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.

Tuesday, June 5, 2018

Get notified about new posts at HATS of the Microbiome

Greetings friends of the Microbiome

You can now get notified when a  new post is published.   On the blog just enter your email address in the box near the upper left-hand side.  You will get a confirmation email and when you confirm by clicking the link in the email, each time there is a new post, you will get notified the day it is posted.

Also if there is a topic within the subject the microbiome, leave a comment on this post, and we will look into it.


Dr. Rick

Monday, June 4, 2018

Probiotics and Colostrum - Naturally

Why Colostrum and Probiotics? Look to Nature

R.H. Bennett Ph.D.
Applied Life Sciences LLC

It was from a hands-on experience many decades ago, that I came to appreciate probiotics and colostrum was Nature’s way.  The birth of a calf or foal was an experience I had many times as a young person, and so when I was present to this miracle as a scientist, I saw it with familiar yet trained eyes.

Within minutes of its first breath, a foal or a calf is up and nosing around mom looking for food.  At birth, the youngʻen gets inoculated with the microflora of the birth canal, and minutes later the baby gets more microbes from the nipple.  This occurs when each time the baby nurses.   One the first day or so, the liquid from the udder is colostrum.

Colostrum is an amazing soup.  It has high-energy milk fat, vitamin A and more.  It has a high concentration of antibodies critical for powerful passive immune protection.  It has immune factors that engage the neonatal immune system to empower active cellular immunity.   The transfer of momʻs immune memory occurs here.  We call these specific information peptides, transfer factors.  All colostrum of all species contains all these factors and more.


There is so much more to tell of colostrum and will do so in the future.  However, for now, let's look at the role of colostrum constituents with the microbiome.

Immune Globulin G or IgG and other immune factors (4,5)

IgG in colostrum is targeted to bind up specific microbes that may be harmful to the microbiome and the newborn.  Once bound up the microbe cannot attach and persist and is swept out.  In short, it helps the balance of the ecosystem.

Lactoferrin (5,6)

Lactoferrin is an iron-binding peptide that also has broad immune modulating functions in the gut.  In the gut, it binds up any free iron and thus deprives specific harmful microbes of the iron they need for enzymes that produce energy substrates needed for growth.


These are complex carbohydrates that the animal cannot digest but a certain member of the microbiome, specifically the Bifidobacteria actively consume as they proliferate in the gut.  These are in effect prebiotics (3). 


This milk sugar is also food for the microbiome, and many species of bacteria use lactose very efficiently.  In this regard, it is a prebiotic too.   Microbes use lactose and produce Latic Acid.  This lowers the pH of the gut, and that helps regulate the microbiome too.

Immune peptides (2,4,6)

There are quite many immune peptides, glycopeptides, and cytokines in colostrum.  All of these have a considerable role in maturing and activating the immune system of the neonate.   Many members of the microbiome have similar and symbiotic roles in the regulation of the immune system.

            Grow Factors

There are many growth factors in colostrum. They have a wide range of functions, including establishing gut integrity (1).

Note:  There clearly appears to be an increase in the research on milk and colostrum bioactive compounds.  Of the citations in the above section, all were published since 2000. As this trend continues we will keep the readers apprised and we should all promote the necessity of breastfeeding for the vitality of all children.

Combining Colostrum with Probiotics

From my experience and training, it made perfect sense to me to combine colostrum and or colostrum components in any probiotic product.  The synergy is undeniable.  However, our first formulation did not contain colostrum, more than likely for market economic reasons.

The second formulation some many years later, it was my view was a combination prebiotic-probiotic indeed must contain colostrum too.  After all, it had many factors that are there in nature needed for the microbiome.  To make a long story short, people who were not immunologists or microbiologists, could not appreciate the good a probiotic with colostrum could bring to people with “troubled microbiomes."  Who are those people?  Just about anyone on a traditional high carbohydrate, high fat, high sugar, Western Diet.

