Do Probiotics Work? Yes! But…

Do Probiotics Work? Yes! But…

The Probiotic Case Test Results

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Do probiotics work?

After a three-week testing period in which I phased in approximately 100 billion CFUs a day in probiotics to my diet, carefully observed my own reactions, and then examined the laboratory test results of samples I sent in to the microbiota testing company, Ubiome, I can finally answer that question with an emphatic…



Nothing is simple when you are dealing with complex systems, never mind the interrelationship between the human body and the trillions of microorganisms within.

Don’t get me wrong. The “yes” part was frankly surprising to me, really surprising, in fact. Based on my test results, the supplements I took seemed to have a genuine impact, one that was material enough that they could show up in the Ubiome test results.

And it was more than just that there was some identifiable effect, that is, these do not appear to be random differences based on the normal variation you’d get testing one day vs. another. There was a consistency to them to an important extent.

Basically, the effect was pretty much exactly what you would expect were you to take large amounts of probiotics for three weeks. The microorganisms you would expect to flourish, flourished.

Keep in mind, I went into this particular phase of my testing (see the rest of the MicrobioME Project category for all that is going on there) with low expectations, that is, I never expected much from probiotics.

I’ve just heard too many claims in the past about miracle pills and supplements that will cure all that ails you to have much faith in yet another.

That said, if you choose carefully, these probiotics, at a minimum, do appear to really contain live microorganisms, and they really will make their presence known in a recordable, testable fashion.

That is to say, what you consume, actually matters.

The “but” part is simply that there is more to it than that. Read to the end, because it’s all pretty fascinating I think, and vitally important if you are to make intelligent decisions regarding your own health. Not all the benefits appeared to be without costs in that some beneficial microbes might have suffered as a result.

Elsewhere, I had some very positive outcomes but not ones you would necessarily expect from probiotic supplementation alone. This will warrant further observation (and I will continue testing) as those kinds of results can potentially call into question their overall validity.

Before we go any further, all the typical caveats and cautions apply. This is a one-person experiment, and I’ve only got two samples and two testing periods to work from at the moment (more is in the pipeline), so yes, small sample error, confirmation bias, testing vagaries, all apply.

Also, these were the results from testing fecal samples, and what comes out isn’t always representative of what is going on inside. It is, however, used broadly in research and it’s honestly the only practical way I have of conducting this experiment. Basically, it’s what I have to work with, so I’ll work with it.

I hope, over time, as I continue to test and examine, the validity (or possibly even lack thereof!) of my results will come into sharper focus. In the meantime, we should all temper our enthusiasm, me most of all.

We’ll start by comparing this latest Probiotic Case with my initial Base Case, the one in which I did not take any supplements of any kind, and even cut out yogurt as it naturally contains probiotics. Most of the graphs I’m going to pull up from the Base Case were in my initial post, but I’ve also added a few that appear more relevant to me now that I have something to compare them to. All graphics are part of the test results provided as part of Ubiome’s Gut Explorer Kit.


We’ll start with the relatively easy parts first.


Base Case results will be on the left, Probiotic Case on the right.

                                Base Case                                                                              Probiotic Case

I want to first draw your attention to the microbial diversity on the right of each graphic.

I had a small but measurable uptick in my diversity from the Base Case to the Probiotic Case. My diversity was already pretty high so I would not have expected this to be dramatically higher, but nonetheless you would expect to see an increase in the Probiotic Case, and that is what we have.

In fact, it’s one of the selling points of probiotics. Diversity of your microbiota is associated with better gut health and superior overall health outcomes, so it is believed that the higher this number the better.

You might have already noted that my wellness score actually dropped! It’s a small delta, and could be little more than a statistical rounding error, but if I’m going to pay attention to the data I have pay attention to all of it.

We’ll get into some of the specifics as to why I think that happened later, but yes, that would be one I could put in the “But…” category

Probiotic Microorganisms

Did my “probiotics” increase?

Yes, and no, but both answers support the notion that what the manufacturers said were in the pills I was taking were in those pills, at least in a broad sense (Ubiome provides little information at the species level and effectively none regarding strains).


The Lactobacillus genus is one of the most popular categories of probiotics you can take, and yes, they were very well represented in the supplements I was taking.

