Base Case Ubiome Test Results

Base Case Ubiome Test Results

Setting The Bar

My personal Ubiome test results are in, creating a “Base Case” against which future tests will be measured.

The information, provided by Ubiome, a gut microbiome gene sequencing company, is impressively detailed and comprehensive (although not perfect), and provides a measure, down to the genus level and occasionally beyond, of the general state and well-being of my gut microbiome.

This is my first test, and the one against which we will be able to compare how things change going forward, and to what extent changing the microbiome is even possible.

In short, this one sets the bar.

If you haven’t already, you might want to read my introductory post to the MicrobioME Project for a thorough explanation of the intent, purpose, and limitations of what will be an ongoing study of my microbiome, and how dietary changes, supplement interventions, and lifestyle choices, can affect it over time, and in the process, affect my general health and well-being.

In short, do these things matter? Does it make sense to take probiotics? Prebiotics? How important is diet? Sleep? Antibiotic use? Can we really improve the health of our microbiome, and if we can, does that improve our overall “human” health?

Will the tests show anything? Will they contradict observational data, that is, how I feel? Better? Worse? The same?

While your results will certainly be different, and your decisions must be right for you, my hope is that this ongoing personal study will provide you with useful reference points against which you can measure and compare your own health, and the health of your own microbiome, whether you engage in actual laboratory testing or not.

And you are invited to share those impressions with us in the comments section so we can all benefit from each other’s experiences.

As I do with my weekly “Snapshot” updates, I’ve included all the relevant variables (towards the end of this post) detailing my supplement intake, diet, lifestyle, etc. The sample I submitted to Ubiome was taken January 11.

(Note: While I routinely update my supplement and lifestyle parameters on Mondays, I test on Fridays as my weekdays are more structured than my weekends and should therefore enhance the validity and ongoing continuity of the tests.)

For this Base Case I ceased all probiotic supplementation (which before then was pretty limited anyway). I did continue with my existing, and very modest, prebiotic supplementation, primarily my daily psyllium fiber (which isn’t considered a traditional prebiotic) and otherwise stuck to my normal routine.

Essentially, I lived how I normally do, engaging in what I considered to be a generally “healthy” manner, absent any extraordinary measures, good or bad, that would affect my microbiome.

The results?

Simultaneously gratifying, disturbing, unsurprising, and astonishing.

Basically, the plot of a good movie.

The Results

Ubiome first provides you with a quick top-level overview.


This was generally good news, and given I feel I eat reasonably “well,” engage in all manner of physical activity (I run a health, fitness, and wellness business), sleep “okay,” and otherwise try to do my best health-wise, I had hoped this would be the general result.

Besides, I “feel” good, and would have been disppointed to say the least if the data did not support that admittedly subjective observation.

But it wasn’t all sunshine and roses either!

While much of my data was largely either in line with averages or compared favorably with Ubiome’s “Selected Samples,” not all of it was.

Not by a long shot.

And it went both ways.

I’ll stick to the most notable results, primarily those in which my results differed materially from what might be expected.

Probiotic Bacteria

Before we go any further, please note that the “Selected Samples” Ubiome uses to compare many of these results are from “individuals who report no ailments and high levels of wellness.” Essentially, a higher bar than just “average.”

A really mixed bag here.


My Lactobacillus levels were nearly non-existent. This is a very popular genus of probiotics, thought to be highly beneficial, and I had close to none. Likewise, I was short of Bifidobacterium vs the Selected Sample, but not by nearly as much.

The one bright spot here was Akkermansia. This is an up-and-coming probiotic not a lot of people have heard of and is not typically included in multi-strain formulations (in fact Ubiome maintains it’s simply not available for purchase) and yet I had this in abundance.

Here’s another look, from the “Advanced” section where I can get some detailed numbers all the way down to the genus rank.

First, the percentage of identified genera:

Or another way, as compared to “all samples” which will differ from the bar charts above as those were against a “selected sample.”

Keep in mind, I was not taking any probiotic supplementation during the weeks leading up to this test. That was on purpose. It will be interesting to see if I can increase the Lactobacillus and the Bifidobacterium with probiotic supplementation (that’s what the next test, already submitted and awaiting results, will be about) and whether that will have any affect on levels of Akkermansia which you cannot supplement for.

Probiotic Foods


I found this interesting in that I ceased consuming my daily serving of Greek yogurt for purposes of this test. Will it go back up now that I’m eating yogurt again? That will be interesting to see.

The only other two foods Ubiome tests for probiotic presence in your gut are pickles and sauerkraut, which I only eat on occasion, and so unsurprisingly I had neither of these in recordable numbers.


Ubiome tests for microbes associated with the production of three substances that can modulate inflammation, butyrate, propionate, and polyamine (in that order, below).


As you can see, I whiffed on those microbes that produce propionate. Ubiome suggests I can help feed and therefore increase the population of these microbes by adding assorted mushroom derivatives to my diet such as LC-AX supplements and mushroom fiber.

Since my next test involves experimenting with prebiotics, I am going to explore the possibility of adding mushroom fiber to my diet in the coming weeks.

