Prebiotic Probiotic Combination – Real World Results and Impressions

Prebiotic Probiotic Combination – Real World Results and Impressions

What Happens When You Supplement With A Lot of Prebiotics and A Lot of Probiotics? As It Turns Out, Quite A Lot!

The results of the Prebiotic-Probiotic Case are in. What was it all about?

A personal experiment in intensive supplementation with both prebiotics and probiotics to see if it was truly possible to impact my overall health and well being, and my gut health in particular.

The short answer? Yes, and yes.

What follows is in part personal observations, and in part a close examination of the data from laboratory testing of my microbiota.

Both hard and soft data, a broad and deep dive into this new frontier of health.

And we’re only just getting started.

Before we go any further, if you are new to the MicrobioME Project, or new to Microbiome Bulletin, you might want to check out The MicroboME Project, the About “Us” page, the Microbiome Glossary, and, “Microbiome Hype,” plus you can check all the MicrobioME Project posts in the MicrobioME Project Category.

This is the third full test, including complete laboratory test results in which the composition of the trillions of microorganisms residing in my gut are identified and quantified. See Base Case Ubiome Test Results, and “Do Probiotics Work? Yes! But…” for the previous two cases, (the Base Case and Probiotic Case respectively).

This latest test consisted of a prebiotic probiotic combination in which I added approximately 24 grams of prebiotic fibers a day to my diet (in and of itself, more than the total fiber the average American consumes) in addition to the 100 billion CFUs of probiotics I had been taking per day for the previous Probiotic Case test.

I was not being subtle.

Personal Impressions

Allow me to answer your most pressing question first.

Yes, gas was involved.

But as I had mentioned at the time in a MicrobioME SnapShot post, that was mostly early on. Regardless, there is no question, even with my already high-fiber diet (60 to 70 grams a day), that there is an adjustment period. In fact, anyone embarking on a similar personal journey should definitely take it more slowly, particularly if they had a previously low-fiber diet (which I would define as anything below 30 grams a day).

However, as I was already accustomed to fiber, and I was willing to accommodate a little intestinal discomfort, I pushed through, basically ramping up to the full 24 grams a day in about a week.

The full test ran three weeks. Was that long enough to see changes?

Definitely, both in terms of laboratory testing, and personal observations.

Regarding those personal observations, an interesting thing happened. By the end of the three weeks, I was thinking that I hadn’t really noticed anything. I felt fine, but I usually feel fine. I largely eat right (largely), I run a health and wellness business and so am very active, and so on.

And besides, I wasn’t trying to address any particular concern, so it was not as if I wanted to cure some existing malady. My thinking is more long term. I am primarily trying optimize my gut health in order for forestall the kinds of chronic autoimmune-related modern diseases that research is increasingly finding to be associated with a dysfunctional and imbalanced microbiota.

However, it’s amazing how quickly you can become accustomed to what I refer to as, “the new normal.”

It wasn’t that I did not feel better, it was I had been feeling better for a while now, having started taking the probiotics nearly two months earlier and having been on the prebiotics for a solid month. That feeling, which is hard to describe exactly, had become my new normal.

I didn’t realize it until very recently. As I write this, I am well into my new “Base Case 2” testing period in which I am not taking any supplementation of any kind. And frankly, I don’t feel as great.

I’ve mentioned this is in some recent comments in other posts, but things just aren’t quite as good. Energy levels, sleep, general well-being, it all feels a little “off.” It’s subtle, yes, but noticeable.

Subjective? You bet! But I am a skeptic at heart, in fact, in the first draft of this post I actually discussed how I hadn’t noticed any particular improvement. That was two weeks ago. I hadn’t intended to delay getting this post out (life happened to intervene), but I had to set it aside for a while.

Lucky happenstance, because having now gone a couple weeks without any probiotic supplementation and having phased out my prebiotic supplementation to zero, I have this new perspective. I am now reminded what it’s like not to take any of this stuff.

I’m actually starting to think those supplements very well may have had a positive effect on me.

But this is about far more than my “feelings,” it’s about the hard data, too, it’s about the changes that occurred to the composition of my microbiota itself.

Laboratory Testing

Ubiome’s testing process involves sending in a small fecal sample which then undergoes gene sequencing to determine the microbial communities that reside in your gut. (While not as accurate as sampling the interior of your colon directly, it is cost effective and really the only practical way for me to conduct this kind of testing. It is widely used among researchers for those same reasons, and so should suffice for our purposes.)

Let’s take a look at what Ubiome came up with.


Earlier Base Case results will be on the left, Probiotic Case in the middle, and the new Prebiotic-Probiotic Case on the far right.