                               Base Case                                                                       Probiotic Case









Before I started supplementing, my Lactobacillus was very low in comparison to Ubiome’s “Selected Group” (According to Ubiome: “These are samples from individuals who report no ailments and high levels of wellness”). That was one of the discoveries from my Base Case.

Levels essentially doubled over the course of my supplementation. They are still at very low levels, but doubling is still doubling.


Bifidobacterium is another immensely popular probiotic genus, and my supplements included those as well.

                               Base Case                                                                      Probiotic Case









My levels here tripled. (Note the numbers, the bar charts were presented using different scales.) I was doing well before, so this really surprised me, in fact I’m inclined to think this might be a statistical outlier, however, I won’t dismiss the fact that I ingested large numbers of Bifidobacterium, and here they are showing up in a test.

I should note that Ubiome does test for two specific species of Bifidobacterium, B. bifidum and B. animalis and did not find any detectable amounts. There are many species of Bifidobacterium however, and the ones that were in the Genuine Health Probiotic I was taking (the big 50-billion CFU dose) were not tested for specifically.

They also did not find any detectable amounts of any other probiotic species they test for including those in the Lactobacillus genus. Disappointing, but I understand it is not terribly surprising for many people. Again, there are many other species they do not test for, ones that I was supplement with, so presumably those were the ones being detected at the genus rank. (One oddity: I was taking fairly high amounts of L rhamnosus, and that is one that should have shown up in Ubiome’s probiotic screen. That one, like so much, will bear watching.)


My Akkermansia microbial population dropped by nearly 30%.

                               Base Case                                                                       Probiotic Case

I’ll point out that I didn’t supplement with Akkermansia. No one does, I don’t believe, as it is not a probiotic that is commercially available, so I did not expect it to increase, but why did it decrease?

There is the very real possibility that the infusion of Bifidobacterium and Lactobacillus (and others) had a crowding out effect, disadvantaging the Akkermansia either directly or indirectly.

This also would be part of the “But…” category I mentioned in the beginning. Yes, the probiotics I was taking showed up in increased quantities, but I had a material drop in another. Is that a net positive still? Impossible to tell, but this is something to keep in mind as it has been raised as a concern before by others in the field.

Yogurt Microbes

Here the data is pretty unequivocal and exactly what you would expect if you assumed that what you ate mattered, and that the testing Ubiome does is credible.

                               Base Case                                                                   Probiotic Case

In the weeks during my Base Case testing phase I completely phased out my consumption of yogurt. The resulting tests indicated that I had just over half the microorganisms that people who consume yogurt regularly would have.

During my Probiotic Case testing phase I resumed eating approximately 8 ounces a day, and sure enough, those microbes more than tripled in number.

This potentially highlights the transient nature of probiotics. I’ve eaten yogurt regularly for years, yet when I stopped, it appears my yogurt microbes plunged and revived only after I started consuming yogurt again.

Ongoing testing will either confirm or cast doubt on that assessment.


other results that were more mixed. Not mixed in the sense of not good, but rather not necessarily consistent with probiotic supplementation that I know of.

Vitamin-Producing Microbes

Ubiome tests for two sets of microbes that are tasked with manufacturing certain vitamins the human body cannot 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

While still low those numbers increased nearly 7 times for my Probiotic Case. It’s not clear that any of the specific probiotic supplements I was taking would have led to this. But clearly something happened. That, or it’s just a testing error or part of the natural variances. Future testing will tell.

Vitamin B9-Producing Microbes

On the other hand, microbes that produce vitamin B9 actually decreased. They are still high, but you have to wonder if some of these changes don’t come at the expense of others. Again, bears watching.

                                 Base Case                                                                 Probiotic Case

Anti-Inflammatory Microbes

There are three particularly important short chain fatty acids (SCFAs) that are produced by microbes in your gut, primarily in your colon or large intestine. These are Butyrate, Propionate, and Polyamine and are considered important anti-inflammatory substances. They also serve to provide sustenance to the cells in your intestinal wall.

Butyrate Microbes

I had hoped to see my butyrate microbes increase, although interestingly enough, Ubiome does not suggest that supplementing with probiotics would help this in any direct way, and that goes for propionate and polyamine as well. Rather, it appears prebiotics would be more effective. Still, mine did increase during my Probiotic Case.

