain

Picture of Hippocrates with his quote “All Disease Begins in the Gut!”

My brain totally broke in 2010 and I felt like I had developed ADHD, depression, and dementia all at once. By scouring the literature, interviewing and consulting with doctors and researchers, and experimenting with my own body and mind, I finally came to understand that it wasn’t just one thing that had caused my brain and body to break, but the accumulation of many things. 

One of my main problems: I had an imbalance of healthy and unhealthy bacteria in my digestive system. 

There are approximately 100 trillion microorganisms and 500 known bacterial species living in our guts. That means there is 10 times more bacteria cells in our bodies than human cells and over 90% of our cells are non-human. Simply put, we are more bacterial than we are human (1, 2).

Gut bacteria affect our nervous, hormonal and immune systems and play a key role in countless bodily functions, including the digestion of food and production of vitamins. So not surprisingly, the makeup of these bacteria in our system can affect how we feel physically and mentally. 

But our modern lifestyle isn’t good for our gut bacteria. Stress, bad diet and medications can reduce probiotic (good) bacteria and increase bad bacteria in our digestive tract. A lot of people today have out-of-balance and dysregulated gut bacteria. So if we want to regain optimal brain health, it’s critical to restore and support the “good germs” in our gut.

In this post, I’ll show you how to increase your good bacteria and reduce your bad bacteria like I did, so that you’ll improve the health of your brain and experience more mental resilience. 

Image of the gut and the brain - Can this influence this?

What the Cutting-Edge Research Says: You Need Healthy Gut Bacteria to Have a Healthy Brain

Impressive new research shows that there is a connection between our brain and our digestive tract, and that the bacteria in our gut can have a profound influence on our behaviour, thoughts and mood.

There’s evidence that healthy gut bacteria produce and regulate the amount of neurotransmitters in the brain (such as serotonin, dopamine and GABA), which can affect mood, pain and cognition (50-52). 

Dr. Stephen Collins, a gastroenterology researcher at McMaster University, has done a lot of research in the field and discovered that unhealthy gut bacteria play a key role in causing abnormal behaviour (including anxiety and depression), while certain strains of good bacteria can reduce stress hormones and anxious behavior. 

In one study, Collins took the gut bacteria of mice that were prone to anxious behaviour and transplanted it into calm mice. After the transplant, the calm mice started acting nervously. He has also seen the same results with humans (28 – 35). 

It’s increasingly clear that our gut bacteria, or microbiota, can communicate with the human brain.
— Dr. Kathy Magnusson, PhD, Oregan State University

Studies by Dr. John Cryan, a neuropharmacologist and microbiome expert at the University College Cork, shows that gut bacteria can alter brain chemistry.  

He found that after eliminating their good bacteria, mice act in ways that mimic human anxiety, depression and autism. And in one of his studies, two strains of bacteria were more effective than an antidepressant at treating anxiety and depression (36 – 42). 

Lastly, research has found that mice with autistic-like behaviour have much lower levels of a common type of bacteria called “Bacteroides Fragilis” than normal mice. They were stressed, antisocial, and had the same digestive problems often found in autism. And when they were fed “Bacteroides Fragilis”, there was a reversal in their autistic symptoms. They became less anxious, communicated more effectively, and showed less repetitive behavior (43, 44). 

This is just the tip of the iceberg. A growing number of scientists and practitioners around the world are researching and speaking out about this, explaining that the gut-brain connection can be hacked to treat psychiatric disorders. 

So without further ado, here are five powerful ways to nurture your good bacteria and eliminate the bad bacteria in your gut. By following these steps, you’ll feel stronger both mentally and physically.  

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1. Take A High-Quality Probiotic

Simply increasing the amount of beneficial bacteria in your gut through probiotic supplementation might be one of the most powerful things you can do for your brain and mental health. 

Probiotic supplements add good germs to your digestive system, and providing your body with a diverse array of friendly bacteria can significantly reduce your susceptibility to the negative effects of stress. Researchers have found that mice are less anxious when they are fed probiotics, and numerous studies have shown that humans experience less stress, anxiety, rumination, hostility, depression and aggression when supplementing with probiotics (3, 4, 5, 6, 7, 8, 9, 10). 

