The MicrobioME Project

The MicrobioME Project

The MicrobioME project will go beyond petri dishes, animal testing and theoretical models. The MicrobioME project will be real life, with real products, real lifestyle changes, and real consequences.

What does it involve?  Well, to start, two things:

  1. The Microbiome.
  2. Me.

Hence the name. But this is no vanity project. I assume you are as curious as I am about the ways the microbiome can affect our health and well being. Do you want to know what probiotics can really do, in real everyday life? Prebiotics? Does sugar and animal fat really feed the “bad” ones? Does it matter?

Do you want to know if we can really improve our lives by improving the lives of the trillions of bacteria, yeast, and archaea with which we share our bodies?

Me too.

We are all different, of course, and you will need to consider factors particular to your own situation, but by being able to observe what amounts to my ongoing microbiome diary, you will at least have some useful reference points to help you make more informed decisions.

What Should You Expect?

I am going to document my diet, supplementation, lifestyle habits, and any other variables that might prove relevant. I will provide that information to you here in detail.

I will then purposefully (and sometimes not!) alter those parameters over time, both to the good (better diet, probiotic supplementation, more fiber etc.) and the bad (worse diet, sleep deprivation, antibiotics), and record my personal observations regarding my general health. But I’m going to go one step further.

I am also going to be testing the makeup, health, and diversity of my microbiome using samples processed by the microbial genetics testing company, Ubiome. (I have no relation with them, but after some research, settled on this as my lab of choice.)

And I’ll be sharing those results with you as well.

As a research project, it will be subject to all the normal caveats regarding difficulty controlling for variables, confirmation bias, small sample errors, and the inherent anecdotal nature of it all. I do recognize that, and you should too. This does not rise to the validity of a peer-reviewed double-blind placebo control-group clinical trial, but it’s not intended to.

It’s intended to provide a window into one person’s experience with these various lifestyle changes and supplementation routines. That is, in and of itself, worthwhile.

And You Can Be Part of It

With your help, we can make this more than just a one-man show.

As we move ahead, I want to encourage you to share your own experiences in the comment sections. I suspect there are going to be some surprises along the way. Things we all thought would help that didn’t. Things we thought would hurt but helped. Readers having the opposite experience from my own. Tests that yield one result one month and something entirely different the next even though no variable that we’re aware of changed.

That’s just the nature of this kind of project, but if we make it a discussion, it can become something more than just random data points. It can become something useful to everyone.

Here’s What I’ll Be Sharing

Probiotic Supplementation

Everything I’m taking and how often. This will change as I test out new products, engage in various experiments (going without, for example, which will be my first one, stay tuned for that), and simply decide one product is superior to another and making that switch. You’ll be kept abreast throughout all those changes in this section.

Prebiotic Supplementation

Likewise, with prebiotics. I have not taken much in the way of specific prebiotics (beyond what is naturally present in my diet) so this part should be interesting. I’ve not yet had an adverse reaction to probiotics, so heavy supplementation with prebiotics will be a new thing for me.


I’ll be recording my diet and sharing it in terms of macros (fat, carbs, protein) and relevant breakdowns (fiber, sugar, etc.), and any other data I think useful. I’ll record all this with the “Lose It!” app. I have no relation with the company, but do recommend the app, particularly if you have an Apple Watch with which it integrates. I’ll add details of what I’m eating specifically when I think it’s relevant. (Say, there was a pie in the house. Or Two. It happens!)

Exercise and Sleep Patterns

Both exercise and sleep patterns can have a profound effect on your Microbiome so I will be including these data points as well. There will be times when I’ll be attempting to hold them constant while I change and test some other variable (diet, probiotics, etc.) times when I’m changing them deliberately to test the effect has on my microbiome, and times when I’m trying to do one or the other and simply fail. Regardless, you will be kept apprised of this.

Testing Results From Samples.

This will be primarily fecal samples to start. Yes, sorry, we’re going there.