Microbial Diversity

Diversity Score

This was included in the Overview already, but it’s worth noting as this is considered an important metric. Generally speaking, greater diversity of the microbiome is associated with improved health outcomes as compared to less diversity. My numbers here are good. But is it possible to increase diversity? That’s another thing we’re going to explore going forward.

Alcohol Metabolism


I include this primarily for the stark contrast between the “accumulators,” which are bacteria that turn alcohol into toxic substances, and the “decomposers,” which break that toxin down into harmless substances. While I have twice what I “should” have of the accumulators (bad) I have 28 times of the latter as compared to the average (really good).

What’s that all about?

I don’t know. I don’t drink much or often. Well, not anymore. There was a time when I did and perhaps I had this same ratio when I was younger. Perhaps these microbes kept me healthier than I otherwise could have expected. If so, thanks, guys!


I was found to be deficient in microbes that produce vitamin K2. I supplement with K2, and exhibit no obvious signs of vitamin K deficiency so I’m not overly worried about it, however Ubiome notes that you can supplement with the Vitamin K-producing Bacillus subtilis, but you have to look for it as it is not commonly found in probiotic formulas. That’s something I might experiment with in the future.

On the other hand, I had an abundance of microbes that produce vitamin B9. What I found intriguing about this was the fact that among the things Ubiome recommends that you consume to help increase vitamin B9-synthesizing microbes was xylooligosaccharide (XOS), one of only two prebiotics I was consuming during my base case test.

Advanced Section

Ubiome also offers an “Advanced” section where you can really dig down into the details, in fact so many it’s frankly overwhelming, but this will be an ongoing endeavor on my part, and I did manage to glean a few insights from the data.


I had elevated levels of four microbial communities that are associated with autism, two at the Class level (taxonomy classification), Betaproteobacteria, and Negativicutes, one at the Family level, Sutterellaceae, and one at the Genus level, Sutterella. Four-and-a-half times the average for those last two.

I should note these are almost all branches of each other in the taxonomy, so I’m basically triple counting in a sense.

I do not suffer from autism of any kind, or to be precise, any noticeable kind. Take this as a helpful reminder that when reviewing test results like these, great care must be taken not to assume association is causation. I’ll keep an eye on these nonetheless.

Kidney Stones

I had 3.82 times the average of Order-level Burkholderiales. These microorganisms are able to digest the oxalates that are found in large quantities in such vitamin-C rich foods such as berries and leafy greens keeping them from building up in the kidneys and becoming kidney stones.

I’ll note here that kidney stones tends to run in families, and my father had kidney stones.

I eat a lot of berries and leafy greens, in fact they are the principal source of my fruit and vegetable intake on any given day.

And I’ve never had kidney stones.

It could be I’m just lucky to have large quantities of these microbes, but I believe there is a strong argument to be made that the act of feeding my microbiome a diet heavy in oxalates is in fact resulting in a flourishing of the microbes that devour them.

To iterate my caution above, I can’t assume correlation is causation, but this is another one to keep an eye on, particularly when I get to the diet portions of my experiment later in the year.

It will also be interesting to see if the Prebiotic Case that I will start building this coming week (in which I ingest undigestible complex carbohydrates including soluble fiber) will result in a measurable increase in the levels of the microorganisms that feed on those foodstuffs.

Metabolism and Inflammation


As compared to all omnivores (which I am one in that I derive my nutrition from both animal and plant sources), my Akkermansiaceaei microorganisms are at levels just over 30 times greater. Akkermansiaceaei was found to be highly elevated in individuals who engage in intense physical exercise (according to a study involving rugby players) and appears to help aid in metabolism and inflammation.

As it so happens, I do engage in intense physical exercise.

Oddly, my levels as compared to pretty much every other classification, from vegans to Ubiome’s “Selected Sample” to those following a Paleo diet, were unremarkable. I suspect there are, to pardon the pun, a few bugs in the system, so I will not make very much of this one.


My Ubiome results produced an enormous amount of data, which I will be poring over as I continue to test and grow more familiar with the format and the numerous microorganisms identified by that testing, but this first pass did yield some interesting results.

To highlight:

The general health of my microbiome is very good. This was my expectation given my general lifestyle in that I eat in a reasonably healthy manner (although by no means perfect, my sugar intake for example is too high), I exercise regularly, and consume plenty of fiber.

However, my “probiotic” levels, as represented by the Lactobacillus and Bifidobacterium genera, are low, particularly Lactobacillus, which was nearly non-existent, although my Akkermansia was elevated.

This is not a small matter. Both Lactobacillus and Bifidobacterium are considered important and while they can become over-hyped, particularly among those who market probiotics, that does not mean the hype is wholly unjustified.

I also need to seriously consider increasing the microbes associated with the production of the inflammation-regulating substance propionate, and possibly even those associated with vitamin K2 production.

That creates the question, a question that is at the heart of the MicrobioME project:

Will I be able to increase those levels?

And if I can, will it matter? Will it make a difference, even if only subjectively, in how I feel?

