Gut-Brain Axis: Why Optimal Health Starts With Digestion

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Gut-Brain Axis: Why Optimal Health Starts With Digestion

digestion, gut-brain axis, gut bacteria, dysbiosis, microbiota, microbiome, probiotics, fecal transplants, blood-brain-barrier, butyrate, serotonin, LPS, lipopolysaccharide
The bacteria that live in our gut have a huge impact on our overall health. So, when it comes to identifying the root cause of any illness, we have to start by looking at the health of your microbiome. Let’s take a closer look at the gut-brain axis, and how to get your gut bacteria functioning optimally.

Dr. Doni explains the microbiota-gut-brain connection; why it’s important, how we can support it, and why it’s so exciting for the future of healthcare.

digestion, gut-brain axis, gut bacteria, dysbiosis, microbiota, microbiome, probiotics, fecal transplants, blood-brain-barrier, butyrate, serotonin, LPS, lipopolysaccharideWhen you meet with a naturopathic doctor you’ll find they often start by asking about your digestion, regardless of why you came in.

You may be looking for help with stomach aches, headaches, weight gain, anxiety, depression, menstrual pain, recurrent infections, skin rashes, Hashimoto’s thyroid, or any other autoimmune condition (the list goes on) but, 9 times out of 10, the first question your naturopathic doctor will ask will be about your gut health.

While naturopathic doctors have been starting with digestive health for over a hundred years (Dr. Benedict Lust and his wife Louisa founded and established naturopathic medicine in New York in the early 1900’s), it is only in the past 5 to 10 years that research has truly started to explain why and how the gut is so inter-connected with the rest of the body via communications from the organisms living in the gut.

Why is the Microbiota-Gut-Brain Connection Important?

As I mentioned in my last post, our health is determined not just by our genes, but by the genes of the microbes that live in our gut – referred to as our “microbiota” or “microbiome” (the genes of the bacteria, fungi, and archaea) – and the stresses we are exposed to that affect both our genes and our gut bacteria.

These organisms actually communicate with the rest of the body via what is known as the microbiota-gut-brain axis, so when it comes to identifying root causes of any illness, we have to start by looking at the health of your microbiome and identifying how to get it back to optimum.1,2

Not Yet Mainstream Knowledge

It can be hard to imagine that what is going on in your digestive tract has anything to do with your joint pain, anxiety, blood sugar levels, immune system, or menstrual cycle – let alone your mood, behavior, and focus. It is definitely not something you’re likely to hear about when you meet with your primary care doctor, gastroenterologist, neurologist, psychiatrist, or any other medical specialist for that matter. It has simply not been integrated into standard medical care yet.

I say “yet” because I believe that over the next decade, addressing gut microbiota particularly for anxiety, depression, Alzheimer’s disease and other neurodegenerative diseases, autism, and pain will become universal. That is because there is such a huge amount of research being done.

In fact, the US National Institute of Mental Health (NIMH) in Bethesda, Maryland has funded seven pilot studies to investigate the microbiota-gut-brain axis. And the US Office of Naval Research in Arlington, Virginia plans to spend $14.5 million over the next 5-6 years examining the gut’s role in cognitive function and stress responses.3

How Does the Microbiome Communicate With the Rest of Your Body?

Well, in simple terms, the bacteria in your gut communicate with the rest of your body by producing substances, triggering inflammatory messages and/or by sending signals via your nerves.

If or when the balance of bacteria is disrupted, that has the potential to send a very different message to your nervous system and influence your mood, memory, and focus. Your metabolism and likelihood of gaining weight is also affected, but for now let’s focus on your nervous system. 4,5

What is an Inflamed Brain?

It was previously thought that the nervous system is protected by the blood-brain-barrier (BBB), but now we understand that inflammatory messages from your gut can be communicated across the BBB.

In other words, inflammation from the digestive tract can spread inflammation throughout your body including your nervous system. I call it “inflamed brain.” This is why, if you get a stomach virus, your whole body feels unwell.

