by Dr. Bill Rawls
Updated 12/14/18

You’ve probably heard me talk extensively about the microbiome as it relates to gut health, but did you know microbes occur in the brain as well? As a matter of fact, the latest groundbreaking news in the world of neurological science, in my opinion, is the discovery of microbes in human brains.

It’s well-recognized that infections of the brain can cause severe, acute illness. But these new findings could shed light on the role that microbes play in many chronic diseases associated with neurological symptoms, including chronic Lyme disease, fibromyalgia, and chronic fatigue syndrome.

I believe that understanding this connection is the key to restoring brain health and alleviating stubborn neurological symptoms such as pain, numbness, and hearing and vision issues that come with so many chronic illnesses. Here’s what you need to know.

Proof That Microbes Invade The Brain

Just two years ago, researchers in Canada were searching for bacteria in autopsy brain specimens from people who had died of multiple sclerosis (MS). What they found, according to their study in the journal Nature, was astonishing: Not just one or a few species of bacteria, but hundreds of different bacterial species inhabiting the brain!

Although every sample contained bacteria, each one carried a slightly different spectrum of microorganisms. Notably, pro-inflammatory bacteria prevailed in the MS group. Those microbes were associated with key characteristics of MS, including inflammation and demyelination, a process that damages myelin, the protective, fatty substance that wraps around the nerves in the brain.

Perhaps even more remarkable, the researchers found a similar array of bacteria in the control specimens, too. The controls were brains from people who had died of something other than MS. Like the MS brain tissue, they contained many different species of bacteria. The difference? Friendly flora dominated the brains of the control group.

Surprised by the findings of so many different species of bacteria, the researchers double-checked their methods for the possibility of contamination, but ultimately found that the results were authentic. And soon thereafter, similar findings were noted in an independent 2017 study from the UK.

This time, researchers were analyzing autopsied Alzheimer’s brains. And just as with the MS study, they discovered a broad distribution of bacteria in each specimen. Again, the control specimens from people who had died of something other than Alzheimer’s also contained a wide range of microbes. And, as with the MS study, the most striking difference between the two groups was the predominance of pro-inflammatory bacterial species in the diseased, Alzheimer’s brains.

These studies raise a crucial question: Do all brains contain microbes? When I consider one more study, some 2018 research from the University of Alabama, the answer is likely an unexpected, yes.

Here, researchers evaluated vascular changes in the brains of 34 people who died of non-infectious illnesses. Across the board, they encountered a range of bacterial species in different areas of the brain. Yet again, each and every specimen contained a variety of microbes. The microbes found in these particular studies were inside brain cells (intracellular or stealth microbes), and the specific species were not identified.

The extraordinary findings of these three studies confirm that the collection of microbes in the human body, called the microbiome, is more extensive and intricate than anyone could have ever imagined. Who would have thought the normal scope of the microbiome extended into the brain? But apparently, it does.

Why bacteria might want to invade brain tissue isn’t difficult to answer — brain tissue provides a wealth of nutrients. It’s abundant in the resources that bacteria need, such as collagen, myelin from around nerve sheaths, vital nutrients, and energy.

How they got there, however, is a more challenging question. Most of the microbes found in the studies were common to the gut and skin. Researchers speculate that they simply traveled through the blood. This would imply that the gut-blood barrier and the blood-brain barrier aren’t nearly as protective as was once thought, especially considering each sample in every study revealed so many different species of bacteria. Plus, it should be noted that these three studies only checked for bacteria — the prevalence of viruses may be even higher.

How Microbes in the Brain Trigger Neurological Symptoms

Regardless of where and which microbes inhabit our bodies, our relationship with them is built on a foundation of sharing. When that relationship is balanced, we share some resources and nutrients with our microbes, but not enough to cause damage to our tissues. In return, many of our microbes reciprocate by providing us with vitamins and other benefits.

