The ancient texts of Ayurveda may not speak directly of the microbiome; however, it is undeniable that its importance is observed, as our microbiome is an interwoven aspect of our Agni or digestive fire.  They are so related, in fact, that if you are experiencing ongoing digestive issues, it is likely some level of dysbiosis (imbalance in your gut flora) is occurring.  Alternatively, a healthy, balanced, and robust digestion is a fairly clear sign of a healthy and harmonious microbiome.    

What is the microbiome?

The microbiome is the term for the trillions of microbes that live on and in our bodies and consists mainly of bacteria, viruses, and fungi as well as archaea and other protists.  These microbes hold a strong influence on all of our bodily functions including digestion, metabolism, immune function, and even our mental-emotional health.  Although the gut microbiome is the largest branch of our microbiome and often the most commonly referred to, the microbiome is also present in our respiratory system (sinuses, lungs), mouth, skin, and genitals.*. Each of these distinct regions will generally host its own unique microbial colonies, although there may be some overlapping microbial species that are found in multiple areas of the body.

*For the relevance of this article, I am referring to the gut microbiome unless otherwise stated.   

Why is the microbiome so important?

Although the microbiome is not technically a part of our human genome, it has such a strong influence on our physiology that we cannot live without it.  The ratio of microbial cells to human cells is said by some scientists to be 10:1 (meaning the total amount of microbial cells is 10 fold of human cells).  Our human genome has about 20,000 unique protein-coding genes while the human microbiome contains roughly 8 million protein-coding genes.    

With our bodies hosting trillions of microbial cells, it is of great importance that we establish a beneficial symbiotic relationship with our microbiome.  A healthy microbiome aids in the digestion of fat, proteins, sugar, and carbohydrates; supports a healthy metabolism; and produces essential vitamins (such as B12), neurotransmitters (such as serotonin), and the oh-so-important short-chain fatty acids (SCFAs).  Further, our microbiome holds a strong influence on our mood, energy, inflammation response, and immune health.   

Common Signs & Symptoms of Dysbiosis (imbalanced gut flora)

• Chronic gas and bloating
• Recurring nausea
• Constipation and/or diarrhea
• Acid reflux or heartburn
• Leaky gut syndrome
• SIBO
• Inflammatory GI disorders (IBD, IBS, Crohn’s, Ulcerative Colitis, Gastritis, etc)
• Food allergies
• Unhealthy food cravings
• Vitamin and mineral deficiencies
• Chronic inflammation
• Diabetes
• Obesity
• Chronic fatigue
• Brain fog
• Candida overgrowth (including yeast infections and thrush)
• Frequent cavities
• Bad breath
• Heavy coating on the tongue
• Frequent sinus infection
• Autism and/or ADHD
• CNS disorders
• Depression, anxiety, and other mood disorders
• Insomnia
• Skin rashes, acne, and other skin disorders

Common Causes of Dysbiosis

• Poor diet heavy in unhealthy fats, processed foods, and refined sugar and carbs
• Low fiber diet
• Food additives, preservatives, and pesticides
• Stress
• Poor sleep habits
• Chronic inflammation
• Illness and infection
• Antibiotic use (especially in excess)
• Certain prescription medications
• Alcohol, tobacco, or drug abuse
• Environment
• Chemicals, perfumes, and pollution
• C-section birth and/or lack of breastmilk
• ACEs (“adverse childhood experiences” aka childhood trauma)
• Poor hygiene
• Overuse of antibacterial soap
• Genetic predisposition
• Certain vitamin deficiencies (such as Vitamin D and A)
• Comorbidities (cancer, heart disease, diabetes, etc)

How to Heal Your Microbiome

A healthy microbiome consists of hosting beneficial microbial types, but equally as important is obtaining a rich and diverse variety of microbes!  Although taking a probiotic may be mildly supportive of this, without the proper dietary and lifestyle changes, probiotic supplements will never be fruitful on their own. 

Luckily there are countless ways to promote a healthy and diverse microbiome without buying unnecessary supplements or spending tons of money.  Although you do not have to adopt all of these suggestions straight away, it is recommended to focus on the ones that are most relevant to your needs and situation.  And remember, these recommendations are all supportive of each other, so the more positive changes you can make, the more noticeable your results will be!  So let’s get to it!!

NOTE: I have divided up the recommendations into their respective categories.  When beginning your healthcare plan, I would suggest choosing two to three dietary goals from the “dietary tips” along with one goal each from the other two categories.  As you turn these recommendations into your new reality, you can move forward with more goals.    

