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

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.

When 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, Hashimoto’s thyroid, or any other autoimmune condition (the list goes on) but, 9 times out of 10, their first question will be about your gut. While naturopathic doctors have been starting with gut 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.

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 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

Why is the Microbiota-Gut-Brain Connection Important?

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. 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

So why is the gut and microbiome so influential to our health? 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

It was previously thought that the nervous system is protected by the blood-brain-barrier (BBB), but now we understand that changes in the gut can be communicated across the BBB. Inflammation, for example, from the digestive tract can spread inflammation throughout your body including your nervous system. 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 ways people experience symptoms in their brain due to issues in the digestion are:

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

The way this connection works is that substances produced by the bacteria in your gut – some considered good and protective, such as butyrate, and others not-so-good, known as LPS (lipopolysaccharide) – 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 focus. Just as an imbalance could be detrimental, increasing the desired bacteria could be beneficial. I’ll get into that more soon. 6,7,8,9,10

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 digestive system 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).

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.

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. 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.

The microbiota is also affected by a number of other things and trying to limit them will help keep yourself in good health:

  • Proton Pump Inhibitors – used to treat GERD
  • 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 analyze the genetics of the bacteria that are present in your gut. Some of these labs will provide a data file that we can then upload into software, such as the soon-to-be-released Opus 23 Utopia program developed by Dr. Peter D’Adamo, that will be able to interpret the bacterial counts and provide suggested treatments based on currently available research.

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:

  • 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.
  • 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.
  • 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 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.
  • 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.

    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.

    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.

    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.

    What do you think? 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? Let me know using the comments box below.

    Dr. Doni
    23rd August 2016


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