Other microbes, however, are not so generous. Remember, the microbiome is a large menagerie of microbes, and there are always more aggressive bacterial outliers that have the potential to take more than their share if they’re not contained.

We all have these outliers — freeloaders looking for an easy meal. We pick them up as we go through life, from contaminated air particles, food and drinks, intimate contact with other people, skin abrasions, and bites from insects bites such as ticks and mosquitoes.

Outliers want the same thing as all the rest of our microbes: to share the abundant resources that we have to offer, especially in the brain and nervous tissues. The vast majority of them do not have a high potential to cause severe, acute illness. They quietly enter the body and join in the mix of other bacteria sharing in the resources of the body.

Which brings us to the immune system, the governing body over our shared community with our microbes. When the immune system’s functions are healthy, it keeps our microbiome in check: favorable microbes flourish, and adverse ones are suppressed. If the activity of the immune system is compromised, however, outliers multiply and take more than their fair share.

Many outliers also have the characteristic of being intracellular, a very effective survival technique that allows them to evade the immune system and resist antibiotic therapy. Some of the more common intracellular microbes that can be associated with neurological symptoms include:

  • Borrelia
  • Mycoplasma
  • Chlamydia
  • Bartonella
  • Babesia
  • Rickettsia
  • Ehrlichia
  • Epstein-Barr virus
  • Toxoplasma

If microbes from the skin and gut can freely enter the brain, as the three studies above imply, then outliers can too. When outliers in brain tissue abound, the result is neurological inflammation. Because many microbes value myelin as a resource, damage can include demyelination of nerve sheaths. This, coupled with inflammation, can cause a wide range of neurological symptoms, including chronic pain, numbness and tingling in the hands and feet, burning sensation in the hands and feet, loss of hearing, ringing in the ears, and changes in vision.

Currently, medical science hasn’t accepted cause and effect on this front, because they are looking for a single smoking gun where one microbe always causes a certain type of illness. With chronic illnesses, though, it’s a disruption of the entire microbiome that causes symptoms of illness. It’s never one microbe, or even a few microbes. Even Lyme disease — long linked with the single bacteria, Borrelia burgdorferi — is now considered a polymicrobial infection.

Microbes in the Gut Cause Neuro Symptoms, Too

It’s important to note that microbes don’t necessarily have to enter brain tissue to influence the brain. The microbiome disruption that occurs with chronic illness involves the gut as well, and bacteria in the gut produce a range of neurotransmitters, including glutamate, serotonin, GABA, and dopamine. They use these neurotransmitters to communicate with each other and intestinal cells.

Factors that contribute to chronic immune dysfunction, such as chronic emotional stress and a diet laden with carbohydrates and refined foods, allow a shift in gut flora toward outliers, which alters microbe signaling. This shift toward pathogens, called dysbiosis, generates inflammation and favors production of excitatory chemical messengers. In turn gut dysbiosis activates the sympathetic nervous system (fight or flight response), and sympathetic overactivity increases sensitivity to pain sensations. Not surprisingly, depression and anxiety have been associated with altered gut microbe signaling, too.

Add up the evidence, and you have a good explanation for the extensive list of neurological symptoms common in many of today’s chronic illnesses. It should be noted, however, that even though microbes are central to the problem, chronic immune dysfunction is at the core — both areas must be addressed for wellness to be restored.

Start with Herbal Solutions

Disruption of the immune system is the root of all chronic illnesses. It can be the result of an acute infection with a microbe, but most often, it’s the result of a “perfect storm” of factors that come together to hamper the body’s natural defense network. These system disruptors can include severe emotional stress, poor diet, exposure to toxins such as mold or chemicals, and physical stress — commonly altogether.

