Prebiotics Side Effects – Things You Want To Avoid

Prebiotics Side Effects – Things You Want To Avoid

The Prebiotic Case Test Results: The Pitfalls of Prebiotic Supplements!

So, what happens when you spend nearly two months supplementing with 24 grams of prebiotic fiber a day?

Well, for one thing, you get a little gassy.

And for another, your microbial diversity, a generally desirable attribute, can actually get worse!

See here for What is a Prebiotic?

Prebiotics 20190322In terms of personal impressions, the increased gassiness would be number one, and while not particularly serious (and certainly not health threatening!) it’s something people ask about and yes, it’s a real thing, although I believe there are ways to mitigate it such as ramping up the prebiotics more gradually.

In terms of laboratory test results, there are also unanticipated prebiotics side effects. I believe these, too, can be mitigated, and I will be exploring that in the future, but I would very much encourage anyone contemplating supplementing with prebiotics to read on because you probably don’t want to do it the way I did.

I don’t even want to do it the way I did!

New to the MicrobioME Project? New to Microbiome Bulletin? If so, you might want to check out, The MicroboME Project, the About “Us” page, the Microbiome Glossary, and Microbiome Hype.

And you can check all the MicrobioME Project posts in the MicrobioME Project Category.


I did not fully appreciate the difference in intestinal gas until after I had ended the supplementation phase of this experiment towards the end of March and spent a few weeks back on my normal diet absent any additional prebiotic fiber.

Gut Flora

While I had reported early on during the testing phase that I had experienced some increased gas, I had also indicated that it had settled down for the most part within a couple of weeks.

And that was true, it had settled down.

But that was a purely relative measure. While it had definitely gotten better as my system adjusted, I had grown so accustomed to it, and I guess was so relieved that it was better than it had been in the beginning, that I thought it had returned to normal.

In reality, I now realize it had never entirely settled down to where it had been before I began the supplementation.

I want to stress that I did not experience bloating or even any kind of gas-induced pain, it was just more gas in general.

Keep in mind, it was not as if I had low fiber intake before I began the MicrobioME Project. My average fiber intake has been north of 60 grams a day for years. I can’t imagine how it would be were someone to embark on the same experiment having been consuming the average amount of fiber a day of between 15 and 20 grams (in America, which is nearly half the recommendation).

Basically, that would be more than doubling your fiber intake, over a very short period of time. (I ramped up to 24 grams a day over the course of one week.)

Gut Flora 20190322

The apparent impact this had on my microbiota, and the negative side effects this had including a reduction in microbial diversity, and the favoring of some microbes to the detriment of others (as revealed by the Ubiome laboratory testing), is likely of even greater concern.

And that is why I would strongly advise against doing what I did. Heck, I have no interest in doing it that same way again. While I plan on revisiting all these various scenarios going forward I’m going to go a lot more slowly at least in part for that very reason.

As I’ve mentioned before, the main thrust of this first phase of the MicrobioME Project was to determine if it was even possible to change the composition of your microbiota. This is an area of some contention, and I decided to go hard and fast with the supplementation to get that answer before I started on anything more subtle.

So far, the answer to that question is an emphatic “yes.” Based on my own observations and perhaps more importantly, the Ubiome testing I conduct, there were measurable and material changes in the composition of my microbiota, at least while I was taking the supplements, and that was what I was trying to determine.

For the first three Case results, see the below.

Base Case: Base Case Ubiome Test Results,

Probiotic Case: “Do Probiotics Work? Yes! But…

Prebiotic-Probiotic Case: Prebiotic-Probiotic Combination: Real World Results and Impressions

Based on these results, and the results we are about to discuss for the Prebiotic Case, I intend to go slower in the next phase, and linger on each case longer, because I believe that the effects of the supplementation were still accumulating throughout the phase. That is, while the microbiota changed rapidly, as research has indicated it would, I don’t think it had changed to its fullest extent during these weeks-long testing periods.

Again, more on that later, let’s focus on the Prebiotic Case for now.


As I already mentioned, in terms of subjective personal impressions, yes, gas was involved, and I now recognize it was at elevated levels throughout the nine weeks I was on the supplements (including remaining on probiotic supplements for the first three weeks when I was conducting the Prebiotic-Probiotic Case study).