                    Base Case                                         Probiotic Case                     Prebiotic-Probiotic Case

Base Case Diversity

Probiotic Case DiversityPrebiotic Probiotic Case Diversity





As you can see, while my diversity increased when I added the probiotics, it actually came back down after I had added the prebiotics together with the probiotics.

This suggests that the prebiotics are favoring certain taxa (microorganism types) over others. While diversity is generally considered a universal good, as it has been associated with better health outcomes, it should be noted that that is not always the case, and in fact, based on recent research, this result should not have been surprising.

Presumably, the key is that a decrease in diversity is tolerable so long as that diversity is coming at the expense of less-useful microbes to the benefit of more-useful microbes. From a purely observational standpoint, that’s not clear, but there are some telling clues in the data that follows.

                  Base Case                                  Probiotic Case                         Prebiotic-Probiotic Case

Base Case WellnessProbiotic Case WellnessPrebiotic Probiotic Case Wellness

Interestingly, my “Wellness Match Score” declined sequentially, from when I added probiotics to when I added prebiotics to the probiotics. I did not concern myself with the first decline, but this latest decline, while still small, did catch my attention so I checked with Ubiome to get a better understanding of how this number is calculated, including its constituents and how those were weighted.

As it turns out, this is actually a pretty simplistic calculation. It just measures how well the makeup of my microbiota matches up with their “Selected Sample,” which is determined by averaging the results of people who are generally healthy.

That’s it.

Of all the data Ubiome provides, this strikes me as the least useful. Microbiotas are very individual, and while you can argue that there are certain specific microorganisms or combinations of microorganisms that are associated with certain positive outcomes, and that you are better off if you can maximize those, the notion that you are more “well” because your overall makeup is similar to someone who is generally healthy is, well, kind of simplistic.

I’d prefer not to see this number plummet as the year goes on, but in light of the rest of the results, I’m not going to trouble myself with it too much at this stage.

Probiotic Microorganisms

Now that I have three data points, the Base Case, the Probiotic Case, and now the Prebiotic-Probiotic Case, I am going to make use of some of the graphical presentations Ubiome provides in their test results.

Prebiotic-Probiotic Case Probiotics

Anything jump out at you?

Let’s go through these one by one!


As I had mentioned in reviewing my results for the Probiotic Case, the Lactobacillus genus is one of the most popular categories of probiotics you can take, and they were very well represented in the supplements I was taking.

                       Base Case                                  Probiotic Case                Prebiotic-Probiotic Case

Lactobacillus 20190111




I had found it encouraging that even though I had very low levels, I was able to double my counts after supplementing with probiotics.

However, three weeks after adding significant amounts of prebiotics, my levels are basically back where they started. Either these numbers are so small that the variation I am seeing is little more than random statistical noise, or the prebiotics benefited other microorganisms (such as the one that follows) to the detriment of Lactobacillus.

I’ll reserve judgment on this for the time being. I plan on conducting multiple tests over the coming months, so this picture might clear up in the future.

(For clarification, please note that Ubiome’s “Selected Group” consists of “samples from individuals who report no ailments and high levels of wellness.”)


Bifidobacterium is another popular and common probiotic genus, and one that should respond to prebiotic supplementation.

My levels had tripled after supplementing with probiotics, which did include Bifidobacteria. What would happen after I added prebiotics to the mix?

                      Base Case                                  Probiotic Case                      Prebiotic-Probiotic Case

Prebiotic-Probiotic Case Bifidobacterium





They would triple again, and then some. (Please note that the scales change with the way Ubiome presents the data. I will be creating my own bar charts next time.)

I had expressed some skepticism regarding the initial tripling, thinking it could have been a statistical outlier, and it still might be, but for whatever reason, it is starting to appear that my Bifidobacterium is unusually responsive to supplementation, both probiotic, and prebiotic.

This can happen. Research has found that depending on your prebiotic fiber intake, some microbes will be favored over others. Which microbes successfully colonize your gut is also very individual. Two people can take the same exact probiotic, for instance, and one will get increased numbers while another gets nothing.

I would suspect this is where, at least in part, my diversity is suffering. Is that necessarily an outright bad thing, given Bifidobacteria is considered a cornerstone of good microbiota health? I don’t know the specific species or strains, but even with that information, it would still be difficult to know, certainly not in so short a time frame.

As with everything I’m doing here at the MicrobioME Project, time will tell, but this is an interesting one.


As is this. My Akkermansia microbial population dropped by nearly 30% after probiotic supplementation, and then another 25% with the addition of the prebiotics.