DIETARY TIPS

Not surprisingly, the majority of my recommendations fall under the “dietary” category, showing the great influence our food choices have on our gut health.  If you are overwhelmed with the amount of suggestions in this article, making at least one dietary change is a great place to begin!

1. Eat at least 30 different plant food weekly – keep it colorful!

If you are aiming for a rich and diverse microbiome, the first step is to make sure you are eating a wholesome, diverse, and mostly plant-based diet.  Since healthy microbes feed (and therefore thrive) off of prebiotic fibers, it is of great importance that your diet is filled with a variety of colorful plant foods. 

Make it a goal to eat at least 30 different plant foods each week.  This includes all fruits, vegetables, whole grains, spices, and herbs.  To break it down a bit, you can aim for 10 different (and colorful) veggies, five different fruits, five different whole grains, and 10 different herbs and spices (but use each one fairly generously).*

*This is just a rough example; find what works for you!

2. Increase fiber intake from a variety of plant foods. 

The word “prebiotic” is being thrown around these days like it is some new phenomenon and something you must get through supplementation.  In reality, however, any food that contains prebiotic fiber, better known as “soluble fiber”, will provide a suitable diet for a healthy and diverse microbiome. 

Soluble fiber is simply the type of fiber that is not digested by the human digestive tract, but instead feeds the microbes in our small and large intestines.  Without this nourishment, the healthy microbes will die off and the not-so-healthy microbes that feed on sugar, unhealthy fats, and refined carbs will take over.

The generally recommended amount of fiber each day should be about 25 to 30 grams for women and 35 to 40 grams for men.  Of this amount, aim for at least 10 to 15 grams to be of the soluble variety (but remember insoluble fiber is essential for our gut health as well!).    

Great sources of fiber include:

• Legumes such as chickpeas, lentils, black beans, and mung beans
• Vegetables and fruit (whole, not juiced) such as apples, bananas, avocado, coconut, broccoli, asparagus, and kale (TIP: keep the skin on when possible, this is where the most fiber is)
• Whole grains such as steel-cut oats, brown rice, quinoa, and buckwheat
• Nuts and seeds such as flax seeds, chia seeds, hemp seeds, pumpkin seeds, hazelnuts, and almonds
• Chickpea flour, almond four, coconut flour, 100% whole wheat flour

3. Avoid processed, pre-made, and packaged foods.

One of the worst foods for our health and the health of our microbiome is processed foods.  This is because processed foods are often refined and filled with preservatives, additives, and other non-food ingredients to ensure a long and unnatural shelf life as well as a “better” texture, taste, or whatever.   

Many individuals feel you cannot live without eating processed foods*, but I have to argue.  It takes more effort and preparation, but living a life free from processed foods is possible and many individuals have improved their health significantly with this one major dietary change.

*By “processed”, I am generally speaking of most packaged foods, but some foods such as organic whole milk, homemade yogurt, homemade kefir, etc are not on this list (although they are technically processed).

Challenge yourself to a diet free from ALL processed, pre-made, and packaged foods for 30 days* and you will undoubtedly improve the health of your microbiome along with your overall energy, health, and wellbeing.  During this time, eat only whole foods and aim for home-cooked and homemade as much as possible. 

*If this is too big of a challenge to start with, go slow and cut back on eating processed foods by 50% to begin, and keep cutting back as eating whole foods becomes more natural.   

Processed foods to avoid (non-exhaustive):

• Chips, pretzels, and crackers
• Packaged cakes, cookies, pastries, and bars
• White bread, bagels, pizza dough, couscous, pasta, and any food made with white flour
• Soda and beverages with artificial ingredients or added sugar
• Packaged meal foods (mac and cheese, boxed mashed potatoes, ramen noodles, etc)
• Canned foods
• American cheese
• Deli meats
• Bacon and sausage
• Cured meat
• Breakfast cereal
• Quick oats and rolled oats
• Candy bars
• Pre-made salad dressings and sauces
• Margarine
• Store-bought yogurt or kefir
• Low-fat dairy products
• Ice cream 
• Decaf coffee or tea

4. Allow full digestion between meals.

Like our digestive fire (Agni), our microbiome needs space between breaking down food to rest and reset.  If we are eating before our previous meal is digested, excessively snacking between meals, or grazing throughout the day, our microbiome becomes overtaxed and overwhelmed.  Healthy microbiota seems to flourish with proper space between food intake. 