That is what we’re going to find out. For those of you who have been following this project from the beginning already know, I have been supplementing with probiotics for the last three weeks (see the MicriobioME section for “Snapshots”). I sent in my sample this past Friday. The results of that test will establish what I will be calling my “Probiotic Case.”

When those results are in, I can compare them with this Base Case.

And I’ll be comparing a lot more than just my probiotic levels. We’ll look at everything, because we’re talking about a highly interrelated ecosystem, and changing one parameter, good or bad, could have unforeseen consequences.

Will taking probiotic supplements improve the diversity of my microbiome? Make it worse? Or have no effect?

Will my levels of Akkermansia go down? Will my levels of Burkholderiales, the microorganisms protecting me against kidney stones, be affected?

That is what this project is all about.

And then we’ll move on to examining prebiotics (which I will start supplementing with this coming week). And we’ll test that. We’ll test some other things, and then we’ll do it all again.

Because these single-point-in-time tests, even if valid, are still subject to random error, and it might take some time to establish a genuine pattern.

So we’ll keep testing.

And I will share this with you along the way, including my impressions. It’s nice to have the date on your side, but if none of it makes any obvious impact on your health, how you feel, how things are functioning, the data are just numbers on a screen, and in the end, that’s cold comfort.

Thanks for taking this journey with me. It should be an interesting ride!

Please note the data below for the snapshot of my supplementation routine, diet, etc, as of the date I took this Base Case sample.

And please share any thoughts, comments, observations and questions with us in the comments section below.

Take care!


Base Case Snapshot

January 7, 2019 through January 11, 2019

In establishing my “Base Case,” I wanted to eliminate any extraordinary interventions, including anything that would be materially from what I normally do.

And more to the point, eliminate those things I want to test for going forward.

In other words, no probiotic supplementation, no big diet changes, just a few “normal” weeks.

Below is my data from the week on which I took my test, which was Friday, January 11. While I do Monday-to-Sunday “Snapshots” I like to test on Fridays as my weekdays are more structured and so less subject to random changes in schedule which should help elevate the validity of the tests over time.

And while I did not record the data in detail in the weeks prior to this last one, I had maintained these general levels for between two and three weeks prior to the testing.


Overall, I continued to feel great with no obvious health issues during this period, and gut health seemed normal. I’ll have more to say on that later, as I believe the Genuine Health Probiotic has yielded some noticeable benefits since this test was take. I’ll be reviewing that in some detail in the near future.

Specifics follow below.

Probiotic Supplementation

Brands, CFUs (number of live organisms, see my post, “What Should I Look For in a Probiotic” for an explanation), and days of the week together with averages.

And yes, purposefully zeroed out. I took nothing for several weeks (and not much before then).

Note that I provide CFU totals both at the time of manufacture and at expiration (estimated in cases where the manufacturer does not specify). I don’t typically take probiotics too close to their expiration and so you can assume my actual intake is closer to the date of manufacture. (I considered fine-tuning the numbers given how close a given bottle was to its expiration date, but as I don’t know the rate of decay, I considered that of very little utility.)

I also eliminated my daily 8 ounces of Greek Yogurt. Is yogurt really a probiotic? A discussion for another time. I include it here for thoroughness. No kimchee either.

(Thinking about trying some of these out for yourself? Please check out our Resource Page. All items are listed by category and available for immediate purchase through Amazon.)

Prebiotic Supplementation

For my total fiber intake, see “Diet” below. This is specifically for prebiotic supplementation. Not all dietary fiber is considered prebiotic.

I’m holding this constant. (I will be conducting a Prebiotic Case Study next in which I will drastically increase both the variety and quantity of my prebiotic intake.)


(The LEF Prebiotic Chewable from Life Extension Foundation is made up of xylooligosaccharide.)

(Thinking about trying some of these out for yourself? Please check out our Resource Page. All items are listed by category and available for immediate purchase through Amazon.)




My macro percentages tend to change only a percentage point or two from week to week.

A few things to note: My fat intake is majority plant-based, nuts and seeds and plant oils for the most part. Close to half my protein comes from shakes and bars, and are primarily whey, casein, and plant based.

I eat about a cup of blueberries a day, plus some blackberries. I also have at least one large salad every day.

My fiber intake is pretty high, and has been for many years, and is about half soluble, half insoluble.

I do tend to eat desserts, and almost always have a bowl of cereal (of all things) with blueberries before I go to sleep. While my intake of carbs is reasonable, my intake of sugar is higher than ideal.

We all have our weaknesses!


I neglected to record data every day that week, but the day before my test was pretty typical, as was most of that week.

Activity LevelActivity

I teach regular group fitness classes as part of my wellness business so my activity level is usually pretty high.

Weekday caloric expenditure averaged close to 3000 Calories a day, weekends closer to 2300.

I exercised around two hours a day during the week, but keep in mind that the Apple Watch counts very modest movement as exercise, so that would be a mix of modest to high intensity (For example, walking the dog counts).

I hit the “Stand” parameters 17 hours each weekday, and closer to 15 on weekends. (Apple measures a “Stand” as moving around for at least a minute within an hour.)

Thanks again for following along.

Don’t forget to share your own thoughts and experiences below!

Take care,