                         Base Case                                   Probiotic Case                     Prebiotic-Probiotic Case

I should point out that I didn’t supplement with Akkermansia. No one does, as it is not a probiotic that is commercially available. And the prebiotics that favor it, mainly oligofructose, or inulin, also favors the others, and yes, I did supplement with that

Like with Lactobacillus (and perhaps others we’ll get to) there might have been a crowding out effect, disadvantaging the Akkermansia either directly or indirectly.

I’m still at relatively high levels, which I’m happy about as Akkermansia is kind of an up-and-coming microbe (to the extent a microbe can be up and coming) but this one bears watching going forward.

Yogurt Microbes

This is another “wow” moment, assuming you are wowed by such things.

Prebiotic-Probiotic Case Yogurt Microbes Graph

My levels of microbes associated with yogurt eaters more than tripled when I reintroduced yogurt into my diet following the Base Case. It has more than tripled again with the Prebiotic Case.

                           Base Case                                    Probiotic Case                        Prebiotic-Probiotic Case

Prebiotic-Probiotic Case Yogurt Microbes


This could be a matter of double-counting, though. Bifidobacterium is a component of some yogurts, and Ubiome considers it as such. While none of the yogurt I ate had it, the mere presence of high levels of the genus could be creating the very high numbers here.

Vitamin-Producing Microbes

Ubiome tests for two sets of microbes that are associated with the manufacture of two vitamins the human body cannot make on its own or has difficulty absorbing from dietary sources.

Vitamin K-Producing Microbes

I had mentioned in my Base Case that my Vitamin K- (K2 specifically) producing microbes were very low. I have no symptoms of vitamin K deficiency possibly because I supplement with K2, so I wasn’t too concerned, but I did think it was something I should watch.

                        Base Case                               Probiotic Case                 Prebiotic-Probiotic Case

Prebiotic-Probiotic Case Vitamin K

This one reminds me a bit of the Lactobacillus. Very low numbers subject to wild swings. So, while they did increase with probiotics and seemed to have pulled back with the prebiotics, I don’t have any obvious reason why they would have done so. We’ll just keep watching this one.

Vitamin B9-Producing Microbes

On the other hand, the changes in microbes that produce vitamin B9 make some sense. They decreased materially while I was taking probiotics, and while I don’t have any obvious explanation for that other than potential crowding out as others thrived (similar to my theory regarding the Lactobacillus) it potentially makes sense that they should bounce back with prebiotic supplementation as inulin is one of the interventions Ubiome suggests if you want to increase these particular microbes.

They are still lower than when I started, so this is another one to keep an eye on to see if I can’t make better sense of it in the future.

                  Base Case                                        Probiotic Case                               Prebiotic-Probiotic Case

Prebiotic-Probiotic Case Vitamin B9

Anti-Inflammatory Microbes

Ubiome tests for microbes associated with the production of three short chain fatty acids (SCFAs), butyrate, propionate, and polyamine. These SCFAs provide a number of benefits including having anti-inflammatory properties.

Prebiotic-Probiotic Case Anti-Inflammatory Microbes

Butyrate Microbes

As I had mentioned when writing up my Probiotic Case, supplementing with probiotics would not be expected to necessarily increase the microbes that produce butyrate, and yet they did increase in that case. It might have been the normal and unavoidable variances you are going to get with this kind of testing, or it could have been a result of the complex interrelationship of gut flora, but regardless, it was a small change.

                  Base Case                                        Probiotic Case                           Prebiotic-Probiotic Case

Prebiotic-Probiotic Case Butyrate





Interestingly, these butyrate-producing microbes also increased with the addition of prebiotic supplementation. This would be more in line with expectations, as Ubiome suggests that is exactly one of the courses of action you can take if you want that result.

At first glance, this one does not appear to be a matter of double-counting. Ubiome does not list Bifidobacterium, the genus I had a large increase in, as directly producing butyrate.

However, I did a little more digging, and there is research that supports the notion that while Bifidobacterium does not produce butyrate, there appears to be cross-feeding interactions between Bifidobacteria and the butyrate-producing colon bacteria Anaerostipes, Faecalibacterium prausnitzii, Eubacterium, and Roseburia.

Perhaps, we’re seeing a cascade of positive effects from my spike in Bifidobacteria.


My propionate, which was already low, continues to be driven lower. Interestingly, while Ubiome seems to consider this a SCFA you want to make sure you boost, there are others who take a darker view, and actually believe the lower the better. Another one to watch going forward.

                Base Case                                   Probiotic Case                           Prebiotic-Probiotic Case

Prebiotic-Probiotic Case 20190223






I had mentioned in my Probiotic Case that, “It should be interesting to see how these come out in my Prebiotic-Probiotic Case…” as Ubiome identifies prebiotics as a supplement that should increase the populations of these microbes.