It was never so bad that it became any kind of problem, personally, professionally, or socially, and I clearly got accustomed to it, but it was noticeable.

Gas Test Prebiotic 20190322

Not to get overly graphic, but this is important as well: There was a distinct change in odor as well. Worse? Well, that’s subjective, but definitely different suggesting that different gases were being produced, or at least the composition or components had changed. I had no means to test these emitted gases, of course, but the fact it was so noticeable meant something different was happening.

In terms of these subjective impressions, there really weren’t any other noticeable side effects. Basically, I felt great. I wasn’t attending to any specific problem, so I wasn’t looking for miracles or cures, but overall my health, and my gut health, were fine. Again, I would note I already consumed a large amount of daily fiber, so I did not expect anything less or more.

I did notice the absence of the probiotics, but I’ll have more to say on that when I get the Base Case 2 test results back and so can carefully examine the full arc of this first phase, from Base Case, through the three separate supplementation phases (probiotics only, prebiotics and probiotics, and today’s write up, prebiotics only), and back to Base Case 2 (coming) in which I again return to taking no additional supplements.

Lab Results

Regarding the detailed changes in the composition of my microbiota and the resulting side effects of this supplementation, we’ll turn to the actual Ubiome test results.

Please note that now that I have test results from four cases, I’ve changed how I present the data, abandoning the individual charts Ubiome provides (which had proved increasingly cumbersome) and instead creating my own sets of bar charts using the same data.

This will allow me to continue to track testing results in the year ahead in an easily accessible form.

Microbial Diversity

Diversity is generally considered a desirable thing and is broadly associated with superior health outcomes.

Diversity 20190322

I did not make too much of the drop in diversity of my microbiota for the Prebiotic-Probiotic Case as it was relatively minor and I had not done enough testing to come to any firm conclusions.

However, here we have the makings of a trend.

While my microbial diversity actually increased when I started taking the probiotics (at least over the three-week testing period), it decreased when I introduced the prebiotics.

And then it continued to decrease after I removed the probiotics and continued to take the prebiotics.

What could cause this? Well, I was supplementing intensively with certain prebiotics, which you can examine in the tables towards the end of this piece and in any of the MicrobioME SnapShots I posted weekly in the MicrobioME Category.

These were all common, straightforward prebiotics, from pectin to inulin, to XOS and so on, but in relatively large quantities, 24 grams a day in all, which is more than most people in the developed world consume in overall fiber a day never mind pure prebiotics. I was taking nearly 8 grams a day in inulin alone.

There is the very real possibility that this specific and intensive supplementation was favoring certain microbes to the detriment of others.

This is a theme we will be returning to time and again.

Wellness Match Score

Prebiotic Wellness 20190322

No one wants to see a decline in their wellness, least of all me!

However, as I’ve mentioned before, I don’t put a lot of stock in this one. It’s basically a measure of how closely the overall composition of your microbiota matches that of people who are generally healthy.

That’s interesting, but people’s microbiotas are very different from each other, so I probably pay the least attention to this one.

In any case, the declines were relatively modest and likely reflected the decrease in diversity, which I am taking note of.

Probiotic Microorganisms

Now we get into the details, and I think this is where the apparent favoritism of some microbes at the expense of others starts to come into focus.

It’s not all bad, in the sense that it appears beneficial microbes are being favored, but it also appears that maybe this is at the expense of other beneficial microbes, at least the ones being tested for by Ubiome.

One important thing to note before we go on, the “Selected Sample” that my amounts are being compared to are the levels that are typically found in people who exhibit overall good health and wellness and report no illnesses. For purposes of these charts, my score is expressed as a portion of that (this is how Ubiome expresses the results as well).


Prebiotic Lactobacillus 20190322Prebiotic Lactobacillusb 20190322





I wanted to present this data two ways, because my lactobacillus is at such low levels that comparing it to the Selected Sample is visually useless.

Lactobacillus is considered a beneficial microbe and is present in many probiotic formulations and while it increased, doubled in fact (again, if only from very low levels) when I was taking probiotics that included lactobacillus, it declined after I introduced the prebiotics, and continued its downward march once I stopped taking the probiotics and was supplementing with prebiotics only.

These results suggest that the lactobacillus was being out competed by other microorganisms that were responding better to the introduction of prebiotic fiber.


