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The Microbiome and Your Health

Updated: Jan 4, 2023

Believe it or not, the bugs in our gut have a lot to do with our normal function and disease development. As more research on the role of the microbiome becomes available, we are learning that the balance of these critters can influence our genes, our neurotransmitters and mood, hormone metabolism and even direct our immune system and play a role in autoimmune disease.


  • What is the microbiome? How do we know if it’s imbalanced and how can we test it?

  • What do antibiotics and probiotics do to the microbiome?

  • Naturopathic Treatments for addressing microbiome imbalances.

What is the Microbiome?

A microbiome is the collection of bacteria, fungi, yeast, and even viruses that live both in and on our bodies and acts as an interface between our cells and the outside world. There are several human microbiomes, the skin has its own microbiome, the mouth and nasal cavities have their own, and the digestive tract is another with varying organisms depending on the location. In general, they help protect us from pathogenic infections and maintain the health of the organism (you!).

The digestive tract microbiome is what we are mostly referring to when we discuss the microbiome as it is the largest collection of microbes for humans. Its best-known responsibilities are for helping us properly digest our food, get the nutrition from our food, and develop and maintain our immune system.

Whare are the Symptoms of an Imbalanced Microbiome?

Common symptoms or conditions from an imbalanced gut microbiome include:

What are the potential causes of imbalances to the microbiome?

The core microbiome is formed in the first few years of life, and heavily influenced by how we are born (i.e. vaginal delivery vs. cesarean), if we were breast fed or not, and our diet and exposures in the first few years of infancy and childhood.

The microbiome can also change over time in response to our diet, stress levels, medications, and environmental exposures. Here’s a list of things that commonly disrupt the microbiome:

  • Dietary changes, eating one’s food intolerance and lack of dietary diversity

  • Stress, poor sleep

  • Antibiotic use

  • Acute and chronic infections

  • Medications (include birth control pills)

How Can You Assess the Microbiome?

The gut microbiome can be assessed through stool testing. A good laboratory will collect several days of stool (usually 3 in a row), and list the various microorganisms found as well as evaluate for the balance of the various families of bacteria. There are several labs which do this, our favorites include:

  • Doctor’s Data – GI 360 which includes complete microbe assessment, inflammatory markers, and comprehensive digestive analysis from stool.

  • GI MAP – A comprehensive stool analysis of microbes, inflammatory markers, and enterotoxins (toxin levels produced by certain bacteria).

Having a baseline assessment of the types of bugs inhabiting our gut can be tremendously helpful to guide dietary changes and specific probiotic support to rebalance and support a healthy microbiome.

Fun Fact: The ratio of Firmicutes to Bacteroidetes (two major phyla, or families of bacteria which make up 90% of the microbiome) can determine how you metabolize carbohydrates and play a role in obesity and weight loss.

What about Antibiotics and Probiotics?

Antibiotics can be more general or more specific to target certain types of bacteria, but their effects are systemic. Even though you might be taking an antibiotic for a urinary tract infection or for acne, those antibiotics are affecting the microbiome of the gut, the mouth, nasal cavity and everywhere else.

This is why a common side effect in women is yeast infections after completing a course of antibiotics. The beneficial bacteria inhabiting the vagina are compromised by most antibiotics and without those lactobacillus species maintaining the balance, opportunistic candida species can take over.

Taking a high dose probiotic (50-100 billion cfu is what we generally recommend) daily for 3-6 months following a course of antibiotics can be hugely helpful in preventing many opportunistic infections. Looks for one with a wide variety of beneficial strains such as many different Lactobacillus species, different Bifidobacterium species and Streptococcus thermophilus for starters.

Sometimes more specific probiotics are needed for various conditions. A yeast known as saccharomyces boulardii can be especially helpful for those with disordered gut motility, common “traveler’s diarrhea” and even IBS. Newer spore type probiotics such as bacillus strains are soil-based probiotics are very helpful for promoting bacterial diversity and enhancing the conditions for other good, or “commensal” bacteria in the GI tract. They are excellent at treating “leaky gut”, or gut barrier dysfunction.