Though addressing symptoms is part of the solution, balancing the microbiome and restoring normal immune function must occur for wellness to be reestablished. There are four key components of recovery:

  • Addressing symptoms
  • Suppressing microbes and restoring balance to the microbiome
  • Restoring normal immune system functions
  • Reducing inflammation

1. Address the Symptoms

For managing neurological symptoms, a plant extract called CBD (cannabidiol) from hemp in oil form is one of the best options available. CBD affects a system in the body called the endocannabinoid system, which oversees a wide range of functions in the body, including brain neurotransmitters.

Taking CBD oil calms an irritated nervous system, which leads to a reduction in pain, anxiety, and other neurological symptoms. Use of CBD is not associated with euphoria, and scientific studies have shown that CBD from hemp has no potential for habituation.

Many herbs compliment CBD oil. Herbs called adaptogens not only support the immune system, but they also balance hormones and neurotransmitters in the body. One of the most well-known adaptogens for protecting the brain and neurological function is ashwagandha. Other herbs for calming an agitated brain include bacopa, passion flower, motherwort, and l-theanine from green tea.

2. Suppress the Microbes

While antibiotics might seem to be a solution worth considering, if you accept that the problem is not a single microbe but rather a disruption of the entire microbiome balance, then synthetic antibiotics can make the situation worse instead of better. Synthetic antibiotics suppress normal flora and allow outliers to multiply, especially in the gut. This ultimately will set you back.

Herbal therapy offers a more workable solution by restoring balance to all systems in the body. Antimicrobial herbs are beneficial for suppressing intracellular microbes and other outliers in the microbiome, without disrupting normal flora.

There are many herbs with antimicrobial properties that suppress harmful bacteria and restore balance to the microbiome, and most herbs contain bioactive chemical components that cross into the brain. An excellent list to start with includes andrographis, cat’s claw, Japanese knotweed, sarsaparilla, allicin from garlic, and berberine.

3. Restore Normal Immune System Functions

Many herbs have immune-modulating properties — the ability to calm an overactive or overtaxed immune system. This is important for reducing inflammation, but also for bolstering the immune system’s ability to manage the diverse load of organisms in the microbiome. Herbs that can support and nourish your immune system include ashwagandha, as well as cordyceps, reishi mushroom, and Chinese skullcap.

4. Reduce Inflammation

Herbs important for reducing inflammation and promoting healing include turmeric, boswellia, and devil’s claw. Essential oils administered by aromatherapy are also excellent for reducing brain inflammation. Top choices include frankincense, melissa (lemon balm), and rosemary.

Go Beyond Herbal Therapy

Because the brain consists primarily of fat, anti-inflammatory substances that are fat-soluble work best to quell irritation and inflammation. At the top of the list are omega-3 fatty acids from marine sources. DHA, one of the omega-3 fatty acids in marine oils, has been associated with improved motor and cognitive function, mood, and focus.

A word of caution when taking omega-3 fatty acids: Do not exceed more than 6 grams of fish oil daily. Greater amounts have been associated with an increased risk of hemorrhagic stroke (blood vessel rupturing in the brain). If you have a family or personal history of bleeding disorders, you bleed easily, or your blood doesn’t clot properly, consult with your healthcare provider before taking omega-3 fatty acids.

If you want an alternative to fish oil, krill oil is one of the best ways to supplement omega-3 fatty acids. Krill oil occurs as phospholipids, the form most readily absorbed and utilized by the body, instead of triglycerides found in fish. It takes about 60-70% of krill oil to generate the same blood omega-3 levels as compared to fish oil.

There are also a number of foods to consider adding to your diet to encourage brain health. The following foods contain a variety of nutrients, which can be beneficial in improving neurological function:

  1. Eggs are a good source of lecithin and choline, both essential brain nutrients.
  2. Salmon supplies omega-3 fatty acids.
  3. Oysters supply omega-3 fatty acids and minerals, including zinc, an essential nutrient for brain function.
  4. Olive oil offers antimicrobial properties and monounsaturated fats, which are anti-inflammatory.
  5. Coconut oil provides medium-chain triglycerides (MCTs), which promote nerve tissue repair.
  6. Ghee (clarified butter) provides saturated fat, which in small amounts (1-2 tsp per day) helps support healthy brain tissue.
  7. Avocados and nuts provide healthful fats that play an important role in brain health.

