Probiotics: The Unconventional Guide to Healthy Poop


Regardless of their merit, probiotics are the supplement people turn to when they want to improve their digestive health.

However, most people don’t realize we’re still living in the Stone Age of probiotics and they’re nowhere close to fulfilling their potential.

Those 100 billion CFU’s on the label might be 50 billion once you open the bottle, and then turn into 25 billion once they get out of your stomach, and then get chopped down to 10 billion by the time they finally reach the back of your colon.

If you want nice bowel movements you need to do more than just down L. Acidophilus and call it a day.

Do They Colonize Your Gut?

People take a probiotic because they believe it’ll colonize their gut with healthy bacteria.  Skeptics point out there’s little chance they’ll make it there in the first place and are buying an expensive bug cemetery.

As it turns out, both are wrong.

Bifido and lactobacteria are surprisingly resilient at surviving the stomach and have survival rates between 20-40%, which is much higher than originally thought.

However,  they do little more than take a joyride through your colon once they get there.   If you stop taking a probiotic, their bacterial content will stop showing up in your feces shortly thereafter.

Luckily, their short-lived existence doesn’t render them ineffective.  Probiotics consistently have a positive albeit modest effect on various health conditions.  But they don’t work in the ways you think.

It turns out probiotics are nomadic, but not imperial.  They don’t stick to your intestinal walls, but they do emit a wide variety of particles that nourish your intestine, balance your hormones, transmit signals to your brain, and counteract a bratty immune system.

And it’s this chattiness that allows them to be therapeutic.  As long as you keep taking them.

What Are They Good For?

The probiotics industry currently runs on hope moreso than science.

Ever wish you knew which strains were best to maximize your health?  So do the people making them!

However, the cupboard isn’t entirely bare.  To figure out how to get the most out of a probiotic it’d be useful to look at a paper that pooled together all the trials conducted with probiotics and analyzed their results.

It produced a buffet table of insights on what’s important in a probiotic and what’s not.



As you can see above, probiotics have the ability to improve the conditions of various gastrointestinal conditions, but the effect varies 10x.  [footnote]The conditions are ordered most effective –> least effective bottom to top.[/footnote]

If you’re lucky enough to get pouchitis there’s good news. People who take probiotics are 80% more likely to have their condition improve than people who don’t.   If you have enterocolitis they’re almost guaranteed to have no effect.

What determines what a probiotic can help with?  There are two good rules of thumb:

  • Prevent, not cure.  Probiotics are good for helping with the prevention of conditions, or keeping them in check, but are not strong enough to reverse them once they’ve gotten serious.
  • General, not acute.  For conditions that have very specific causes you’ll need traditional medicine for the bulk of your healing.  If your ailment has no specific cause then a good probiotic is likely to help.

probiotics strains

What Strains Work?

Commercially bifido and lacto bacteria reign supreme, but therapeutically nothing compares to C. Butyricum and VSL #3 (which can’t be bought over the counter).

C. Butyricum works because it produces butyrate, which is a fatty acid your gut needs in large quantities but doesn’t typically get.  Here’s a useful thread that explains how it’s helped people with chronic conditions.  It’s really useful for killing gut pathogens and works well with resistant starch (more on that later).

Whole health source has a good article on butyrate, and why the best way to get it is with lots of lard.

VSL #3 is a proprietary blend that was formulated specifically for IBS, pouchitis, and other gastrointestinal conditions and…….is only available through a doctor.  It has the most comprehensive clinical research of any probiotic strain, but forget about picking up a bottle of it at Vitamin Shoppe.  Prescription only.

The rest have more modest levels of success, and quite frankly, suffer from being overused in formulations.  Many of the most popular bifido and lacto strains have been thrown against the wall for so many different things that it’s no wonder they’ve had no effect for a lot of it.

probiotics effectiveness

How Best to Take Them?

Since probiotics pass right through your colon it’s not surprising that you need to take them for a long time to be effective.  You’ll need at least 8 weeks of exposure to see a significant impact, and their benefit increases with length of time taken.

Notice that dose doesn’t move the needle much.  You have 10,000X more bacteria in your belly than you can fit in a pill.  Until they can create 100 trillion CFU in a serving adding a few extra billion is just tossing nickels in the fountain.

More strains are better if the people making the products are paying attention to what they’re doing.  However, most of the increases in strain varieties is a rat race that exercises little caution for how they actually work together.

The truth is that very little is known about how strains can be used to manage various health conditions and most strain combinations is guesswork.

This is the next frontier of probiotics, and will be covered in a later post.

The Importance of Resistant Starch

Truthfully, while probiotics are helpful, their effect is always going to be modest.  Taking a probiotic to change your gut flora is like filling up your swimming pool with the ice mug from your freezer…….it’s just too puny to have much of an impact.