Two (perhaps surprising) examples are anxiety and depression, which are now known to be caused by inflammation in your nervous system.

Other common symptoms in their brain due to inflammation that came from the gut are:

  • Brain fog
  • Difficulty focusing
  • Obsessive Compulsive Disorder
  • Forgetfulness
  • Worries and fears
  • Repeating thoughts
  • Restless sleep

Beyond Inflammation, Other Ways Bacteria Communicate with Your Body

In addition to inflammation from the gut, the bacteria in your gut produce substances– some considered good and protective, such as butyrate, and others not-so-good, known as LPS (lipopolysaccharide) – that cross your intestinal lining and travel throughout your body.

But the connection goes beyond inflammation and substances; these bacteria are actually able to send signals to your genes telling them to turn on or off pathways that influence certain functions such as the production of serotonin and Brain-Derived Neurotrophic Factor (BDNF), both of which effect your mood and focus6,7,8,9,10

Just as an imbalance of bacteria could be detrimental, increasing the desired bacteria could be beneficial. I’ll get into that more soon.

And One More Form of Communication Between Gut and Brain: VAGAL NERVE

Another communication route between your gut and your brain (and other areas of your body) is via your vagal nerve.

This important nerve sends signals from your brain (your nervous system) to your digestion and back again.

If there is stress (such as inflammation or an imbalance of bacteria) then a stress signal is sent from your gut telling the rest of your body to respond.

That response could lead to a number of symptoms including nausea, reflux, difficulty swallowing, muscle spasms, anxiety, racing heart, frequent urination, fatigue, faintness, and/or tinnitus (ringing in your ears).

How Will Your Body Respond To All This?

Each person experiences the microbiota-gut-brain axis differently.

For some, it takes a major change in the bacteria to result in health issues.

Others will notice a headache, mood change, brain fog or joint pain after even the slightest diet change or stress.

This variation is at least partially determined by your genetics (as well as that of your ancestors) and your exposure to stress (even in childhood), or what I think of as your susceptibilities.

What Disrupts the Microbiota?

Psycho-emotional stress, sugar, and gluten (in anything made from wheat, rye, barley or spelt) are all well-established causes of a disruption in your gut flora, which is why I refer to all of them as stresses.

When you are stressed, the stress hormone cortisol sends signals to decrease activity in the digestive tract and increase activity to your muscles and brain.

If you are stressed a lot of the time, you will not digest food well, be prone to intestinal permeability (known as leaky gut), and the balance of bacteria in your gut will be disrupted.

Some bacteria will overgrow and others will undergrow, leading to increased inflammation and further damage to the intestinal lining.

Then the part of your immune system that sits under the intestinal lining becomes activated and starts sending signals to the rest of the immune system, both locally and throughout your body. The immune system also sends stress messages back to your brain, indicating to your central nervous system that there is even more stress and disruption to the bacteria (dysbiosis).

It becomes a vicious cycle of “internal stress.” 

The over-use of antibiotics (such as for sinus, dental, skin or bladder infections) is another top way that microbiota are thrown off track, so preventing the use of antibiotics and other medications that disrupt those bacteria is a priority for healing and preventing this situation.

What Can You Do To Protect Your Microbiome?

Anything you can do to fight off infections through diet, sleep, nutrients, and herbs will protect your microbiome, which in my mind is essentially the greatest health prevention tactic you could implement. Learn how to recover from a cold virus (for example) here.

The microbiota is also affected by a number of other things. Avoiding and addressing these substances and issues will help keep you and your microbiota  in good health:

  • Proton Pump Inhibitors – used to treat GERD (read my approach to GERD here)
  • Alcohol
  • Lack of fiber – such as in a diet filled with processed foods
  • Food poisoning or traveler’s diarrhea

Can You Test Your Microbiome?

There are labs that offer stool testing that tells us what is going on with your gut bacteria.