                 Base Case                                 Probiotic Case                     Prebiotic-Probiotic Case

Prebiotic-Probiotic Case 20190224





And that appears to be exactly what happened. While you could argue that this is more double-counting, since Ubiome identifies Bifidobacterium as one of the polyamine-producing microbes, if that was what was happening here, it should have gone up in the probiotic case as well when I had my initial spike in Bifidobacteria, and yet it did not. In fact, it went down. I think there are some other polyamine microbes benefiting here from the prebiotics.

If nothing else, it does demonstrate some consistency with Ubiome’s analysis.

Sleep Microbes

Serotonin-Producing Microbes

This was and remains an odd one. The only actions Ubiome identifies as methods to increase the levels of serotonin-producing microbes is to eat an omnivorous diet, engage in regular exercise and avoid antibiotics. I do all those things. In fact, I track these components very closely and report on them weekly in my Weekly SnapShot reports as part of the MicrobioME project. Plus, I haven’t taken any antibiotics in years.

Despite the dip in this since I added the prebiotics, I’m still above my original Base Case, so perhaps by consuming probiotics (and maybe prebiotics) I am somehow enhancing the health benefits of the exercise.

Or, it’s just more statistical noise!

                  Base Case                                        Probiotic Case                          Prebiotic-Probiotic Case

Prebiotic-Probiotic Case Seratonin


GABA-Producing Microbes

My increase in GABA-producing microbes makes a certain amount of sense in that Ubiome identifies the consumption of prebiotics as being helpful in increasing their numbers, however these numbers had increased under the Probiotic Case as well. The addition of prebiotics did not appear to increase the number beyond that, although given Ubiome’s indication of “greater than 2” there is a possibility that they simply do not measure beyond that. I will make an inquiry regarding that and update this post as necessary.

                  Base Case                                        Probiotic Case                           Prebiotic-Probiotic Case

Prebiotic-Probiotic Case GABA


TMA Producing Microbes

TMA is converted by the body into TMAO which is associated with “poor cardiovascular wellness” according to Ubiome. Therefore, the fewer microbes you have producing TMA the better, or at least that is the current thinking.

                  Base Case                                          Probiotic Case                           Prebiotic-Probiotic Case

Prebiotic-Probiotic Case TMA





Interestingly, there is nothing specifically associated with either probiotic or prebiotic supplementation that should reduce the population of these TMA-producing microbes. And yet, as I added probiotics, their numbers decreased materially. While the numbers went up slightly with the added prebiotics, it was a relatively small move.

This will be yet another one to watch going forward to see if I can’t make more sense of it.


This project remains in its early stages, but I believe I have already answered some questions.

The first one was really the biggest, and that was, can you affect your microbiota through supplementation?

When I started this project, I did not know the answer to that question. You find some individuals, often with their own vested interests, contending that of course you can. Makers of probiotics certainly support that contention, as do those pushing lines of prebiotic supplements.

Others dismiss the importance or even usefulness of supplementation and believe that lifestyle changes are all that are necessary, or at least more important, particularly when it comes to diet.

And that very well may be true in part, in fact, I’m quite certain that lifestyle, including diet, activity level, sleep, and the like (the things I track so meticulously every week and with every test) are probably all more important to your gut health, and in a perfect world, that is all we would need to focus on.

However, we don’t live in a perfect world. I have long believed supplementation has a place in modern hectic lifestyles, a way to take the edge off of sleep deprivation, fast-food meals, stress, and all the rest. As I tell clients, supplements are just that, supplements. They should supplement your other endeavors.

My approach in these early cases was not subtle nor particularly precise. In the probiotic phase I began ingesting 100-plus billion CFUs of probiotic supplements. That was followed by adding 24 grams of prebiotic dietary fiber supplements.

This was pure brute force. I was going for quantity, quality (I did vet these supplements in advance) and variety. “Let’s see what happens!” was my mantra.

So, to answer the question, “Can you affect your microbiota through supplementation?” the answer is a resounding yes. You absolutely can.

Real, noticeable, material, and measurable effects.

So What?

This was the question I posed towards the end of the post discussing my Probiotic Case results.

So what if I can change the constituency of my microbiota through supplementation?

For one thing, as I mentioned early on, I really did “feel better” while I was taking them. I didn’t really notice it until after I had ceased taking them for a while. I’m back to my old self, but frankly, I rather liked my new self.

Again, and I can’t stress this enough, this part is subjective and prone to error and bias, but I can’t ignore it either. I want to report on everything during this process, and my impressions are going to be an important and ongoing part of that.

