by Jenny Lelwica Buttaccio
Posted 4/17/20

“The collection of microbes in the human body, called the microbiome, is more extensive, intricate, and important than anyone could have ever imagined,” says Dr. Bill Rawls, MD, Medical Director of RawlsMD and Vital Plan. This vast ecological community primarily consists of bacteria, but it includes fungi, viruses, archaea (single-celled organisms similar to bacteria), and protozoans, too.

“Your microbiome is the sum of all the microbes that inhabit your body,” explains Dr. Rawls. The term microbiome is an often discussed concept among chronic Lyme disease patients and healthcare providers, and for good reason: Your body’s unique flora — more than 100 trillion microbes in total — assists with multiple life-supporting functions, including:

  • Fighting diseases
  • Assimilating nutrients
  • Managing weight
  • Regulating inflammation
  • Improving mood
  • Supporting heart function

Although the majority of the microbes are located in your gut, they also reside in the mouth, vagina, skin, brain, and all through your entire body. “Though the microbiome of an adult is relatively stable, it continues to be influenced by environmental factors,” says Dr. Rawls. “Everything encountered in the surrounding environment influences the microbiome.” Chief culprits that impair your flora include food, toxins, stress, and medications, which contribute to a state of imbalance called dysbiosis.

Enterobacteriaceae: large family of Gram-negative bacteria that includes many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis, Klebsiella and Shigella, Proteus, Enterobacter, Serratia, and Citrobacter.

When factors like these shift the balance of the microbiome from normal flora toward pathogens, it’s the impetus for not only intestinal disease, but many other chronic diseases,” notes Dr. Rawls. If you already have a chronic illness like Lyme disease, ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome), or fibromyalgia, is your microbiome forever doomed?

Rest assured, there are several options for enhancing the health of your microbiome. Let’s take a look at some of the extraordinary characteristics of the microbiome and natural solutions to help you rebuild and restore it, so you’ll be better equipped to fight chronic Lyme disease, Lyme coinfections, or other health conditions.

Unique Features of the Microbiome

#1 Your Microbiome is Considered an Organ in Its Own Right

Of course, the microbiome affects gut health, but it’s the impact it has on the rest of the body that continues to intrigue the scientific community. A 2006 medical review in the journal Embo Reports referred to the microbiome as the “hidden organ.” The reason? The review reported the metabolic activity of the microbiome was equal to that of a “virtual organ” within an organ.

gut flora

In other words, the flora housed in the gut and elsewhere collectively carries out several critical biochemical processes, including regulating the gut mucosal lining, maintaining homeostasis, and supporting a healthy immune response. Just as we care about the health of organs in the body (i.e., the brain, heart, lymphatic system), we must work to nurture and restore our microbiome, too, if we are to have the best chance at chronic illness recovery.

#2 The Microbiome Impacts Communication with Your Immune System.

With 70% to 80% of your immune system residing in your gut, the microbiome influences how well your immune system functions by providing it with signals as to whether or not something is beneficial or harmful. Essentially, the microbiome seeks to maintain peace among the expansive community of microbes. A healthy microbiome is primed and ready to keep stealth microbes and other pathogenic microorganisms and infections in check, many of which contribute to chronic diseases.

But immune system communication isn’t its only purpose. Simultaneously, the gut microbiome works to ensure that the body doesn’t attack itself, as is the case in autoimmune disorders like rheumatoid arthritis (RA), celiac disease, and multiple sclerosis (MS).

#3 The Microbiome Exchanges Information with Your Brain.

Neurons and nervous system. 3d render of nerve cells

Your gut and brain are linked through a connection called the gut-brain axis, which influences brain health. There are several ways the microbiome affects how well your brain functions, according to a medical review in the Journal of Medicinal Food. Though science continues to emerge in this area, some of the following ways the gut and brain impact one another are as follows:

  • Systemic Inflammation: Harmful microbes in the gut may produce cytokines, pro-inflammatory substances in the body that can initiate low-grade inflammation elsewhere, such as in the nervous system and brain. Over time, chronic, low-grade inflammation increases the stress hormone cortisol, which disturbs communication with the hypothalamic-pituitary-adrenal axis (HPA). An out of whack microbiome balance, and a subsequent increase in cytokines, may lead to problems like poor sleep, Lyme brain or brain fog, and cognitive issues.
  • An Influx of Neurotoxins: Though the problem might be rooted in your gut, an imbalanced microbiome may contribute to chemical byproducts like ammonia and D-lactic acid, both of which can be neurotoxic, stymying the functions of your brain and nervous system. In addition to Lyme disease, increased levels of neurotoxic substances tend to be problematic in people with ME/CFS and fibromyalgia, too.
  • Hormone and Neurotransmitter Imbalances: Your gut interfaces with your brain in a concerted effort via the vagus nerve, the longest and most intricate cranial nerve in your body. It begins in the brainstem, moves through the neck and thorax, and ends in the abdomen. The vagus nerve acts as a superhighway, allowing for two-way, or bidirectional, communication.

    When you have a healthy
    , balanced microbiome, the vagus nerve can transport beneficial, calming chemicals like serotonin and GABA to the brain and reduce inflammation and intestinal permeability in the gut. You’re more likely to sleep better, have improvements in your mood, and experience less gastrointestinal (GI) discomfort.

    , as the day-in and day-out challenges of living life with a chronic illness persist, your flora becomes altered. Before you know it, you may experience an onslaught of bacteria that release stimulating chemicals like norepinephrine and dopamine — chemicals that can leave you feeling weird, tired, anxious, and in overdrive.