                               Base Case                                                                 Probiotic Case


I was very low on this one and went marginally lower. The difference was very small, so perhaps just statistical noise, but clearly the probiotics had no effect here, but really weren’t expected to.

                               Base Case                                                                 Probiotic Case


This one was disappointing. My levels were solid during my Base Case, best of the three SFCA-producing categories, but declined materially during my Probiotic Case.

                               Base Case                                                                 Probiotic Case

Again, there really should not have been much if any effect, but the microbiota is a dynamic place. More statistical noise? The difference was large. It should be interesting to see how these come out in my Prebiotic-Probiotic Case (the results of which should be about a week away) as Ubiome identifies prebiotics as a supplement that should increase the populations of these microbes.

Sleep Microbes

Serotonin-Producing Microbes

I had not highlighted this in my Base Case because I thought my initial results had been unremarkable. However, nearly doubling serotonin-producing microbes in the Probiotic Case is. An interesting result. The only ways Ubiome suggests you can increase these directly is through lifestyle and diet, but I held those constant. We’ll see if this one holds up.

                               Base Case                                                                 Probiotic Case

GABA-Producing Microbes

Likewise, with GABA. The only supplementation Ubiome suggest can help boost the microbes that manufacture GABA is with prebiotics, not probiotics. Given I am awaiting results from my Prebiotic-Probiotic Case and am in the final week of my Prebiotic Case testing period, this one should be very interesting to watch.

                               Base Case                                                                 Probiotic Case

TMA Producing Microbes

These you want to be low as possible as TMA is associated with poor cardiovascular wellness. As with the sleep microbes, Ubiome does not indicate that taking probiotics should be helpful, but rather that taking resveratrol supplements would be. I do take resveratrol supplements, but I’ve been taking the same amount for years, so that would not explain the difference from the Base Case to the Probiotic Case. This would be another one worth watching.

                               Base Case                                                                Probiotic Case


It’s much to early to come to many conclusions but a few things are worth noting.

Apparently, probiotics do contain, well, probiotics. This is not a small matter. Just because a label says the capsules within have 50 billion CFUs of probiotics or a yogurt has been certified as having live cultures doesn’t necessarily mean that is so.

Those are the times we live in.

However, it appears the ones I consumed (they are all listed below and included in my weekly MicrobioME Snapshots) do in fact contain live microorganisms.

The probiotics also appear to survive the transit through the digestive tract suggesting that the encapsulation and other protections to ensure such are legitimate.

We still need to keep in mind that these probiotics are largely assumed to be transient visitors to our gut, that is, they are for the most part just passing through. They can have a positive impact on their journey, but they do not necessarily remake your existing microbiota.

The important takeaway of that being if you believe you are getting real, positive, tangible results, and if you want those results to continue, you need to ensure you keep that steady supply of probiotics coming.

Just look at what my resuming my yogurt consumption did for my yogurt-consuming microbes in just a few weeks.

I’ve been eating yogurt for years. Now maybe some of that has had a lasting effect, but it appears from these tests that when I ceased consumption for the Base Case, they suffered, but when I resumed, they revived.

Will that continue? We’ll see. I stopped my yogurt consumption for the current Prebiotic Case I’m running in which I ceased all ingestion of probiotics but kept consuming the prebiotics. But for now, it appears these probiotics aren’t much more than visitors.

There remains the question of why did so many of my beneficial microbe populations increase even though the consumption of probiotic supplements should not have had a direct effect on them? Could it be that by increasing general gut health, by creating an overall environment more friendly to the “good” microbes, I also managed to increase the populations of other good microbes? Or is it all just coincidence?

And what of the good ones, like Akkermansia, that actually decreased?

And were decreases like those responsible for dropping my overall wellness score a few ticks? That last one I need to look into and see if I can’t get a much

The Big Question

There is one final question you have to ask yourself as you examine these test results:

So what?

So what if my microbial diversity increased? So what if I increased the microbes that create certain SCFAs, or serotonin, or are associated with yogurt consumption?

Well, time will tell. Research supports the overall contention that these changes (most of them) should yield health benefits, most of which are probably longer-term.