Digestion of a decent size meal takes an average of 4 to 6 hours.  Most individuals will do best by waiting this amount of time between meals before eating again.  However, if needed, you can aim for a small and simple snack such as a handful of nuts or a cup of lassi, or some homemade yogurt to eat at least 2 to 3 hours post-meal to get you through until it is time to eat again.  

5. Practice intermittent fasting.

Similar to the previous recommendation, it has been shown that many healthy bacterial varieties flourish during intermittent fasting periods.  It is recommended to routinely allow at least 12 to 14 hours between eating dinner and the next day’s breakfast.  Since it is equally as important to avoid food after 6 pm, it is more specifically recommended to eat dinner by 6 pm each night and follow with a 6 am to 8 am breakfast.     

6. Avoid improper food combinations.

Eating improper food combinations is said to cause indigestion, create fermentation, and clog the channels of the GI tract.  The by-product of undigested food becomes toxins (ama) in our body and feeds the unhealthy microbes. 

There are many improper food combinations to avoid, but one of the most important is to avoid eating fruit with any other foods.  This includes nuts, cereal, and yogurt.  Instead, fruit should be eaten at least 30 minutes before a meal or at least 1 to 2 hours post-meal. 

Keep reading to discover more food combinations to avoid.

7. Perform a kitchari cleanse.

Kitchari cleanses are a great way to reset your digestive fire and your microbiome.  A kitchari cleanse is a dietary cleanse in which you only eat kitchari for a set amount of days while also drinking cleansing teas and possibly taking cleansing herbs.  Depending on your strength and needs, you can perform a one-day kitchari fast, or aim for longer such as three, seven, or ten. 

If you are new to a kitchari cleanse I suggest starting small with a weekly cleanse once a week for 4 weeks or a single three-day cleanse. 

IMPORTANT NOTE: Since it is essential to avoid refined grains for promoting a healthier microbiome, I would suggest to perform the kitchari cleanse using quinoa or millet rather than the more traditional Basmati rice. 

Get our 3-day Quinoa Kitchari Kit here.

Get our 7-day Quinoa Kitchari Kit here.

8. Eat with Awareness (and chew your food).

What does eating with awareness mean exactly?  It means to sit with your food (do not eat on the go or “on the run”); avoid distraction while eating (meaning—put down your phone, close your computer, stop all work, and avoid distracting conversation); and take the time to appreciate your food, taste your food, and chew your food thoroughly. 

All of these recommendations will allow your body to break down and digest your food better and result in a happier, healthier microbiome. 

9. Eat food-sourced probiotics daily. 

When looking to encourage healthy microbes in your gut, eating probiotic-rich foods is incomparable in effectiveness to taking even the most expensive and “diverse” probiotic supplement.  Fermented foods will often have a wider variety of microbial strains as well as countless more CFUs (colony-forming units), ranging in the trillions (for food) rather than billions (for supplements).  Further, without proper monitoring, many probiotic companies may fall short of the claims they state on their products, and even worse, some companies have been found to have little-to-no actual living bacteria in their supplements. 

Click here for my homemade kefir recipe!

Purchase Live Kefir Grains here.*

*This is an affiliated link, but is honestly where I purchased my grains back in 2018. . . and  I am still using the same batch today!

A good general recommendation is to take 1/4 to 1/2 cup of a fermented food or beverage daily. 

 

I personally LOVE this “I-Boost Herbal Kraut” but it is a bit spicy!  If you are looking for a less spicy ferment, you can find other great varieties from Pickled Planet here.  My favorite non-spicy flavors are Love Kraut and Veda Kraut.    

Here are some good examples:

Click here for my homemade kefir recipe!

10. Eat your Omega-3s!

This may seem unrelated, but Omega-3 fatty acids have a positive effect on our microbiome in several ways.  They positively influence the type and amount of gut microbes; they reduce inflammation (including in the gut); they regulate the amount of short-chain fatty acids (SCFAs), and indirectly, they stimulate the vagus nerve and calm the nervous system. 

Although there are many seeds and plant-based foods that contain Omega-3s (ALA), the type of omegas in seafood (EPA and DHA) is incomparable in terms of health properties and absorption rates.  Here are the most effective sources of EPA and DHA omega three fatty acids:

• Algae Oil (the ONLY known vegetarian source of EPA and DHA Omega-3s)
• Salmon
• Salmon Roe
• Anchovies
• Herring
• Mackerel
• Oysters 
• Black Cod
• Sardines
• Tuna
• Trout
• Whitefish
• Swordfish

*All seafood should be wild-caught.  Those high in mercury such as tuna and swordfish should be eaten on occasion only.