No one ever said science was pretty!

A few cautions regarding this part.

First, fecal testing does not always correlate with actual intestinal testing, that is, what comes out isn’t always representative of what’s going on inside. It’s imperfect, but it’s really the only practical way I can approach this and is a very common approach used by researchers and so has been broadly validated as a measuring tool, even with its limitations.

Second, sampling is just that. It’s a snapshot in time. I will endeavor to hold as many variables constant as I can such as time of day and day of week I collect a sample, diet, sleep patterns, exercise patterns, and so on (unless those are the specific variables I want to test) so as to reduce that variability. This is intended to be an ongoing project and so over time that should work itself out. We just need to be careful that we don’t place too much stock in a single test result.

Finally, the testing itself is imperfect. Two labs can be given the same sample and come out with different results. This is difficult to avoid, but my plan is to use one lab throughout (Ubiome, as previously mentioned) so that we can at least track differences in my microbiome makeup over time regardless if the specifics at any one point are perfectly accurate.

When Do We Begin?

We already have.

I have already sent in my first sample and am awaiting the results. I wanted to create a kind of “base case” and so while I did not change my diet, exercise routine, or sleep patterns, I did eliminate any probiotics I was taking and even stopped eating yogurt (which naturally has probiotics, even though many don’t consider it a probiotic per se) for several days.

In other words, I wanted to get a snapshot of my microbiome without supplementation as that will be the first thing I want to test out going forward.

When I get those results, I will include them along with the data (diet, supplementation, etc.) as of the date of the sample collection, almost always in the form of a running week-long average.

While we wait, I have already started supplementing with probiotics again. I have taken modest amounts of probiotics over the past few years but am really ramping it up for this next phase. Below you will see what I took over the past week. Next week you will see an increase in my probiotic supplementation (while holding the other variables as constant as I can) with the intention of doing a second Ubiome test.

Stay Tuned!

Thanks for stopping by, and I do hope you will follow along and add your own experiences. The microbiome is genuinely changing the way we think about “human” health, and you can be on the forefront of that exploration along with me.

Let’s take it slow, be honest, and dispense with the marketing and the hype. There is so much we don’t know, so much we think we know but don’t, and so much to learn. We can all be a part of that.

Here’s my first snapshot:

MicrobioME Snapshot

January 13, 2019 to January 20, 2019


A fairly typical week. I returned to my regular probiotic supplementation routine having already turned my sample over to Ubiome for testing the previous week (still awaiting results). The Genuine Health Advanced Gut Probiotic is a relative newcomer.

Overall, I feel great, no obvious health issues, gut health seems normal.

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.

Probiotics 1-14-19-1-20-19


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 consume around 8 ounces of Greek Yogurt a day. Is yogurt really a probiotic? A discussion for another time. I include it here for thoroughness. Likewise, with kimchi which I’m consuming once or twice a week.

(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 fiber is considered prebiotic.

Probiotics 1-14-19-1-20-19

(The LEF Prebiotic Chewable from Life Extension Foundation is 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.)


Diet 1-14-19-1-20-19

Pretty typical week for me. You will see some variation here, but usually within a few percentage points. There will be greater variability from day to day but the weekly averages typically hold up pretty well.

My fat intake is majority plant-based, nuts and seeds for the most part. Close to half my protein comes from shakes and bars, so whey, casein, and plant based.

Fiber is about half soluble, half insoluble.


Pretty typical week. As much as I’d like to get over 7 hours of sleep, it averages closer to 6.5. I measure this with a Fitbit Ionic activity watch.

Activity Level

Exercise 1-14-19-1-20-19

I teach regular group fitness classes as part of my wellness business so my activity level is usually pretty high. I subbed a couple of fitness classes (I am a fitness instructor, one of the many hats I wear) so this would be a slightly elevated week.

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.

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 as always, and please stay tuned, lots more to come!