Thursday, June 14, 2018

Measuring Your GI Microbiome

How To See Your Gut Microbiome
“What gets measured gets done."

R. H. Bennett Ph.D.
Applied Life Sciences LLC
One of the unique attributes of the Human Mind is the ability to “see” abstractions.  There are many good examples.  We cannot see the light energy that will sunburn skin, but we know its there.  A painful sunburn is an excellent educator.  We cant see gravity, but one good fall as a toddler, and we learn. We cannot see our microbiome and even if we could, its appearance would be as meaningless as a five-pound bag of bean soup mix spilled on the floor.
Realistically there would be no distinction the microbiome unless scientists could "see” it. The Human Microbiome Project (2) was a project you and I funded via the National Institutes of Health, that gave a consortium of scientists the funding to develop the tools to “see” the microbiome.

The Seeing Tool:  Genetic Pattern Recognition

Imagine that big bag of mixed beans, but in this case, all the beans are similar in size and shape, and they are colorless.  Now we pour it all out on a huge table and decide we are going to sort the beans.  How are we going to do that?  Size, shape, and color are just too vague and in distinguishing.   However, suppose we had a bunch of templates, one for each species of bean that could recognize unique DNA sequences in specie of bean.  All beans like all living things have unique DNA sequences that make a lima bean a lima bean and a lentil and lentil.
  The ID templates are microscopic too and need to be exposed to the bean’s DNA to find a match.  So we grind up the beans dissolve them all in water, stir well and then add the templates.   The templates for Pinto Beans line up on the beans DNA/RNA that are unique for the Pinto Bean.  The templates or probes as they are called have unique tags on them that allow the  “counting machine” to count them once they find and attache to the DNA sequence it is programmed to find.  The result is a DNA copy count for each been type.  Now we know precisely how many of each bean type was in the bag.

A very similar process is used to identify and count the microbiome bacteria in a stool sample.  This is some very sophisticated science and less than a decade old.   Depending on the process used we can count significant groups like Phyla, Family within the phyla and species within the family.   The deeper the counting, the more complicated and expensive that test becomes.   Just the same we can count bacteria groups, and the size of these groups tells us much about the vitality of the microbiome and its influence on the health of body systems (1).  

Testing Kits and Services
Today three organizations offer MB testing services.  All offer similar services. One has a value-added service that requires an order from a health care provider as they attempt to relate the MB pattern to possible and potential disease states or propensities.
    This company is uBiome (u, in this case, represents the Greek Mu for micro) They are located in San Francisco.  They offer for-profit testing services.  Their interface is mostly web-based that some will find frustrating if they need to speak to a representative.  They have added a means of contact.
·        Email:
·       Phone: 1-844-248-5432

The costs range from $ 89 to $399 depending on the number of assays.  For those that would do a "before and after test", such as before and after taking a probiotic or synbiotic, you sign up for auto-ship for $71 per month (cancel anytime). Thus you can do two tests for $142.

The data displays are easy to understand and informative. In the graphic below it shows the distribution of the major bacterial phyla and compares it to some other dietary types.

 Other displays show groups down to the Family or even the Genus level.  An example of an important genus is Bifidobacteria.  It is a member of the Acinetobacter phylum.

 The second organization is the American Gut. It is a non-profit citizen science project within the medical school at the University of California, San Diego.  Discussions with the project leaders were very informative and revealed they are collecting massive amounts of MB data that will help us all better understand the workings of the human microbiome and its implications for health and wellness. 

The test kit cost approximately $  99.00 for one and $180.00 for two. They highly encourage taking a rather extensive questionnaire about diet and lifestyle.  This data with thousands of others will allow for some fascinating results that may indeed tell us we and our MB are who we are and what we eat.

 The data displays include this one and more.  In this case, your MB is contrasted with others.  The customer interface is entirely web-based.

The third organization is uBiota in Salt Lake City Utah.  This business an has strong affiliations to the University of Utah Medical School.   Multiple interactions with uBiota and Dr. Kael Fischer reveal this company 
intends to be a major provider of MB testing.  

The cost for one kit is $99.00 or $329 for three kits. They provide web-based data displays that let the user look deeper within each phylum to examine their MB.  They also provide many other useful displays of the test data.  uBiota can be reached at  801-410-0149

A word of caution about companies with big claims

There are a couple of web-based microbiome health websites that portend to make a diagnosis of disease based on MB tests and another website that offers particular dietary recommendations for a fee.  The specific recommendations arise from your MB data.  It is far too early in the science of microbiome to make a disease diagnosis and dietary recommendations tailored to the microbiome make up.  The consumer is advised to beware.

Your personal research project

 Science is showing us that the more we know about our microbiome and what influences are impacting the MB, the better we can be in assuring its vitality of functions.
One such test on your MB could have many permutations, but has been pointed out in a previous blog; we have to keep our experimental designs clean and simple.  One such simple design could be a Test and Switch Back. 

For a one-person test,  it might go like this:

ü  Before Test Day One.  Do the MB fecal test BEFORE changing diet 
or any other manipulation

ü  Day Two through 14.  Add the change.  It might be removing all 
sugar from the diet, or the addition of a 
Synbiotic like Pre/o Biotic™ or going on a vegan diet.
ü  Day 15 Rerun the MB fecal test and switch back to the diet and lifestyle that existed on Day 1.

ü  Day 30 Test again.

You won't get your data back for a few months, but this is to be expected.   While you are waiting to go back to the change instituted on Day 2 and keep a journal on how it feels. 

 When you get your data back, take a look and see if any significant changes in the percent of the major phyla can be seen.  If you would like some help with the interpretation, send me an email via this Blog, and we can set up a consultation.

Simple Interpretation

Science is and will be teaching us much more about how to interpret MB data, but a straightforward concept is a starting place.   One aspect of a healthy resilient MB is diversity.  We look for patterns that show a large number of different type of bacteria in the MB.  In diversity is stability and resilience(3).  MBʻs with a dominance of one or more types may be perturbed and imbalanced by diet, stress, antibiotics or other medications.  If such pattern shows up in a test, relax it is not an emergency.  Before you head out to the clinic looking for a fecal transplant as we saw on a NOVA special about the microbiome.  Try this; research shows adding much more fiber to the fare (4) while substantially reducing the fats and sugars of the Western Diet(5) will improve the microbiome.
There is an excellent chance this simple dietary change will restore diversity and a good HATS probiotic taken for a month will be a jump start for microbiome rejuvenation.

1.     Al Khodor, Souhaila, and Ibrahim F. Shatat. "Gut microbiome and kidney disease:
 a bidirectional relationship." Pediatric Nephrology 32.6 (2017): 921-931.

2.     Turnbaugh, Peter J., et al. "The human microbiome project." Nature 449.7164 (2007): 804.

3.     Lozupone, Catherine A., et al. "Diversity, stability and 
resilience of the human gut microbiota." Nature 489.7415 (2012): 220.

4.     Tap, Julien, et al. "Gut microbiota richness promotes its stability 
upon increased dietary fiber intake in healthy adults."
Environmental Microbiology 17.12 (2015): 4954-4964.

5.     Sonnenburg, Erica D., and Justin L. Sonnenburg. "Starving our microbial self:
 the deleterious consequences of a diet deficient in 
microbiota-accessible carbohydrates." Cell metabolism 20.5 (2014): 779-786.

1 comment:

  1. An excellent blog with great information , thank you Dr. Bennett!