LIFESTYLE TIPS

1. Take time to de-stress and decompress each day.

With the well-known “mind-gut connection” (via the Vagus Nerve) it is critical to the health of our microbiome to regulate our stress levels each day.  The brain holds influence over our intestinal activities and the health of our gut influences our mood, cognition, and overall mental health.  When our mind is calm and in harmony, our digestive system and microbiome feel stable, secure, and can function at their best.  Alternatively, when stress is high and there is emotional upheaval, our body goes into a state of fight or flight and responds with stress hormones, inflammatory response, and reduced gut motility.  These stress-induced changes have been shown to decrease diversity in the microbiome, promote pathological bacterial growth, and increase intestinal permeability. 

In order to de-stress on a deeper level, daily stress-reducing practices are necessary, even if you are feeling great, carefree, and on top of the world.  It is recommended to perform 1 to 3 of these self-care practices each day.  And if these are not your cup of tea, make this your own and do what works for you!! 

• Meditate
• Yoga—gentle, restorative, and Yin Yoga are best for stress-reduction
• Breathwork—this can be as simple as deep belly breathing or more complex such as Nadi Shodhana or Bhramari
• Rest—this may be the most effective of all (and the hardest for many)
• Warm baths or sauna
• Walking in fresh air
• Nature walks or sitting in nature
• Laying in the grass or sitting by the water
• Gentle exercise
• Chanting
• Abhyanga (oil massage)

2. Get moving – exercise daily.

Exercise is much more than a weight-loss necessity, it is a healthcare necessity for our body, mind, AND microbiome.  Recent studies suggest that exercise can enhance the number of beneficial microbial species, enrich microflora diversity, and improve the development of healthy bacteria.  Exercise has a positive influence on our microbiome in several ways including increasing circulation, reducing stress, and improving digestion. 

So no matter your age, body type, or healthcare goals, make sure to get at least 30 minutes of suitable and enjoyable exercise each day!

Discover the best exercises for your body type here.

3. Stimulate and strengthen your Vagus Nerve.

A strong and healthy Vagal Nerve creates calmness, stability, and security throughout the system and results in a healthy microbiome via the gut-brain access.  Keeping stress low and our emotions in balance is a great sign that our Vagal Nerve is functioning well, but since this is not always the case, there are many researched methods to stimulate and activate your Vagal Nerve and improve Vagal tone.  These include:

• Meditation
• Chanting out loud or humming
• Gargling
• Ujjayi breathing   
• Splashing the face with cold water
• Laughing
• Listening to soothing music
• Warm baths and sauna soaks
• Shoulder, neck, and ear massage
• Foot massage

Luckily, many of these are on our de-stress activity list.  Make sure to include at least one of these suggestions in your daily de-stressing, self-care routine!

4. Perform a nightly abdominal massage.

Although any massage is very soothing and relaxing, abdominal massage has a bit more direct influence on our microbiome health as it supports healthy circulation to the visceral organs and improves gut motility.  When performing this massage apply warm oil to the abdomen while laying down (in Shavasana or “legs up the wall”).   Using the tips of your fingers, massage the abdomen in a circular motion starting around the navel and moving outwards.  The circular rotation should move up on the right and down on the left to encourage the natural movement of circulation and digestion.  Perform this massage for 5 minutes each night before bed. 

5. Avoid excessive antibiotic use.

Although antibiotics can be lifesaving and vital at times, they can also be overused and unnecessary at other times.  Overuse of antibiotics can kill off beneficial microbiota in the gut and leave behind strong and persistent pathogenic microbe types such as Clostridioides difficile (C. diff) and Candida auris.  Some studies have also shown a strong correlation between antibiotic use and anxiety and depression. 

The best suggestion I have for individuals on this sensitive subject would be to use proper discrimination when deciding if antibiotics are the best option.  Weigh out the pros and cons and see which one holds more weight.  When it proves that taking an antibiotic is necessary (and in this case, take them!), strictly follow the recommendations in this article—during and after taking the medication—to support the health and healing of your microbiome and help prevent future dysbiosis.

HERBAL TIPS

1. Drink a digestive herbal tea each day.

Digestive teas offer great support for our digestion and our microbiome.  They stimulate the gastric fire (Agni), flush toxins, and soothe inflammation to create a suitable environment for healthy microbes to flourish.  Further, many herbs and spices contain polyphenols, antioxidants, and a bitter taste which contribute to a healthy and diverse microbiome.

