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Once you understand how your microbiome works, you can gain a sense of mastery over the entire co-partnership. That is where self-care really emerges.”

Rodney Dietert, The Human Super-Organism: How the Microbiome Is Revolutionizing The Pursuit Of A Healthy Life.

For the last decade, I have been on a search to improve my gut health naturally, with some temporary success and many failed experiments. Recent explorations have led me to the Viome Gut Intelligence™ Test, a cutting-edge analysis of the intestinal microbiome with specific recommendations for diet and supplements.
improve your gut health

Your Microbiome

In recent years, I have noticed a worsening of a low-grade digestive discomfort. While my symptoms do not stop me from my day-to-day activities, there has been a consistent nagging that does not ever go away. As we get older, it seems that digestive issues become more obvious. For the last decade, I have been on a search to improve my gut health naturally, with some temporary success and many failed experiments.

Earlier this year my mother was diagnosed with a gastrointestinal disorder. We have been on a journey of discovery about gastrointestinal health since. In the last decade, there have been many breakthroughs in understanding how digestion works.

Have you heard about the Human Microbiome Project? A new and exciting area of medical research is focused on understanding the human being as a superorganism, hosting billions of microorganisms that work together to sustain our health. An estimated 40 billion organisms are living in our digestive tract, alone. Early findings show that this microbiome in our intestinal tract plays an important role in digestion, immunity, mental health, heart health and so on.

The bacteria and other microorganisms in our gut are an integral part of how well we digest and assimilate our food. These microbes exist in harmony in our digestive tract, helping to breakdown complex foods into nutrients that we can use. Also, these colonies create by-products that determine: the health of the intestinal lining, control toxic bacteria, support immune system function, limit the toxins that enter the bloodstream, create vitamins and digestive enzymes, help with hormone function and even have an influence on which genes affect our health.

Keeping the Balance

In balance, these organisms are neither good nor bad, they all work together. But, the modern Western diet with high amounts of processing, chemicals and sugars upsets this internal ecosystem. Sugars, in particular, are the favorite food of what we call the “bad” microbes. These are the strains that tend to aggressively crowd out other organisms when allowed to grow uncontrolled by the “good” bacteria.

The worst part is that sugars starve the “good” bacteria, too. An overgrowth of the “bad” organisms creates an imbalance in the digestive tract which causes a wide variety of unpleasant symptoms.

Signs of Microbe Imbalance

Bloating and Gas

Bloating and gas are often the first signs of an intestinal imbalance.


An overgrowth of "bad" bacteria can allow toxins to enter the bloodstream and lymph system causing inflammation.

Constipation and/or Diarrhea

Many individuals with gi imbalances cycle between constipation and diarrhea.

Brain Fog

Improper digestion interferes with the communication signals in the Gut-Brain Axis.

Nutritional Deficiencies

Blood work can identify specific nutritional deficiencies that are typically caused by a microbiome imbalance.

Mood Disorders

Depression, anxiety, ADD and ADHD are believe to be linked to microbial levels.

Food Allergies and Intolerances

Undigested foods can create many digestive disturbances

Autoimmune Diseases

Microbiome imbalances are believed to be linked to a number of autoimmune diseases including: fibromyalgia, rheumatoid arthritis, lupus, Parkinson's, multiple sclerosis, and scleroderma.

Insomnia and Fatigue

Disrupted sleep can cause a variety of physical, emotional, and mental health issues.

Skin Irritations

As a major organ of elimination, the skin can be adversely affected by digestive issues.

Improving Your Gut Health

There are 3 key strategies to improve gut health.

Restore Microbiome Balance

When things get out of whack, dietary changes can help to restore balance in the GI tract. Eating a wide variety of foods helps to maintain a balanced biome by providing adequate food for all of the different organisms in our intestines. The “good” microbes stay healthy and are able to control the growth of the “bad” ones.

Repair Intestinal Lining

All the things we eat are outside of our bodies until they are digested and can pass through our intestinal walls into our bloodstream. Those walls have a mucus-like lining that acts as a protective layer, similar to skin, that stops toxins from entering our body. When this lining is deteriorated, we are at risk for inflammation and associated diseases.

Strengthen Digestion

Digestion is a series of chemical reactions that break down complex foods into the nutrients that we need. From the mouth to the anus there are important activities that must happen so that we can digest our food. Things like low stomach acid, inadequate digestive enzymes, and microbiome imbalance prevent complete digestion. Undigested foods can become toxins in our body. Eating more plant-based foods, chewing food completely, drinking enough fluids, getting enough sleep and exercise can all help improve digestion and assimilation.

There is no one size fits all in health and nutritional needs, so we each have to work to find the optimal balance to support our wellbeing.