So, who did benefit from the prebiotics?Bifidobacterium 20190322

The answer is pretty clear here, and I think this is at least one major source of the reduction in my diversity.

To be clear, bifidobacterium is a bedrock probiotic, broadly believed to be beneficial in a variety of ways, however it is legitimate to ask if I need 10 times the amount a typically healthy person does.

I will admit I was pleased when my bifidobacterium tripled with the probiotics (which I will get into deeper when I do my overview of this entire phase), but I’m a little troubled by it skyrocketing with the introduction of prebiotics, and it’s continued increase, albeit more slowly, when I took away the probiotics but kept taking the prebiotics.

And this does seem to come at a cost that goes beyond reducing my already meager populations of lactobacillus.


Here we come across what appears to be another price to pay.

Akkermansia Prebiotic 20190322

As I’ve mentioned before, Akkermansia is a rising star among probiotics, but you can’t supplement for it, at least not with probiotics (it’s not currently a part of any formulation I’ve come across) and apparently when you supplement with prebiotics, even a variety as I had done, it appears to suffer in comparison with others.

This also troubled me. I had pretty high levels of akkermansia, and while they suffered somewhat with the introduction of probiotics, they took a real hit once I started taking the prebiotics. The Akkermansia was there at pretty elevated levels before I started taking any supplements, and so was presumably a long-time resident of my gut. I’m not sure I want to disturb that to so great an extent.

Keep in mind, I took A LOT of prebiotics. I am going to continue my experiments to see if this is something I can manage, if there is a happy medium, but clearly I don’t think I’d want to have this be my regular routine.

Yogurt Microbes

While the increase in microbes associated with people who consume yogurt appears to have leveled off, it’s still quite elevated.

Yogurt 20190322I’m guessing this is purely a result of the elevation of bifidobacterium which Ubiome identifies as one of the microbes they measure for this test.

I’ll note that while the yogurt I consume does not include any bifidobacterium, if Ubiome is counting it as a yogurt microbe, then it is being counted here.

Regardless, the question remains whether I need or benefit in any tangible way from having 7 times the yogurt microbes of a typical healthy yogurt consumer.

I’m going to guess not.

Vitamin-Producing Microbes

Ubiome tests for two sets of microbes that manufacture vitamins the human body cannot make on its own or has difficulty absorbing from dietary sources. One set produces Vitamin K, K2 in particular, and another set produces B9.

Vitamin K-Producing Microbes

This is one I can make neither head nor tails of, and it’s been that way for a while.

Prebiotic Vitamin K 20190322It’s up, it’s down, with no apparent pattern.

The amounts are very small, and so perhaps not statistically significant, but it’s been an annoyance for a while.

While Ubiome has a number of suggestions regarding how you can affect your vitamin K-Producing microbes (adopting a Mediterranean diet, supplementing with Bacillus subtilis, etc.) I wasn’t doing any of those things one way or another.

I will continue to chalk this one up statistical noise and monitor it going forward.

Vitamin B9-Producing Microbes

This is another one that does not make a whole lot of sense.

Prebiotics Vitamin B9 20190322Among the things Ubiome suggests you can do to increase these microbes is to take inulin supplements.

For this case, and the one before, I was consistently ingesting nearly 8 grams of inulin a day. It made sense that it would go up for the Prebiotic-Probiotic Case when I started on the inulin, but why would it go back down so dramatically for the Prebiotic Case when I kept my inulin intake constant?

I’ll have to keep an eye on this one, but I’m clearly missing something, or this is simply one part of the Ubiome test that needs work.

Anti-Inflammatory Microbes

Ubiome tests for microbes that produce three short chain fatty acids (SCFAs), butyrate, propionate, and polyamine. These SCFAs yield a number of benefits including providing sustenance for the cells lining your intestinal wall and helping to reduce systemic inflammation.

Butyrate Microbes

These results are more consistent with what you would expect.

Prebiotics 20190322Supplementing with prebiotics should increase your microbes that product butyrate.

This is broadly considered a desirable outcome.

Does this have anything to do with the increase in my bifidobacterium?