If you want a healthy gut you need to make sure it has enough fuel to replenish its bugs on its own.

That’s why eating the right foods is important.

Some carbohydrates aren’t entirely digested in your stomach.  When they reach your colon bacteria are able to breakdown their remnants into sugar and ferment it for fuel. These are called prebiotics, and they might be more useful for increasing the spread of healthy bacteria than healthy bacteria themselves.

Despite many imprecise claims of being the real thing, the only supplementary ingredients that qualify are inulin, fructo oligosaccharide (F.O.S.) and lactulose.

The benefits of resistant starch are threefold:

  • It lives in your hind gut, which is where lots of digestive orders are formed.  Many probiotic bacteria are most active in your foregut and have wilted and died by the time they can  see your anus on the horizon.
  • They feed the bacteria which are already there, which are much greater in number and diversity than anything you could get with a probiotic alone.
  • They produce short chain fatty acids, which are fuel for your gut and help reduce stress.

It’s useful to think of prebiotics as the supplementary equivalent of shampoo and conditioner.  It’s best to use one to prep your body for the other.  The Paleo Mom has a good article on resistant starch, and the astute Vin Cutty also has an awesome article on probiotics and why he doesn’t take them.  

Please note that you need 10-20g’s of this stuff to make a difference.  Supplement companies that fairy-dust it into their capsules are just label chasing.   Sweet potatoes, squash, yams, and artichokes are great sources of resistant starch in real food.

Moving Beyond Bifido and Lacto Bacteria

If you didn’t know any better you might think bifido and lacto bacteria were the genesis of all things gut health.

After all, why on earth would they be included in so many supplements if they weren’t?  

The truth, it turns out, is a bit more depressing.  They were originally included in products because they grow well in milk.  The fact that they’re good for cheesemaking does more to explain their prevalence in commercial products than anything having to do with human health.

The genome of a hunter-gatherer tribe called the Hadza was recently sequenced, and it turns out bifidobacteria were entirely absent.   Apparently they weren’t the probiotic of choice of our ancestors.

And this absence isn’t even limited to people who walk around in butt-flaps!

As we continue to sequence the gut-o-somes of people around the world it turns out bifido and lactobacteria are totally MIA.  (HT:  Vin Cutty).

Bifido and lactobacteria are useful, but if you’re going to use a probiotic you ought to aim a little higher than the Bert & Ernie of gut bugs.  Good strains to get outside of those two are the following:

  1. C. Butyricum – see above.  It kicks ass.
  2. S.  Boulardi – actually a yeast, but it has proven benefits for mental function.
  3. P. Acidilacti – possesses many of the benefits of lactobacilli, but it’s better at removing pathogens.

What Brands Work?

There is a marketing arms race to boast the highest CFU count on your label, but the most important parts of a probiotic are well chosen strains that are carefully grown not to interfere with one another.  Here are three companies that basically get it right:

Prescript Assist – 29 different organisms + proven stability + useful clinical trials.

AOR Probiotic – The only OTC product I’m aware of that sells C. Butyricum in its formula in  the US.

Hyperbiotics – They use well produced strains and strong formulations.

Truth be told, there’s no probiotic you can take that’ll fill up your belly with the bacteria you need.

Fermented foods, a healthy relationship with dirt, and plenty of starch in your diet are the best ways to make your colon whole.

Probiotics are useful for people that are managing gastrointestinal disorders, on antibiotics, or abnormally hate potatoes.

When I walk into Four Seasons, I calmly stroll past the supplement refrigerator without suffering pangs of doubt.  I maintain my colon with a willingness to make the chess players in McDonald Park uncomfortable by my lack of awareness when I sit in the dirt next to them.

If you have more manners than I do, then god bless you.  Your gut might not thank you for it………but there might be a probiotic that can help.  Just make sure you get the basics right.


1).  Bezkorovainy, et al.  “Probiotics:  Determinants of Survival and Growth in the Gut.”

2).  Ritchie, Marina, et al. “A Meta-Analysis of Probiotic Efficacy for Gastrointestinal Diseases.”

3).  Lin, Jun-Song, et. al. “Different Effects of Probiotic Species/Strains on Infections in Preschool Children: A Double-Blind Randomized, Controlled Study.”

4).  Timmerman, H.M.  “Monostrain, Multistrain and Multispecies Probiotics –A Comparison of Functionality and Efficiency.”

5).  Roberfroid, Marcel.  “Prebiotics:  The Concept Revisited.”

5 thoughts on “Probiotics: The Unconventional Guide to Healthy Poop”

    1. Hi DB……great question.

      Off the top of my head, I’d think it’d be a very good substitute, and possibly even better than butyrate producing probiotics if taken with a prebiotic.


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