Simple Steps To Improve Your Gut Health

To increase good bacteria and other microorganisms and restore balance in the gut, a few simple guidelines should be followed.

plant based food


Eat a wide variety of real, whole foods, particularly plant-based foods.

reducing stress can improve gut health


Reduce Stress.

exercise improves gut health


Exercise regularly.

reduce the use of antibiotics to improve gut health


Avoid Overusing Antibiotics and OTC Medications



Get adequate sleep.

discontinue use of antibacterial cleaning supplies to improve gut health

Cleaning Products

Avoid Antibacterial Cleaning Products

These small steps may help improve and prevent intestinal discomfort. However, chronic problems will likely need a more aggressive and detailed approach.

Get to Know Your Microbiome

In our search for tools to improve our gut health, we explored many ideas. I am always looking for ways to be proactive about sustaining and improving my health. Western medicine is effective at treating symptoms but we are at the early stages of understanding how to prevent diseases.

One of the most exciting things we discovered in our investigation is the ability to test for microbiome health. There are a few cutting-edge companies that have at-home testing kits at reasonable prices to help us learn more about our insides. If you are serious about restoring your gut health, these tests can be a helpful guide in the painstaking process of fine tuning your diet and lifestyle.

We ended up selecting Viome to do our testing because of its Gut Intelligence™ Test. This process uses artificial intelligence and metatranscriptomic sequencing (RNA) technology to determine the specific microorganisms that are active within your gut and how they function. RNA (ribonucleic acid) reveals which by-products (metabolites) your microbes are producing and whether they are beneficial or harmful to your body.

Viome’s unique process is the only available test that can do a comprehensive analysis of the intestinal ecosystem and offer personalized recommendations. According to the company’s website following the recommendations can help each individual find foods that support improving your gut health naturally.

Viome Recommendations Help

microbiome diversity is linked to improved gut health

Microbiome Diversity

Improved microbiome diversity, is associated with better health.

lower inflammation linked to improved gut health


Chronic inflammation is linked to a deterioration in overall health. Reducing inflammation with the right diet The right diet for our gi tract reduces inflammation.


Nutrient Availability

Different microbes produce different health-promoting nutrients. Viome helps to strike the right balance



Food is our energy source. The greater the nutrients we can absorb the better our bodies function.



The right diet can reduce toxins by supporting the health of our "good" bacteria.


Optimize Macronutrients

Viome helps to optimize individual daily macronutrient ratios. Different microbiomes require a different balance of proteins, carbohydrates and fats.

Viome recommentations also provide guidance on:

  • Creating more health-promoting microbial by-products
  • Specify helpful prebiotics
  • Particular food recommendations to optimize wellbeing
  • Identifying beneficial microbes that are missing in the microbiome
  • Highlighting supplements that may improve intestinal health

My Viome Journey

The Viome test is a stool (poop) based test. The kit comes in an attractive box and includes instructions and the tools for stool collection (a paper stool collector to place under the toilet seat and a tube with a scoop and a liquid preservative for the actual sample). The instructions are straightforward and collecting the stool is not difficult but it is critical to read the steps thoroughly before attempting to collect the sample. Most importantly, you have to register your kit BEFORE mailing the sample

Mailing the sample is not a problem, the box is small and discreet. We mailed the samples on Friday and Viome confirmed receipt on the following Monday. While waiting for the sample to be processed, there is a questionnaire to complete with a wide variety of questions including detailed health and diet information. They even ask for a comprehensive food journal for a few days. The more detailed information you provide, the more precise your recommendations will be.

Viome has a recently revised website and app, that makes it easy to see your recommended superfoods and foods to avoid.

At the time that we selected Viome the estimated time for processing the kit was 4-6 weeks. The company is now in the middle of a major growth spurt which has created a longer wait time. My mother’s kit was processed in about 4 weeks but it took almost the full 6 weeks for my results to come back. Viome sends an email when the results are in.

My Results

I have been dieting since I was 11 years old taking ballet and gymnastics. I thought I knew a lot about my body and food, although I have struggled with my weight most of my adult life. I have tried every diet imaginable, including elimination diets to find the foods that I should eat. Honestly, I could not have been more surprised at the Viome recommendations.

First, it is important to understand that the Viome results are VERY detailed. I am a few weeks into this and every time I revisit the site and app I learn something new or find something I missed before.

As I write this, I am on day 20 of my 90-day plan from Viome and I could not be more pleased that I have tried this path.  The changes I have noticed are significant. This experience has been enlightening. They recommend that I follow their dietary guidelines for 45 days and then they will ask me to add certain foods back into my diet and monitor how I feel, similar to an elimination diet but much more specific.

The most surprising thing is the foods that are on my foods to avoid list. Some vegetables that I had been eating regularly are on the list including cauliflower, bell peppers and corn (a little less surprising). The minimize list includes a wide variety of vegetables that I had been eating regularly because of my focus on mostly plant-based foods.

