Microbiome Snapshot Week Ending March 24, 2019

Microbiome Snapshot Week Ending March 24, 2019

Week Four of the Prebiotic Case Testing Period

March 18, 2019 through March 24, 2019

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We’ll call this the “bonus” fourth week of my Prebiotic Case testing period as I had hoped to wrap this up last week, however a bad head cold and some sleep deprivation intervened and I decided to delay a week.

But first, a status update on the various test cases (changes from last week are underlined.)

Base Case

No supplementation, just my regular diet and lifestyle habits (I even gave up yogurt as that is considered a probiotic).

Completed and posted: Base Case Ubiome Test Results.

Probiotic Case

Adding roughly 100 billion CFUs a day of a variety of probiotics.

Completed and posted: Do Probiotics Work? Yes! But….

Prebiotic-Probiotic Case

Adding approximately 24 grams a day of various prebiotics to the probiotics I had been taking for the Probiotic Case.

  • Testing Period COMPLETED
  • Sample Collection COMPLETED
  • Ubiome Laboratory Results COMPLETED
  • Case Results Posted: IN PROCESS

Prebiotic Case

Removing the probiotics from my supplementation leaving only the prebiotic supplements in place.

  • Testing Period COMPLETED
  • Sample Collection COMPLETED
  • Ubiome Laboratory Results IN PROCESS
  • Case Results Posted

Base Case 2

  • Testing Period
  • Sample Collection
  • Ubiome Laboratory Results
  • Case Results Posted

Observant readers will note that I’ve added a new case, “Base Case 2.” I plan on weaning myself off of the prebiotics I had been taking for the Prebiotic Case and return to square one, just my normal diet with no supplementation to reestablish a “base case” that I can compare to previous and future cases. That has only just gotten under way.


As you can see above, I finished the testing period for the Prebiotic Case, collected a sample for testing, sent it off to Ubiome for analysis, and just recently received confirmation of their receipt of the sample. If past experience holds, it will be another two-plus weeks before I get results and at least a week before I can go through them thoroughly and get a post out.

Speaking of which, I will be finishing up the write up for the Prebiotic-Probiotic Case towards the end of this week. There was a lot of data to go through, as usual, but also a lot of issues I had to think through carefully. Rest assured, supplementing with large amounts of prebiotics, the food of probiotics, did have a measurable impact on my microbiota, in some cases, a very large impact on some specific gut flora. A sneak peek:

Prebiotic-Probiotic Case

As for how I felt this past week, my head cold lingered the way head colds do, but I slept fine and I was able to hold all my other parameters constant. Please note as you go through the details below that I tested Friday, and saved the data through that day for posting along with my final report on that test. I usually prefer to test on a weekday as they are more structured than my weekends and so it’s more likely I’ll get a valid, consistent, and representative sample.

The data below is for the full week through Sunday.

Probiotic Supplementation

This would mark the second week of zero probiotic supplementation including yogurt, but as noted above, only through Friday. I did add back a probiotic Saturday and Sunday after the sample collection for the Prebiotic Case. These were the Great Oral Health Probiotic lozenges.

My mouth just didn’t feel right after having gone off them for four weeks and since I am so early in the Base Case 2 testing period I did not think it would do any harm. I’ll take them for a few more days only.

Likewise, with yogurt, which I REALLY missed. However, the yogurt will serve another purpose as well: Since I plan on coming off the prebiotics, all of them, this week, I thought some mild probiotic supplementation in the form of yogurt would ease the transition.

My intention is to be off all probiotic and prebiotic supplementation, including the yogurt, by the end of the first week and then spend two solid weeks without any supplementation at all before collecting another sample.

The table below includes 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.

Probiotic 20190324

(Interested in 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.)

I provide CFU totals both at the time of manufacture and at expiration. I don’t typically take probiotics too close to their expiration so you can assume my actual intake is closer to the date of manufacture.

(Note that the CFU counts at manufacture and expiration for the Life Extension Foundation “GI With Phage,” “Heart Health,” and “Immune Health” probiotics were provided directly by the company in response to an inquiry I had made and are not yet reflected on their packaging. This is information you are unlikely to find anywhere else.)

Prebiotic Supplementation

Held steady as planned. I’ll start coming off these next week, but for purposes of the Prebiotic Case, I continued with my additional 24 grams of prebiotic fiber. I’ve been taking psyllium once a day for about 30 years and so consider that part of my regular diet. That is why I don’t count it as part of my “additional” prebiotic supplementation, and why I took it throughout my Probiotic Case which involved supplementation with probiotics only. It is considered to be, at most, a mild prebiotic. I include it here mainly for completeness.

(As I’ve mentioned in earlier updates, green banana flour contains a prebiotic known as “resistant starch” (RS) which only recently has been granted “fiber” status by the United States Food and Drug Administration (FDA). This is an important development as RS has not before been permitted to be listed as a fiber on nutritional labels in this country.

I reached out to the company to find out what the new labels might look like, and they gave me some preliminary feedback which is now reflected in my prebiotic tables. The tables include this RS only, as the other fiber is not considered prebiotic.)

Prebiotic 20190324

(Interested in 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 20190324

Macros remained pretty constant, within a percentage point or two of prior weeks. Fiber levels remained high, but that was to be expected given all the prebiotic fiber I was consuming as part of the Prebiotic Case I just completed. I also added some insoluble fiber to even out all that soluble prebiotic fiber, but I did that for the Prebiotic-Probiotic Case as well so I am holding that element constant. Insoluble fiber is not considered prebiotic so it should not have a material effect regardless.

My fat intake remains majority plant-based (if only by a little), nuts and seeds and plant oils. Close to half my protein comes from shakes and bars, and are primarily whey, casein, and plant based. I do eat meat most days. This week was a typical mixture of, beef, chicken, and fish.

I continue to eat about a cup of blueberries a day, plus a quarter cup each of blackberries and raspberries. I also have at least one large salad in the afternoon and vegetables with dinner and lunch, and this week was no different.


Sleep 20190324

Back on track with sleep. My target is 6 hours and 40 minutes, and I managed to exceed that modestly.

Activity Level

Activity 20190324

My activity level came in just a hair under my target range of between 2750 and 2850 calories a day. I would not consider that material, and in any case, at the time I took my sample for testing a couple days before the end of the week, my activity was right on target.

For the record, I am a group fitness instructor and personal trainer (part of my health, fitness, and wellness business) mostly during the weekdays. We also have a dog who I walk a couple miles a day, so my activity level is usually pretty high.


Weight 20190324

Typical week. It had crept up the week before when I had the head cold, but I always start Mondays a little high coming out of the weekend mainly because I’m not as physically active. As usually happens, my weight creeps down during the week when I’m running around.

I don’t typically weigh myself on weekends, and this one was no different. My schedule is usually less structured and so it can be difficult to get a valid weight measure at the same time, under the same circumstances.


Thank you for reading! Next week will mark the first week of my new “Base Case 2” preparation and so you will see some probiotic supplementation, but only briefly, and you will note my prebiotic supplementation reducing quickly to zero.

The results of my Prebiotic-Probiotic Case should be out towards the end of the week!

Please feel free to ask questions, or add your own observations, below.

Take care!