Maybe. As I mentioned in the Prebiotic-Probiotic Case, while bifidobacterium does not directly produce butyrate, there is research that suggests that there is cross-feeding interactions between Bifidobacteria and the butyrate-producing colon bacteria Anaerostipes, Faecalibacterium prausnitzii, Eubacterium, and Roseburia.

That is, the butyrate produces substances that help feed and nurture these other microorganisms which in turn produce butyrate.

Keep in mind, your microbiota is a vastly complex and interrelated ecosystem, and we are only just getting a handle on these interrelationships.


Prebiotic Propionate 20190322

I can repeat what I said for the Prebiotic-Probiotic Case: My propionate, which was already low, continues to be driven lower.

While Ubiome seems to consider this a SCFA you want more of, not less, there are others who take the view that less is better.

Regardless, another outcome, I believe, of one set of microbes being out competed by others due to my supplementation.


This is another entirely consistent result.

Prebiotic Polyamine 20190322

I had noted before that Ubiome identifies prebiotics as a supplement that should increase the populations of these microbes.

That happened in the Prebiotic-Probiotic Case, and continued to build in the Prebiotic Case.

Once again I don’t believe this is more double-counting. Yes, Ubiome identifies Bifidobacterium as one of the polyamine-producing microbes, but my levels of bifidobacterium increased in the Probiotic Case pretty dramatically, while these Polyamine-producing microbes decreased during that period, suggesting that something else is going on here.

Caution is advised, of course, as there are a lot of moving parts. But there does appear to be some consistency, more often than not, with Ubiome’s analysis.

Sleep Microbes

Ubiome measures for two sleep-inducing microbes.

Serotonin-Producing Microbes

I can repeat what I said for the Prebiotic-Probiotic Case and that is, this was and remains an odd one. Prebiotic Serotonin 20190322

The only actions Ubiome mentions as means to increase the levels of serotonin-producing microbes is to eat an omnivorous diet, engage in regular exercise and avoid antibiotics. I did and 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. I don’t specifically mention my antibiotic use in those snapshots because I haven’t taken any in years.

(And rest assured, if I ever find I have to, that will automatically become anew test case!).

Why are these declining steadily even though I haven’t changed anything that should affect them? I don’t know. Maybe they are being out competed by microbes (such as the bifidobacteria) because of the supplementation. I don’t know if anyone else has tested for this.

It will be interesting to see what things look like for Base Case 2, to see if they rose after I ceased the supplementation.

GABA-Producing Microbes

Prebiotics GABA 20190322

As I mentioned for the last case, 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.

It appears that Ubiome does not measure any amounts above 2 times (they present the data as “greater than 2) so I don’t know if they continued to increase. I still need to make an inquiry about that.

I do wonder if I sleep reasonably well because I’ve got enough GABA even though my serotonin producing microbes are lower than they were.

But that’s pure speculation.

TMA Producing Microbes

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

Prebiotics TMA 20190322These have bounced around a bit, but overall the trend is down, particularly in light of my prebiotic supplementation.

While there is nothing specifically associated with either probiotic or prebiotic supplementation that should reduce the population of these TMA-producing microbes, their numbers have decreased materially.

I do wonder if that is, again, the byproduct of these “bad” microbes being out competed by the microbes benefiting from the supplementation.

Again, it should be really interesting to see how things look when I get the Base Case 2 test results back.


Some questions have been answered with yet more raised!

The answers:

  • Asked and answered is whether or not prebiotic supplementation can alter the composition of your Microbiota. Clearly it can, at least so long as you are supplementing.
  • Do these results manifest themselves quickly? Very much so, yes, by measurable amounts in a matter of weeks.
  • Do certain specific microbes, or microbial families (and more specifically genera and species) benefit from supplementation? That appears to be the case, the bifidobacterium genera in particular.
  • Are there any side effects? That is a definite yes. There is the extra, but manageable gassiness of course, and also the fact (as it appears now) that even microbes thought to be beneficial can suffer at the same time others flourish.

The questions:

  • Do the results linger once you cease supplementation? We’ll get a preliminary look at that shortly when I get the results of Base Case 2 back.
  • Do the effects of supplementation continue to mount the longer you take them? It appears that way, but I’ll need to test for that specifically going forward.
  • What are the long-term health effects? At this point, I just don’t know, it’s way too early.
  • Can supplementing help people who have low fiber diets? This is an interesting one. I already ate a lot of fiber and had a diverse microbiota. The massive supplementation seemed to hurt more than it helped. Might someone who does not eat a lot of fiber with a less diverse microbiota be helped with supplements? I’d love to hear from anyone with personal experience with this.
  • Is there a balance of prebiotic supplementation that could also help someone like me who already has a high-fiber diet? That I aim to find out!