My list of superfoods includes eggs and wild salmon, both of which have been and still are an important part of my diet.  Almost twenty percent of my superfood list are fats: olive oil, MCT oil, ghee, and flax oil.

Most of the dietary advice I have received over the years has been to eat low-fat, low-carbohydrate foods. I have known for a while that I needed to take my fat intake higher, but I did not guess exactly how important the right fats are for my health and wellbeing.

Viome's recommendations have helped me sleep through the night

Initial Thoughts

I read some reviews online that claimed that the Viome recommendations are not specific and follow general nutrition advice. Let me be clear, nothing could be further from the truth (although some individuals may have results that look similar to generally accepted nutrition advice). My mother and I did the tests at the same time and we had dramatically different results from each other and dramatically different results than we expected. Viome offers highly personalized recommendations. For each superfood and food to avoid, they give a detailed description explaining why the recommendation is important for you, individually.

I have noticed a dramatic difference in my digestive discomfort. Within the first week, some of the permanent gassy, bloated feeling in my gut had eased. By the second week, I noticed that my stools had become more formed. The majority of the burping and gas I was experiencing after each meal also stopped.

Perhaps, the most important change is in my sleep. I had not realized that I was not sleeping well because of gut activity at night. I had been waking up a few times a night turning over trying to settle my stomach. Not that I woke up completely, but when I turned over I had to fall back asleep. This left me feeling tired in the morning and throughout the day.

Since following the Viome recommended dietary changes, my sleep has been much better. According to the Viome site, gut disturbances also affect serotonin levels in the brain which impact sleep. I am now able to wake up only once a night to go to the bathroom and there is little tossing and turning.

I will be providing updates as I notice how my body continues to respond to the new diet over the next 70 days. Viome sends a weekly questionnaire so that they can keep track of the changes too. I have chosen to start keeping a food diary before the 45 days so that I will be in the habit when I need to send feedback to Viome. I am looking forward to seeing the progress as I improve my gut health. Stay tuned.

My Recommendations

Although I have not completed the first 90 days, I recommend this test for those who are interested in taking their health to the next level. My gut health has improved noticeably and seems to be continuing to improve incrementally. Viome suggests that it takes the 3 month period of time to make a change in the microbiome and recommends a retest afterwards to confirm the differences.

The Viome recommendations are complex and are best tackled one step at a time so that you are not overwhelmed by the changes before you experience the benefits. My advice is to start by adding more of the recommended Superfoods and try to eliminate the Avoid foods. Do not worry about the Enjoy and Minimize foods at first. It is particularly helpful to explore the unfamiliar foods on your Superfood list, you may find something you like. Each food on that list has a purpose, so try if you can to eat all of them in a week. I have elderberries on my Superfood list that I have not been able to find, but I have tried everything else.

Once you have a handle on the Superfoods then it is easier to focus on the Enjoy foods. For me, this list is very long and fills gaps in my Superfood list.

Now that I have focused my diet on the Superfoods and Enjoy list, I am working on the recommendations for the number of servings of each food group. I am supposed to eat 9 servings of vegetables, 6 proteins and fats, 4 fruit and grains and 8 herbs, spices, and other foods. They even tell you how many servings of Superfoods, Enjoy and Minimize by food group. I am sure that there are more ways for me to continue to refine my diet as I adjust to the new way of eating.

This is a great time to explore Viome, currently there is a $50 coupon on Amazon for the complete Gut Intelligence Test kit making the final price $149. Prime members get free one day shipping too.


Frequently asked questions about Viome.

Yes, it really is. The box contains everything you need to collect your stool (poop) sample. 

There is a flushable paper collector that you can stick to the commode under the toilet seat. You only need a pea sized sample for the tube.

Just be sure to read and follow the enclosed directions carefully.

No, you don’t.

The website has all of the functions that the phone app does. Having the list of foods on a phone is convenient but not absolutely necessary.


Jason Lloyd-Price, Galeb Abu-Ali, and Curtis Huttenhower

The Healthy Human Microbiome

Apr 27 2016
Genome Med. 2016; 8: 51.
Published online 2016 Apr 27. doi: 10.1186/s13073-016-0307-y

Miguel Toribio-Mateas
Harnessing the Power of Microbiome Assessment Tools as Part of Neuroprotective Nutrition and Lifestyle Medicine Interventions
Microorganisms. 2018 Jun; 6(2): 35.
Published online 2018 Apr 25. doi: 10.3390/microorganisms6020035
Dethlefsen LHuse SSogin MLRelman DA.

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.
Nov 18 2008
 2008 Nov 18;6(11):e280. doi: 10.1371/journal.pbio.0060280.

David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger S, Dutton RJ, Turnbaugh PJ.

Diet rapidly and reproducibly alters the human gut microbiome.

Dec 11 2013

Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11.

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