They show us patterns of ‘dysbiosis’ – imbalanced bacteria – and identify the bacteria that are present in your gut based on their DNA, which is rather amazing.

Some of these stool panels are more clinical – and you’ll need to work with a naturopathic doctor to access them. Others, such as Viome and Ubiome, are available direct to consumer and while they don’t provide all the information that the clinical panels do, they will give you a sense of whether you need to pay more attention to your gut bacteria.

How to Optimize Your Microbiome

Over the years I’ve seen thousands of patients with varying degrees of dysbiosis and through that process I’ve learned that there are basically 3 categories of disruption that each require a different approach:

  1. Mild disruption usually just requires consistent dosing of a high-quality lactobacillus and bifido probiotic product, along with diet changes (avoiding gluten and sugar), digestive enzymes and herbs/nutrients to heal leaky gut and get things back to balance again.
  2. Moderate disruption means you probably feel okay most days, but just when you think you’re doing all right, pain, bloating and bowel irregularity remind you that you’re just not feeling your best. You can start in with digestive support, but if you feel worse, you’ll want to slow down until your body has healed a bit and is ready for more support.Avoiding foods that increase inflammation (which may include foods that trigger histamine, such as aged meats and fermented foods) and completing a genetic stool analysis (and possibly also a breath test) to determine the best probiotic for you will help the healing process, along with digestive enzymes to ensure food is being digested and anti-inflammatory herbs, such as DGL (licorice), slippery elm (ulmus) and/or marshmallow (althea) may all help balance things out again. You could look in the digestion section at for ideas.
  3. Severe disruption presents something of a paradox in that you need to start with less treatment when you have more. This is because your digestive system is so reactive you’ll likely react to anything that we add to your regime. So the goal is to start out with the “safest” low-reactivity foods and products until things settle down enough that we can start to treat. You’ll want to do a food sensitivity panel to find out exactly which foods to avoid.You may need to rely on protein shakes, such as my all-in-one pea protein shake, or even an elemental diet shake to get nutrition while your gut heals. In many severe cases we actually need to work on getting rid of unhealthy microbes (using herbs whenever possible) before adding in more bacteria or probiotics.

    There are new, innovative ways to do this, including fecal transplants – a method of introducing stool from a healthy person in order to transfer a more optimal set of bacteria. This approach has been established as effective especially in the case of antibiotic-resistant c. difficile infection. This type of treatment is already available in other countries and could become more available for other conditions (such as anxiety and depression) in the U.S, in the near future.

    All of this is very good news for healthcare but it is still not as simple as it may seem. This is why there are hundreds of studies currently under way, looking at which bacteria you want in your microbiome and which you don’t, and which forms of can shift things in the right direction.

Essential to Heal Your Gut and Rebalance Your Response to Stress

Basically, regardless of the severity of your dysbiosis, we need to heal the environment (your gut) and decrease inflammation, while also supporting digestion, feeding healthy bacteria and ensuring regular bowel movements.

It’s quite a complex system that works best when we are the least stressed.

In fact, you can start to support your digestion by simply taking a few deep breaths before you start eating, then chewing well, and enjoying your food – all of which ensures your nervous system encourages the whole system to work well.

You may want to print this one-page Stress Remedies tip sheet to remind you to send calming messages to your gut.

I was so excited about the research in this area a few years back that I included it in my first book, The Stress Remedy. In it I refer to leaky gut and associated dysbiosis as one of the three “problem networks” caused by stress which lead to health issues throughout the body. The whole premise of The Stress Remedy is that, by understanding the impact stress has on our bodies we are better able to avoid or address those effects.

I have also developed the 7 and 21 day Stress Remedy Programs to assist you with making the sorts of changes that can have such a profound influence on your health in terms of mood as well as energy, focus, weight, and simply feeling good.