Researchers are starting to uncover how probiotics work to support the brain. One study showed that probiotics can help you naturally produce more GABA, a relaxing amino acid and neurotransmitter. Amazingly, this same study showed that probiotics not only help your body produce more GABA, but they enhance the sensitivity of the GABA receptors in your brain, making you more susceptible to calming effects of your natural GABA production (8, 53). On the other hand, if you go to the doctor for anxiety, you’ll likely receive anti-anxiety medication, which works by activating GABA receptors in the brain. 

Other species of probiotics have demonstrated an ability to reduce stress hormones and increase tryptophan, serotonin and omega-3 fatty acids in the brain, all of which play a role in proper mood and cognition (54, 55). So it’s critical to keep your insides flourishing with a healthy colony of good bacteria.

These bacteria could eventually be used the way we now use Prozac or Valium. I think these microbes will have a real effect on how we treat these disorders. This is a whole new way to modulate brain function.
— Dr. John F. Cryan, PhD, University College Cork

I’ve tried a number of different probiotics over the years. Some have helped me somewhat, while others haven’t helped me at all and even made me feel worse.

I’ve now created my own probiotic supplement, called Optimal Biotics.

I created it because I want to give my clients and readers the very best probiotic supplement so that they can experience superior results.

I have found that many probiotic supplements on the market fall short and even cause side effects.

But Optimal Biotics doesn't, and it contains the 8 most well-researched and beneficial probiotic strains.

2. Avoid antibiotics (unless absolutely necessary)

Seven years ago, I went to the doctor because my asthma was getting significantly worse. A lot of inflammation and phlegm was building up in my lungs. It felt like I was breathing through a straw all of the time. 

The doctor incorrectly assumed I had a bacterial infection (I actually had gluten and dairy allergies), so he gave me a course of antibiotics. And then another course. And then another. They did anything. 

Broad-spectrum antibiotics don’t differentiate between good and bad bacteria. These drugs not only kill bad bacteria, but they destroy good bacteria too. By the time I was done all three courses of antibiotics, a lot of the good bacteria in my gut was completely wiped out. And not only did my asthma get worse (and my body less able to handle the gluten and dairy I was eating), but my mental health deteriorated as well. 

Moral of the story: Antibiotics can save lives, but they can also destroy your health if they aren’t completely necessary. Yet many conventional doctors hand them out like candy on Halloween. 

In most cases, those who suffer from mental health disorders like depression and schizophrenia, and from developmental disorders like autism, something has harmed the beneficial bacteria in their gut, sometimes before birth and sometimes later on in life.
— Dr. Natasha Campbell-McBride, MD, Author of the Gut and Psychology Syndrome Diet

Studies show that antibiotic use can lead to profound changes and rapid loss of diversity in the composition of the gut bacteria and this can lead to other chronic health complications. American children are typically prescribed one course of antibiotics every year, and excessive and inappropriate use can cause serious long-term consequences without probiotic intervention. For example, antibiotics used to treat acne are associated with the development of inflammatory bowel disease (12, 13, 16, 17). 

An article published in Nature highlights the negative long-term consequences of antibiotic over-prescription. It points out that antibiotics cause significant and possibly permanent changes in gut bacteria, and infants delivered via caesarean section and/or by a mother given antibiotics during pregnancy significantly will have an insufficient level of good bacteria (14, 15). 

I don’t want to suggest that antibiotics are absolutely terrible and we should always avoid them. But they are excessively and inappropriately prescribed and their benefits come at a cost. You should be aware of this so you can make an informed choice. If you do decide to take antibiotics, make sure you take probiotics afterwards. 

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3. Feed the good guys with prebiotics and resistant starch

The existing probiotics in our gut need to be nourished and supported, and this can be done by eating or supplementing with prebiotics. 

Prebiotics are substances that humans can't digest, so they pass through our gastrointestinal tract and promote the growth of many different strains of good bacteria in our lower bowel. They are essentially food for the good bacteria in our intestines. 

Dr. Phil Burnet, a neurobiologist at Oxford University, published a paper in 2015 showing that people who ingested prebiotics have lower levels of cortisol, a key stress hormone, and focused more on positive feedback and less on negative stimuli. He said the results were very similar to when people take anti-depressants and anti-anxiety medication, but without the side effects.

Other research by Burnet shows that prebiotics support overall brain health in humans and foster the growth of probiotics in mice, which leads to increased levels of several neurotransmitters that reduced anxiety-like behaviour (19, 20, 21, 22). 