4 Natural Ways to Improve Microbiome Health

The good news is that with a little TLC — including stress reduction, herbal therapies, and making some different food choices — you can enhance the health of your microbiome and restore homeostasis. Let’s take a look at four ways to do just that.

#1: Eat Prebiotic and Probiotic Foods.

There are two types of foods that can help you manage your gut ecosystem. The first, prebiotic foods, contain fiber that the body doesn’t digest. While that might sound alarming initially, the undigested fibers serve as fuel for the healthy microorganisms in your microbiome.

Variety of fermented food korean traditional kimchi cabbage and radish salad, white and red sauerkraut in glass jars and ceramic plates over grey spotted background. Flat lay, space

The second, probiotic foods, are the ones with which you’re probably most familiar. Unlike prebiotics, foods rich in probiotics contain living, active microorganisms that join the community of friendly microbes in your gut.

When working to strengthen your microbiome, prebiotic foods to consider include:

  • Onions
  • Garlic
  • Asparagus
  • Cocoa
  • Chicory Root
  • Konjac Root
  • Burdock Root
  • Seawood
  • Bananas
  • Apples

When it comes to probiotic foods, the following items may help you add to your friendly flora:

  • Kombucha
  • Kefir
  • Yogurt
  • Kimchi
  • Sauerkraut
  • Pickles
  • Other fermented vegetables

#2: Take Herbal Therapy.

herbal capsules on wooden spoon and leaves

“Taking herbs and other natural supplements is possibly the simplest, most effective way to restore your gut health and improve your microbiome,” says Dr. Rawls. “What’s most interesting to me is how well our bodies recognize and utilize these beneficial plant compounds.” To restore your microbiome, Dr. Rawls suggests the following herbs:

  • Antimicrobial Herbs: Herbs that suppress the overgrowth of harmful microbes that contribute to gut dysfunction, dysbiosis, irritable bowel syndrome (IBS), and small intestinal bowel overgrowth (SIBO) should be the cornerstone of any natural, microbiome restoration protocol. Potent herbs with the power to rebalance your gut flora include: berberine, andrographis, Japanese knotweed, cat’s claw, and garlic.
  • Herbs that Contain Mucilage: If your gut mucosa has been compromised, and you’re experiencing gut discomfort, Dr. Rawls’ go-to mucilage-containing herb is slippery elm bark. The herb is a demulcent that forms a protective film in the gut, soothes irritation in the mucosal lining, and keeps foreign substances out of the bloodstream.
  • Chlorella: A freshwater green algae, chlorella is rich in chlorophyll, a potent detoxifier. Chlorophyll binds to organic-type toxins (herbicides, pesticides, mycotoxins), heavy metals, and plastics in the gut, so they don’t get absorbed and are more quickly removed with waste.
  • Digestive Enzymes: When you have a microbiome imbalance, natural processes like enzyme production can lag and further contribute to poor digestion. Supplementing with digestive enzymes can help fill in the gaps while you’re restoring your gut health — enzymes are especially important for breaking down the carbohydrates that feed harmful bacteria. Taking an assortment of enzymes (such as protease, amylase, alpha-galactosidase, lipase, and others) is ideal.
  • Bitter Herbs: Herbs like burdock, dandelion, gentian root, fennel seed, and ginger are bitter herbs that activate bitter receptors throughout our GI tract. This releases the saliva, enzymes, and bile we need to break down our food.
  • Supplemental Probiotics: Because every person’s gut microbiome is different, some people gain benefits from probiotics, and others do not. It’s really a matter of trial and error. Typically, the best probiotic to consider is one that contains both lactobacillus and bifidobacteria species. However, be aware that using probiotics can make GI conditions like SIBO, irritable bowel, or leaky gut worse. If you experience symptoms such as trapped gas and bloating, discontinue use of the probiotic.

#3: Utilize Stress Reduction Techniques.

Woman With Digital Tablet Using Meditation App In Bedroom

Regulating stress is a crucial aspect of restoring your microbiome. Studies done in animals noted that even short-term exposure to psychological stressors could begin to shift the composition of your intestinal flora away from beneficial microbes like lactobacilli. But stress doesn’t come from psychological factors alone. Other triggers include environmental stressors and an exacerbation of physical symptoms, among others.

To get your stress levels under control, engaging in mind-body activities like meditation, prayer, deep breathing, guided imagery, and restorative yoga can help bring on the calm. If you find it particularly challenging to strike a balance in your life, you might find it helpful to talk with a therapist and implement a more personalized treatment protocol like cognitive behavioral therapy (CBT) or mindfulness-based cognitive therapy (MBCT).

#4 Get Physical.

Sporty fit woman stretching in Ashtanga Vinyasa yoga asana Parsvottanasana - intense side stretch pose

Research from the past few years indicates that physical activity has several positive effects on the microbiome. More specifically, exercise correlates with a rise in the number of beneficial gut microbes, which helps to augment the body’s micro-ecosystem. But when you’re dealing with symptoms like fatigue or chronic pain, exercise is one of the last things you probably want to do.

Fortunately, while researchers aren’t sure of the exact amount of exercise needed to change the microbial balance, even low-impact activities, like walking, Pilates, or qigong, can bring about results. So if you need to, ease into exercise — as you regain your strength, you can up the intensity.

Although there’s still a lot to learn about the benefits of the microbiome and the best ways to restore it, managing the health of yours (like you would other organs of the body) may yield greater energy, enhanced immune function, improved sleep, better digestion, and more.

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.


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