Here are some of my favorite digestive blends:

• Ginger tea (get recipe here)
• CCF tea (get recipe here)
• Tulsi, Turmeric, Ginger Tea (get recipe here)
• Cinnamon, Cardamom, Ginger Tea
• Detox Tea (purchase here)
• AWAKEN Tea (purchase here)
• Healthy Digestion Tea (purchase here)
• Tulsi Synergy Spice (purchase here)

Discover your favorite digestive tea blends and aim to drink at least one cup each day between meals. 

2. Take a digestive stimulant before meals.

Taking a digestive aid before meals is one of the most common (and effective) methods for kindling Agni (digestive fire), preventing indigestion, and encouraging proper absorption.  When paired with a healthy, microbiome-friendly diet, this recommendation will help support and expedite the healing process of your microbiome and encourage beneficial microbes to flourish.   

Here are some digestive stimulants that I have found to work well:

• Eat a slice of ginger (simple, tried and true!)
• Take this ginger, lime, and honey digestive “appetizer”
• Take 3 to 5 droppers of Digestive Tonic Tincture in 1/4 cup of warm water
• Take 1 to 2 tbsp Agni Elixir in 1/4 cup of warm water
• Take a 1/2 tsp of Trikatu Churna with honey; follow with a few sips of warm water

No matter your preference (and you may rotate between a few), aim to take a digestive aid about 15 minutes before each meal.  As your digestion improves, you can reduce this amount to 1 to 2 times daily until you obtain a healthy and robust digestive fire.

3. Take Triphala Churna before bed each night.

Triphala is a traditional Ayurvedic formula that supports healthy digestion, detoxification, and elimination.  Made of three (mainly) sour, bitter, and astringent fruits, this formula contains polyphenols, antioxidants, and fiber and has been shown to act as a beneficial prebiotic for our microbiome.   

To support digestion and microbiome health, take 1/2 tsp of Triphala each night before bed in 1/2 cup of warm water.  If constipation is present, you can take this dose again in the morning.

Purchase my handcrafted Triphala Churna here!

4. Take herbs that help balance the microbiome. 

There are numerous Ayurvedic herbs that have been shown to reduce dysbiosis and encourage a healthy microbiome.  Here are some of my Ayurvedic favorites, with a few Western additions:

• Guduchi
• Musta
• Neem
• Vidanga
• Ginger
• Turmeric
• Cinnamon
• Oregano
• Thyme
• Cayenne pepper

These herbs and spices can be taken regularly in a custom blended herbal formula and the spices can be added to your meals.

5. Take a vitamin D supplement.

Recent studies have found a positive correlation between high vitamin D levels and a healthy microbiome.  Optimal vitamin D levels (40 to 80 ng/mL) support healthy immunity, reduce inflammation, and strengthen the gut lining, all of which are important for encouraging a suitable environment for healthy microbes to thrive. 

It is estimated that between 40% and 80% of the American population is vitamin D deficient.  The best natural sources of vitamin D include the sun (in which you need a good amount of exposure), oily fish, and fortified milk.  Since it is proven that most children and adults are not getting enough of these sources to maintain healthy vitamin D levels, it is often strongly recommended to supplement. 

I use and love this liquid Vitamin D3 K2 supplement that contains no additives or preservatives and is in a coconut oil base.  With this supplement, I have raised my vitamin D levels from 24 ng/mL to 80 ng/mL in a few months.  I am now on a lower dose for maintaining (rather than increasing) healthy vitamin D levels since it is also important to avoid over-supplementing.

Purchase my favorite Vitamin D3-K2 liquid supplement here!*

*This is an Amazon-affiliated link, but is truly the supplement I use daily.  Thank you for your support!

Keep Reading

• Top 10 Ayurvedic Food Rules
• The Importance of Agni
• 28 Days to a Healthy Digestion Challenge
• Treating Candida with Ayurveda

Discover healing recipes with my 30-Minute Ayurvedic Cookbook!*

Discover over 100 herbal remedies in my Ayurvedic Herbal Medicine for Beginners book!*

*By ordering directly through these links, you are helping to support Svastha Ayurveda – Thank you!!

REFERENCES

I obtained much of the information in this article from this AMAZING course by Dr. Robert Svoboda and Dr. Scott Blossom.  It comes highly recommended for anyone wanting to learn more about Ayurveda and the Microbiome!