Prebiotic-rich foods include sweet potatoes, carrots, onions, asparagus and squash. These foods are included in my free grocery shopping guide for optimal brain health and you should be eating them regularly. If you feed the good bacteria, you will feel healthier physically and mentally.

Resistant starch is one of the most potent ways to boost your prebiotic intake, and it’s been shown to help prevent and manage chronic disease (18). 

A convenient way to incorporate more resistant starch into your diet is by using Bob’s Red Mill Unmodified Potato Starch. I’ve tried and recommend it. You can get it through Amazon. It's one of the easiest and cheapest ways to incorporate more resistant starch into your diet. It is bland so you can simply add it to beverages, smoothies and meals. It has to stay raw though, so don’t cook it. 

Other high-quality resistant starches that I’ve tried include banana flour, plantain flour and waxy maize. I usually rotate between them.

Image of candy in a bowl and candy in an injectable needle

4. Don't feed the bad guys with sugar

Avoiding sugar is a critical aspect of preventing and treating brain and mental health challenges. Not only does high sugar consumption increase inflammation, but sugar is fuel for bad bacteria. Significantly limiting your sugar intake will starve the bad bacteria and allow the probiotic bacteria in your gut to thrive. 

Diets high in sugar cause negative changes in gut bacteria that impair “cognitive flexibility”, which is the ability to adapt to changing situations. Sugar can also impair short and long-term memory (23). 

In his book The Sugar Blues, William Duffy argues that sugar is an addictive drug and eliminating it can have a profoundly beneficial impact on mental health. For some people, cutting out refined sugar may be all they need to do to overcome their depression and other mental health challenges. 

When I first cut out sugar several years ago, I actually went through withdrawal. I was incredibly tired, had increased anxiety and depression, and was sweating profusely at work. This makes sense in light of the research showing that people who drink more sweetened beverages are more likely to suffer from depression (24). My boss at the time thought I was sick, so he actually sent me home for the day. Eventually, I overcame the withdrawal and my mood and energy improved significantly. 

So radically reducing your sugar intake will support your gut bacteria, brain chemistry and overall health. 

5. Eat whole, probiotic-rich foods

Overall, you should also be eating a wide-variety of whole foods to support your gut health. Eating a standard Western diet for just one day can dramatically change your gut bacteria in a bad way, while eating lots of whole foods increases the diversity of good bacteria (45, 46, 47). 

Bowl of fermented vegetables

If you haven’t already, grab my Free Grocery Shopping Guide for Optimal Brain Health for a full-list of healthy whole foods. 

And probiotics don’t just need to come in supplement form. You can also experiment with incorporating probiotic foods into your diet. Fermented foods include sauerkraut, kimchi, kombucha, natto and pickled cucumbers. The probiotic bacteria in these foods cause their fermentation. If you can tolerate dairy, foods like kefir and yogurt (unsweetened) are also high in nourishing bacteria. 

By eating them, you’re promoting the proliferation of good bacteria in your gut, which will then support your brain. One study suggests that young adults experience less social anxiety if they eat fermented food, and another study shows that yogurt eaters experience positive changes in brain function that cause them to react more calmly to visual stimuli (25, 26).

This was not what we expected, that eating a yogurt twice a day for a few weeks would do something to your brain.
— Dr. Emeran Mayer, MD, Psychiatrist at UCLA

Probiotic foods tend to have a broad combination of bacteria too – more than what can be found in typical probiotic supplements. And people have been fermenting food for more than 8,000 years, yet most of us stopped after the invention of the refrigerator, which may explain the decreased diversity of good bacteria in our digestive tracts today. 


Promoting the growth of beneficial bacteria through positive lifestyle choices can make our brains feel great and function optimally. Too much bad bacteria can make you feel mentally weak, tired and ill, and you may even see changes in your personality. I know I did.  

Bacteria have lived inside humans for hundreds of thousands of years and therefore have lots of experience modifying our brains. They are more precise and subtle than pharmaceuticals, meaning means fewer side effects. As a result, changing the composition of our gut bacteria through lifestyle and dietary interventions is emerging as a very effective and practical way to treat anxiety, depression, autism and other mental health disorders (27, 48, 49).

So in conclusion, support and feed the good bacteria with:

And starve and fight off the bad bacteria in your gut by avoiding:

  • Sugar

  • Antibiotics

By taking these steps, your gut, body and brain will become stronger and more resilient over time.

Let me know what you think in the comments.