As I’ve mentioned before, for the most part I am not taking probiotics because I was looking to solve a specific problem. And yet, I had a positive (albeit subjective) experience taking the Genuine Health Advanced Gut Probiotic, and the one specific problem I was trying to address with the Great Oral Health Probiotic seemed to actually abate when I started taking those.

I wish I had easy answers for you, but if you’ve read this far, you already know those don’t exist. What I do have is the data I have presented above, my admittedly subjective opinions about it all, and my disclosures and personal reviews of the products I take and the lifestyle I pursue.

My goal here with Microbiome Bulletin is to provide you with the tools and knowledge and information so you can be better equipped to make your own decisions.

My decision is to continue to experiment, to try different probiotics, prebiotics, diet, lifestyles and so on, and report them back to you right here.

I think we’re off to a pretty good start.


I very much appreciate your stopping by. My plan is to continue testing, running some new scenarios and returning to old ones.

I suspect I will occasionally get some results that don’t make any sense, or try things that clearly aren’t effective, but hopefully over time the picture will become more clear.

Please feel free to offer your own opinions, observations, experiences, and any question you may have in the comment section below. That give-and-take can be very helpful to the process.

To your health, and the health of the 39 trillion creatures who call you home!

Please see below for the supplement and lifestyle data at the time the sample was taken. It is my intention to hold constants as constant as I can. That is very hard in real life, which is why human studies are often so expensive, difficult, and prone to errors!

Take care!



I took my sample Friday morning on February 1, 2019, and placed it in the mail shortly thereafter. I like to take samples on Fridays as my weekdays are more structured than my weekends, and it’s difficult enough to control all the variables without throwing in some more.

Speaking of which I chose to highlight the variables below precisely because they can affect the microbiota and therefore the outcomes 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 a Friday morning.

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.

(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. I have made a similar inquiry about the Immune Health and will update the chart if and when necessary.)

Probiotics 20190201

(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.)

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, so for the past week I would assume my CFU count is probably at least 75 billion CFUs a day.

I also consume around 8 ounces of Greek Yogurt a day pretty reliably and while I had thought that really wouldn’t add much, based on the Probiotic Case above, it appears it can have a material effect.

Prebiotic Supplementation

Since I was conducting a Probiotic Case, I had not yet introduced any new prebiotics to my diet. Note that I did take the Psyllium and one small prebiotic chewable. I’ve been taking psyllium for literally decades, and since I considered it part of my normal diet I did not want to eliminate it. Some argue it is not a prebiotic at all. Although I argue the opposite, it is a mild prebiotic at best.

I’ve been taking the LEF Prebiotic Chewable for a couple years now and so kept that up as well. It is a xylooligosaccharide (XOS) and is a true prebiotic. In retrospect I probably should have eliminated that as well, even though it was a small amount.

Prebiotics 20190201

(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 20190201

My macro amounts were pretty consistent for this final week. Compared to the Base Case I am within a percentage point of each of the major macros (fat, carbohydrates and protein) and within a few grams of both fiber and sugar.

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. This was little changed from my Base Case.

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, again, in keeping with what I was eating during my base case.


Sleep 20190201

This is basically my target. I was a little under during the Base Case (6 hours and 31 minutes) but that is still within an acceptable range.

Activity Level

Activity 20190201

Back when I was completing the Probiotic Case I was still using these activity circles to track my activity. (I have since moved to reporting average daily calories.) Regardless, this was a little lighter compared to when I was establishing my Base Case but not by much (I tended to wrap that middle green ring (exercise) a few times so the difference is not as much as it seems looking at this representation.)

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.



Diet 20190201

I wasn’t posting my weight for the MicrobioME Project back when I established my Base Case, however I was keeping track of it. While I can’t recreate the chart at the left, I can report that at the time of my taking my Base Case sample, my weight was 153.4 pounds, so almost no change from when I took my Probiotic Case sample (and the prior days were similar as well).



Thanks again for stopping by. There is a lot of information here to digest (sorry, couldn’t resist), with more to come. My Prebiotic-Probiotic Case is already with Ubiome and I expect to be in a position to forward them a sample for my Prebiotic Case shortly.

Comments, observations, and questions are always welcome and can be left below in the comments section.

Take care!