The second thing is, I have test results, most of which appear to be consistent with what is known about the microbiota. This is the hard data part, and while it is, as they like to say, an n-1 trial (consisting of one subject, me), and so prone to all manner of error, it is still real data and hopefully the two together can help make more sense of it all.

The bottom line at this point: This supplementation I engaged in really made a difference.

Now, whether that translates into material, tangible differences in my health beyond my own impressions is something I may never be able to entirely prove but as I’ve said before, I am going to continue testing and keeping up on the research in the hope that this can be of some use to you.

And as others engage in it as well, a fuller picture may begin to emerge.

Before You Go…

A couple of things:

  • If you would like more information on all the supplements I’ve been taking for these tests and places to purchase them, please visit our Resource Page.
  • For details on the supplement and lifestyle data at the time the sample was taken, please see below. It is in the same format as the weekly SnapShot reports I post during the testing phases. I try to hold the constants as constant as I can, and vary only the variable I’m trying to test. That is very hard in real life, which is why human studies are often so expensive, difficult, and prone to errors. I post this information so you can make your own judgment regarding how successful I’ve been on that front.

Thank you, and take care!


SnapShot Overview

I took my sample Friday morning on February 23, 2019, and placed it in the mail shortly thereafter. I like to take samples on Fridays as my weekdays are typically more structured than my weekends, and it’s difficult enough to control all the variables without exposing myself to more.

Speaking of which I chose to highlight the variables below precisely because they can affect the microbiota and therefore the outcome of these Ubiome laboratory tests. In fact, I plan to address these variables in the future (sleep deprivation, diet, and so on).

For these tests to have any validity, I have to hold these other variables as constant as possible while I examine the effect changing one can have on my microbiota.

The data below is for the five days ending on Friday.

Probiotic Supplementation

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.

I took my sample for Ubiome testing on Friday, and so only included my intake through that day. I continued to hold daily intake steady at the same rate as I have been since early in the Probiotic Case testing phase.

Probiotic 20190223

(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.)

Please note that the CFU counts at manufacture and expiration for the Life Extension Foundation “GI With Phage” and “Heart Health” probiotics were both provided directly by the company in response to an inquiry I had made and are not yet reflected on their packaging.

While CFU numbers can degrade rapidly, 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, so for the past week I would assume my CFU count is probably near or over 100 billion CFUs a day.

I also consume around 8 ounces of Greek Yogurt a day.

Prebiotic Supplementation

Since ratcheting up my intake of prebiotics early in the Prebiotic-Probiotic Case testing phase, I held it steady for this final week, at about 24 additional grams a day. (I’ve been taking Psyllium for literally decades and it’s become what I consider a part of my regular diet, and so did not count it as an addition. I should also point out that psyllium is not typically considered a true prebiotic, although I make the argument it does qualify as a mild one.

The LEF Prebiotic Chewable is another one I’ve been taking for some time, and so did not consider it an addition, although in retrospect, given I haven’t been taking it that long and XOS is considered a true prebiotic, I will consider it as one going forward and in fact did eliminate it for the Base Case 2 phase I’m in the middle of conducting now.

Prebiotics 20190223

(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.)

As I’ve mentioned in earlier MicrobioMe SnapShots, 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.


Weight 20190223

My macro amounts, fat, carbohydrates, and protein were pretty consistent, although a little carbohydrate heavy by a couple of points. Nothing I would consider material, but something to watch. Sugar, was pretty much on point. Fiber, unsurprisingly given that I added fiber to my diet specifically for this test, was elevated vs. the Base Case and Probiotic Case but otherwise was consistent with the past few weeks during the testing period.

My fat intake is 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, typically a mix of beef, poultry, fish (once or twice a week) and pork.

I ate about a cup of blueberries a day, plus some blackberries. I also had at least one large salad in the afternoon and vegetables with dinner and often lunch, which has also been largely consistent since I started testing.


Sleep 20190223

This was a little light. I prefer to get closer to 6 hours and 40 minutes, but still within an acceptable range.

Activity Level

Activity 20190223

My target range is to expend between 2750 and 2850 calories a week, and I came well within that range this past week.

As a reminder, I teach regular group fitness classes as part of my wellness business (mostly during the week) and do some personal training so my activity level is usually pretty high.


Weight 20190223My weight fluctuates within a pretty tight range, and this week was no exception.


Thank you for reading, there is a lot to go through here, but I am finding it worthwhile and I hope you are as well.

I plan to continue on with these tests, changing variables, and “seeing what happens.”

If you are doing the same, or have any of your own questions or observations, please leave them below in the comments section.

Take care!