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Live Optimally,
Jordan Fallis

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(1) http://gutpathogens.biomedcentral.com/articles/10.1186/1757-4749-3-1

(2) https://www.sciencedaily.com/releases/2015/04/150414083718.htm

(3) http://gutpathogens.biomedcentral.com/articles/10.1186/1757-4749-3-1

(4) https://www.sciencedaily.com/releases/2015/04/150414083718.htm

(5) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179073/

(6) http://www.ncbi.nlm.nih.gov/pubmed/25449699

(7) http://www.ncbi.nlm.nih.gov/pubmed/25862297

(8) http://www.ncbi.nlm.nih.gov/pubmed/21876150

 (9) http://www.ncbi.nlm.nih.gov/pubmed/20974015

(10) http://www.ncbi.nlm.nih.gov/pubmed/16117982

(11) http://www.ncbi.nlm.nih.gov/pubmed/17692729

(12) http://www.nature.com/ajg/journal/v105/n12/full/ajg2010303a.html

(13) http://www.pnas.org/content/108/Supplement_1/4554.full.pdf#page=1&view=FitH

(14) http://www.nature.com/nature/journal/v476/n7361/full/476393a.html

(15) http://www.nature.com/nrmicro/journal/v7/n12/full/nrmicro2245.html

(16) http://jac.oxfordjournals.org/content/15/3/319.abstract

(17) http://www.ncbi.nlm.nih.gov/pubmed/19018661

(18) http://www.ncbi.nlm.nih.gov/pubmed/24228189

(19) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410136/

(20) http://www.ncbi.nlm.nih.gov/pubmed/26476141

(21) http://www.ncbi.nlm.nih.gov/pubmed/24144322

(22) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858812/

(23) https://ir.library.oregonstate.edu/xmlui/bitstream/handle/1957/55795/MagnussonKathyBiomedicalSciencesRelationshipsBetweenDietRelatedChanges.pdf?sequence=1

(24) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990543/

(25) http://www.sciencedaily.com/releases/2015/06/150609092803.htm

(26) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839572/

(27) http://www.ncbi.nlm.nih.gov/pubmed/25415497

(28) https://www.sciencedaily.com/releases/2015/07/150728110734.htm

(29) http://www.ncbi.nlm.nih.gov/pubmed/23845749

(30) http://www.ncbi.nlm.nih.gov/pubmed/24997039

(31) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181531/

(32) http://www.nature.com/ncomms/2015/150728/ncomms8735/full/ncomms8735.html

(33) http://www.ncbi.nlm.nih.gov/pubmed/21988661

(34) http://www.ncbi.nlm.nih.gov/pubmed/20600016

(35) http://www.ncbi.nlm.nih.gov/pubmed/21683077

(36) http://www.ncbi.nlm.nih.gov/pubmed/25251188

(37) http://www.ncbi.nlm.nih.gov/pubmed/20696216

(38) http://www.pnas.org/content/108/38/16050

(39) http://www.ncbi.nlm.nih.gov/pubmed/22968153

(40) http://www.ncbi.nlm.nih.gov/pubmed/21303428

(41) http://www.ncbi.nlm.nih.gov/pubmed/22483040

(42) http://www.ncbi.nlm.nih.gov/pubmed/26372511

(43) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897394/

(44) http://www.ncbi.nlm.nih.gov/pubmed/24315484?dopt=Abstract&holding=npg

(45) http://stm.sciencemag.org/content/1/6/6ra14.long

(46) http://www.nature.com/nature/journal/v518/n7540_supp/full/518S14a.html

(47) http://www.ncbi.nlm.nih.gov/pubmed/24939238

(48) http://www.nature.com/nrn/journal/v13/n10/full/nrn3346.html

(49) http://onlinelibrary.wiley.com/doi/10.1111/gbb.12109/abstract;jsessionid=F9A259194D111B1544816067055A05B7.f04t02

(50) http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003726

(51) http://www.sciencedirect.com/science/article/pii/S0166432814004768

(52) http://www.pnas.org/content/108/38/16050.long

(53) http://www.ncbi.nlm.nih.gov/pubmed/22612585?dopt=Abstract&holding=npg

(54) https://www.ncbi.nlm.nih.gov/pubmed/23686721

(55) https://www.ncbi.nlm.nih.gov/pubmed/23686721

Medically reviewed by Dr. Fred Hui, MD, CCFP, CAFC

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