All that aside, my biggest takeaway from this Prebiotic Case came as a surprise.

I went into this expecting far more benefit from supplementing with prebiotic fiber than probiotic supplements. As I already mentioned, I have a high-fiber diet, over 60 grams a day. I am a fan of the overall health benefits of fiber. Surely adding prebiotic fiber would be a pure, unadulterated good thing.

More is better, right?

And yet it was the probiotics that seemed to yield better overall results with fewer side effects.

See Genuine Health Probiotic and Great Oral Health Probiotics.

Now, that could be I didn’t take them for very long before I started on the prebiotics, so I will be retesting that assumption, but regardless I come away from this prebiotic case believing I completely overdid the total supplementation, and ramped it up too fast, having gone from just about zero prebiotics to 24 grams a day.

This, too, I will revisit, going more slowly, being more prudent, and testing along the way.

To be clear, I remain a big fan of fiber. I believe the generally healthy state of my microbiota is probably in part a result of my high-fiber diet. The surprise was that you can get too much of a good thing, you can focus entirely too much on high-intensity supplementation too quickly, and end up with results you do not desire.

But this does go to show that you have to go into these things with an open mind. It’s okay to go into this with some preconceived notions, as long as they are in the form of a hypothesis. It’s desirable as you have to have some structure and reason for your experiment, but you must be prepared to go where the data takes you, and if supplementing with large amounts of prebiotics all at once turned out to have mixed results, well, you accept that, adjust your experiment, and move on.

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. I do advise you proceed with caution and make your own judgments, or judgments made in consultation with your healthcare provider.
  • 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 periods. 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.

The comments section is all the way at the end, and you are encouraged to add your own thoughts and opinions or ask any questions you like!

Take care!


SnapShot Overview

I took my sample Friday morning on March 22, 2019, and placed it in the mail shortly thereafter. I prefer 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.

To that point, I chose to highlight the variables below precisely because they can affect the microbiota and therefore the outcome of these Ubiome laboratory tests. I hold these as constant as possible while I examine the effect changing one can have on my microbiota. (And yes, I’ll be testing those other variables in the future as well).

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

Probiotic Supplementation

Zero probiotic supplementation. This test was all about prebiotics and prebiotics alone.

If you are interested in probiotics, check out my Probiotic Case results, Do Probiotics Work? Yes! But… and my post, “What Should I Look For in a Probiotic.”

Prebiotic Probiotic 20190322

(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.)

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.)

I took my sample Friday morning, so this is the supplementation I took through that time.

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.


Diet Prebiotics 20190322

My macro amounts, fat, carbohydrates, and protein were pretty consistent compared to when I took my sample for the Prebiotic-Probiotic Case. Fiber remained very high compared to the Base Case and Probiotic Case but that is not at all surprising given that I added prebiotic fiber to my diet specifically for this test.

My fat intake remained 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 poultry, fish (once or twice a week), pork, and occasionally beef, and this week was no different.

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


Sleep Prebiotics 20190322

Sleep was just about spot on to my goal of 6 hours and 40 minutes, and consistent with previous periods.

Activity Level

Activity Prebiotics 20190322

My target range is to expend between 2750 and 2850 calories a week, and I came almost right straight in the middle of that range.

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. Outside of work I am also pretty active, walking the dog several miles a day and keeping generally busy. There is relatively little variation in this routine.


Weight Prebiotic 20190322

My weight continues to fluctuate within a pretty tight range, and this week was no exception, although it did come in a little light right towards the end, but not in any material fashion that it should have an effect on my test results.


 I really appreciate your stopping by and taking the time to read this. The microbiota is an integral part of our health, and everything we do and everything we eat affects it one way or another. Hopefully you found my experience as useful and helpful as I am in understanding the complex interplay of all these variables, even if we seem to raise more questions than we can answer sometimes.

Speaking of questions, please feel free to ask those in the comments section below, or just share your own thoughts or experiences!

Take care!