What is on the Market?

Well, it should not be too surprising to find at least four companies are making a probiotic that contains colostrum or colostrum components.   In the last 10 years, the world’s colostrum production shifted from New Zealand to the Western United States.  With industry consolidation, most all colostrum collection, processing, and production is controlled by an Arizona company.

  According to the US Dairy Export Council, the APS Biogroup is the world’s largest colostrum processor.  Their website reveals they do custom colostrum and colostrum containing products for a number of international and US companies.  There is a reasonable likelihood that the Arizona firm produces the colostrum found in most commercial retail products.

 Figure 1. Probiotic products containing colostrum currently on the market

Table 1.  A comparison of probiotic products containing colostrum/fractions
Probiotics – HATS*
4Life Research
Five Typed Strains – Yes
100 mg 1
Three Species - ?
Rice sols, FOS 200mg
1400 mg2
Five Typed Strains some HATS
800 mg2
Six Species -?
One Species-?

*HATS Human Adapted Targeted Symbiotic, 1 Ultrafiltrate of colostrum with defatted colostrum added dried, 2 Defatted colostrum dried, Strains: genus and species with strain ID, Species: Genus species only, no strain ID, therefore, HATS indeterminable

The data in Table 1 is from the product labels, and it shows some very distinct differences between the products.  While the ChildLife product contains the most colostrum, it has un-typed strains and a low concentration of prebiotics.  The Symbiotics product has typed strains some or all of which maybe HATS.   As a synbiotic, the 4Life products are the best combination of HATS strains and prebiotic type and dose.  These prebiotics are known from in vitro research[3] to facilitate the growth of the strains in the product[4]. The dosage of colostrum or one of its components is low compared to the others.

In many situations, it may be advantageous to add additional colostrum/components to the daily dietary supplement regimen.  Many companies in the West sell such colostrum supplements. The rationale to do so arises from the components in colostrum that synergize with the microbes of the microbiome.  In particular the 4Life synbiotic can be augmented by the addition of one or more of their colostrum containing products. One recommended product for this purpose is Transfer Factor Classic; it contains 600 mg of colostrum and colostrum components, in the daily dosage.

Take Home Message

Probiotics, prebiotics, and colostrum are nature’s way to jump-start the microbiome.  It may well be going back to nature in this simple way the microbiome can be rejuvenated and restored at a time we not so young folks need it the most.
1.     Blum, J. W., and C. R. Baumrucker. "Colostral and milk insulin-like growth factors and related substances: mammary gland and neonatal (intestinal and systemic) targets." Domestic animal endocrinology 23.1-2 (2002): 101-110.

2.     German, J. Bruce, Cora J. Dillard, and Robert E. Ward. "Bioactive components in milk." Current Opinion in Clinical Nutrition & Metabolic Care 5.6 (2002): 653-658.

3.     Gopal, Pramod K., and H. S. Gill. "Oligosaccharides and glycoconjugates in bovine milk and colostrum." British Journal of Nutrition 84.S1 (2000): 69-74.

4.     Jørgensen, Ann Louise Worsøe, Helle Risdahl JuulMadsen, and Jan Stagsted. "Colostrum and bioactive, colostral peptides differentially modulate the innate immune response of intestinal epithelial cells." Journal of Peptide Science 16.1 (2010): 21-30.

5.     Stelwagen, K., et al. "Immune components of bovine colostrum and milk." Journal of animal science 87.suppl_13 (2009): 3-9.

6.     Van Hooijdonk, Antonius CM, K. D. Kussendrager, and J. M. Steijns. "In vivo antimicrobial and antiviral activity of components in bovine milk and colostrum involved in non-specific defence." British Journal of Nutrition 84.S1 (2000): 127-134.

[3] Dr. C. Oberg Weber State University in vitro (lab culture methods) unpublished research
[4] Disclaimer. In a former position, the author was part of the research and development team for the product.