Brain inflammation and irritation can be a difficult part of coping with neurological Lyme, fibromyalgia, chronic fatigue syndrome, and other chronic illnesses. I hope these suggestions give you some tools to feel in control of what’s going on in your body.

To maximize your body’s healing power, remember this: Pair these brain-boosting tips with stress reduction techniques, a healthy diet, and plenty of sleep to boost your immune system and keep the microbes and inflammation in check.

Dr. Rawls is a physician who overcame Lyme disease through natural herbal therapy. You can learn more about Lyme disease in Dr. Rawls’ new best selling book, Unlocking Lyme.
You can also learn about Dr. Rawls’ personal journey in overcoming Lyme disease and fibromyalgia in his popular blog post, My Chronic Lyme Journey.


1. Branton WG, Lu JQ, Surette MG, et al. Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis. Scientific Reports. 2016 November 28; 6: doi: 10.1038/srep37344
2. Caro XJ, Winter EF, Dumas AJ. A subset of fibromyalgia patients have findings suggestive of chronic inflammatory demyelinating polyneuropathy and appear to respond to IVIg. Rheumatology. 2008 Feb; 47(2): 208-11. doi: 10.1093/rheumatology/kem345
3. Dinan TG, Cryan JF. The Microbiome-Gut-Brain Axis in Health and Disease. Gastroenterology Clinics of North America. 2017 Mar; 46(1): 77-89. doi: 10.1016/j.gtc.2016.09.007
4. Dittfeld A, Gwizdek K, Michalski M, Wojnicz R. A possible link between the Epstein-Barr virus infection and autoimmune thyroid disorders. Central European Journal of Immunology. 2016; 41(3): 297–301. doi: 10.5114/ceji.2016.63130
5. Draborg AH, Duus K, Houen G. Epstein-Barr Virus in Systemic Autoimmune Diseases. Clinical and Developmental Immunology. 2013; 2013: 535738. doi: 10.1155/2013/535738
6. Emery DC, Shoemark DK, Batstone TE, et al. 16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain. Frontiers in Aging Neuroscience. 2017 June 20; 9:195. doi: 10.3389/fnagi.2017.00195
7. Fierz W. Multiple sclerosis: an example of pathogenic viral interaction? Virology Journal. 2017 Feb 28; 14(1): 42. doi: 10.1186/s12985-017-0719-3
8. Ivanova MV, Kolkova NI, Morgunova EY, Pashko YP, Zigangirova NA, Zakharova MN. Role of Chlamydia in Multiple Sclerosis. Bulletin of Experimental Biology and Medicine. 2015 Sep; 159(5): 646-8. doi: 10.1007/s10517-015-3037-z
9. Libbey JE, Cusick MF, Fujinami RS. Role of pathogens in multiple sclerosis. International Reviews of Immunology. 2014 Jul-Aug; 33(4): 266-83. doi: 10.3109/08830185.2013.823422
10. Pender MP. The Essential Role of Epstein-Barr Virus in the Pathogenesis of Multiple Sclerosis. Neuroscientist. 2011 Aug; 17(4): 351–367. Doi: 10.1177/1073858410381531
11. Roberts RC, Farmer CB, Walker CK. The human brain microbiome; there are bacter bacteria in our brains! Program No. 594.08. 2018 Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience, 2018. Online.
12. Sriram S, Ljunggren-Rose A, Yao SY, Whetsell WO Jr. Detection of chlamydial bodies and antigens in the central nervous system of patients with multiple sclerosis. The Journal of Infectious Diseases. 2005 Oct 1; 192(7): 1219-28. doi: 10.1086/431518
By |December 14th, 2018|Health-Articles|0 Comments