A Word about Prebiotics:

Prebiotics are the foods we eat that help feed the good microbes in our gut. Dietary fiber is where most of this comes from and as it’s broken down in the gut it creates short chain fatty acids that are nutrients for the good bacteria and promote healthy colon cells. Chicory root, leafy greens, leeks, asparagus, barley, oats, flax seeds, wheat bran, apples, bananas and jicama are great prebiotic foods.

New Research in Postbiotics:

Postbiotics are an emerging interest in the microbiome as these are supplements containing only byproducts of bacterial fermentation – basically the waste products that the probiotics leave behind.Research is showing that taking supplements of post biotics can also regulate the composition of the microbiome.

Naturopathic Treatment for the Microbiome

The microbiome can change under the right conditions! You shouldn’t have to take massive amounts of probiotics for the rest of your life to address your microbiome and once we’ve identified the imbalances, an individualized treatment plan can be created to support increasing the strains of bacteria that need growth and decrease any strains that are overgrown.

Dietary Recommendations

  • Food diversity creates the proper terrain for a healthy microbiome. If you find you are eating a lot of the same foods over and over, it’s time to find some new recipes, incorporate some new fruits and veggies and explore new flavors.

  • Avoid your individual food intolerances which are foods that drive dysbiosis (or imbalanced gut flora) in your body.

  • Targeted prebiotic foods for bacterial strains that are low in numbers. General prebiotic foods include chicory root, leafy greens, leeks, asparagus, barley, oats, flax seeds, wheat bran, apples, bananas and jicama. Walnuts and pecans are great for several beneficial bacteria strains as well.

  • Avoid processed and refined foods, eat more fresh vegetables, fruits, wild caught fish and seafood, pastured meats, dairy and omega-3 eggs. Especially avoid artificial sweeteners and but organic whenever possible as pesticides can also impact the microbiome.

  • Fermented foods have natural probiotics in them such as sauerkraut, kimchi, yogurt, kefir, kombucha, fermented pickles, miso, tempeh, raw cheeses and sourdough. Try to get 2-3 different fermented foods in each day.

Lifestyle Recommendations

  • Sleep: Not only is your sleep affected by your microbiome, but your microbiome is affected by your sleep! Keep a good routine and prioritize getting sufficient and good quality sleep each night.

  • Stress: It’s not easy to reduce stress these days, but anywhere you can reduce responsibility, ask for help and find time to do the things you enjoy (or even do nothing at all) can help. Stress can make the gut and intestines more permeable, activating immune and pro-inflammatory responses which trigger additional stress hormones to be released.


We love these probiotics for patients needing to support a healthy microbiome:

  • HMF caps or powder by Seroyal

  • Therbiotic caps or powder by Klaire labs (we love their infant powder for babies)

  • Fem-Ecology caps by Vitanica for women

  • RestorFlora or MegaSporeBiotic caps for bacillus or spore probiotics


Constitutional hydrotherapy treatments can be a great addition to your treatment plan in supporting normal digestive function, reducing stress and general healing. Your provider can let you know if this treatment is appropriate for your condition, and you can read more about it here.

Individualized care which considers your unique metabolic and dietary needs is essential for effective and efficient improvement of the microbiome. At PCNM you’ll be working with a team looking to solve the problem, and not just manage it with a prescription. Schedule a complimentary consultation to see how we can help!


Disclaimer: The entire contents of this website are based upon the opinions of physicians at Pacific Clinic of Natural Medicine, unless otherwise noted. Individual articles are based upon the opinions of the respective author, who retains copyright as marked. The information on this website is not intended to replace a one-on-one relationship with a qualified health care professional and is not intended as medical advice. It is intended as a sharing of knowledge and information from the research and experience of our providers and their community. PCNM encourages you to make your own health care decisions based upon your research and in partnership with a qualified healthcare professional. If you are pregnant, nursing, taking medication, or have a medical condition, consult your health care professional before using products based on this content.

If you want to use an article on your site please direct to and cite the original article page. This content may be copied in full, with copyright, contact, creation and information intact, without specific permission, when used only in a not-for-profit format. If any other use is desired, permission in writing from Pacific Clinic of Natural Medicine, LLC and the Teresa True, ND is required.

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