The Stress Remedy Programs include diet plans to help you avoid the foods that disrupt your microbiota and eat the foods that support your microbiota. They also include support for sleep, exercise and recovery from stress. The 21-day program includes supplements to help heal digestion and leaky gut, including digestive enzymes and the highest-quality probiotics. Check out those supplements here

If you’d like my help to address your microbiota-gut-brain axis, please reach out and schedule a one-on-one consultation. We can then determine which tests are needed for your case and whether one of my specially developed consultation packages meets your needs. You might also consider what I refer to as the Leaky Gut and Digestive Solutions Package for a comprehensive approach to healing your digestion.

A Patient Story…

I wanted to end by sharing the story of a patient I spoke with recently. She originally came in to see me because she was struggling with anxiety and bloating. She had seen numerous practitioners without any resolution. Through stool and breath testing we discovered a bacterial imbalance in both her small and large intestines. She made changes to her diet and started to take digestive enzymes, an herb to address the unhealthy bacteria, and a spore-forming probiotic to decrease inflammation and help heal her gut.

After a few weeks she felt somewhat better, but not completely. She decided to take a one-month vacation and spend time with her family in her local town. What she discovered was nothing short of remarkable. Within two weeks of being home, eating local foods her family prepared in a traditional way, she felt completely better. What she noticed was that she had completely stopped eating processed foods and instead ate whole fruits, vegetables, and fish. She also described how she became more aware of day and night, noticing that she was more able to calm and relax when it became dark. Her new challenge is to find ways to maintain and implement all that she learned back in her city work schedule.

You Can Heal Your Gut and Balance Your Microbiome Too! 

Have you noticed that your digestion, mood and outlook improve when you eat healthy foods and take time to connect with yourself and nature? Can you imagine that the bacteria in your gut also benefit from these choices and send signals that could positively influence your mood and memory for years to come?

I encourage you to keep making choices to benefit your good bacteria, because the bacteria don’t just live in your intestines. They communicate with your body and have a huge influence on your health. 

Dr. Doni
23rd August 2016


  1. Callaghan BL, Cowan CS, Richardson R . Treating Generational Stress: Effect of Paternal Stress on Development of Memory and Extinction in Offspring Is Reversed by Probiotic Treatment. Psychol Sci. 2016 Jul 15.
  2. Cryan JF. Stress and the Microbiota-Gut-Brain Axis: An Evolving Concept in Psychiatry. Can J Psychiatry. 2016 Apr;61(4):201-3.
  3. Smith, PA. The tantalizing links between gut microbes and the brain. Nature. Oct 2015; 526 (7573): 312-314.
  4. Sherwin E, Sandhu KV, Dinan TG, Cryan JF. May the Force Be With You: The Light and Dark Sides of the Microbiota-Gut-Brain Axis in Neuropsychiatry. CNS Drugs. 2016 Jul 14.
  5. Boulangé CL, Neves AL, Chilloux J, Nicholson JK, Dumas ME. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med. 2016 Apr 20;8(1):42.
  6. Forsythe P, Kunze W, Bienenstock J. Moody microbes or fecal phrenology: what do we know about the microbiota-gut-brain axis? BMC Med. 2016 Apr 19;14:58.
  7. Stilling RM, van de Wouw M, Clarke G, Stanton C, Dinan TG, Cryan JF. The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? Neurochem Int. 2016 Jun 23;99:110-132.
  8. Borrelli L, Aceto S, Agnisola C, De Paolo S, Dipineto L, Stilling RM, Dinan TG, Cryan JF, Menna LF, Fioretti A. Probiotic modulation of the microbiota-gut-brain axis and behaviour in zebrafish. Sci Rep. 2016 Jul 15;6:30046.
  9. Kennedy PJ, Cryan JF, Dinan TG, Clarke G. Kynurenine pathway metabolism and the microbiota-gut-brain axis. Neuropharmacology. 2016 Jul 5.
  10. Masotti, A. Interplays between gut microbiota and gene expression regulation by miRNAs. Front Cell Infect Microbiol. 2012; 2:137.
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