Everything You Always Wanted to Know About Probiotics

Probiotics. We’re betting you’ve heard of them, have a vague idea that they’re good, and wonder if you should be taking them. But this is one area where we also see a lot of confusion. Supplementation of healthy bacteria willy-nilly, without knowing what or why you’re doing what you’re doing, can be just as detrimental to your health as doing nothing at all. So before you stock up on pills or start mainlining sauerkraut, let’s get the complete low-down on all things probiotic from today’s guest expert, Dr. Tim Gerstmar of Aspire Natural Health.

What are probiotics, and what role do they play in the body? 

Let’s back up a second before talking about probiotics and talk about gut flora.  Inside our digestive tract we have somewhere around 100 trillion bacteria happily living in us.  We’re like a giant high-rise building, and the bacteria are our tenants.  About 7 lbs of “you” is really bacteria that live in your intestines, from your mouth to the other end.

Our understanding of gut flora has advanced by quantum leaps in the past decade or so but we’re still just scratching the tip of the iceberg here.  We now know that our gut flora helps us properly digest our food, protects us from pathogens (harmful microorganisms), helps us detoxify harmful compounds, produces vitamins and other nutrients, keeps our guts healthy, and balances our immune systems.

Probiotics are a culture of “good” bacteria.  Most often when we say the word probiotics we are talking about a supplement (a pill or powder) of beneficial bacteria, but we also use the word probiotics when talking about fermented foods.

What gets your gut bacteria out of whack in the first place? 

There are a number of things that will disrupt our balance of gut bacteria, but two of the biggest things for most people are stress and antibiotics.

There was a nifty study I saw on rats a while ago.  These rats are genetically identical, living in the same controlled environment, and eating the same standardized food.  One group (the control) was left alone, while the other group was regularly stressed.  Examination of their poop (there is a fun job!) showed marked differences in their gut flora – which means stress alone is enough to derange your gut bacterial balance.  Personally I think chronic stress is at least on par with diet (if not more significant) a factor in causing disease.

The other big thing that will destroy your gut flora faster than you can say lickety-split are antibiotics.  Don’t get me wrong, I’m a big fan of antibiotics when used appropriately.  But we’ve way overused and abused antibiotics – taking them for viral infections (antibiotics do nothing for viral infections), not completing courses (leading to antibiotic resistance), and using them wholesale in all of the animals in the factory-farming system. Studies have shown that the good flora is decimated by antibiotics – and in some people, never recovers back to baseline without intervention.  If you take one thing away from this article, please always use probiotics with antibiotics! (Don’t take the two types of pills at the exact same time, but do take probiotics at an alternate time of day while you’re taking your antibiotics).

Some other things that get our gut flora out of whack are: C-section birth, bottle feeding, early introduction of food (some controversy here), low soluble fiber diet (not enough fruits and veggies), toxic exposures, and poor digestion (low stomach acid, poor pancreatic output of enzymes, issues with bile secretion).

What are some symptoms of gut dysbiosis?

Symptoms of gut dysbiosis fall into two broad categories. First, almost any major disease or dysfunction.  I know this sounds a bit glib, but knowing how tied up the gut flora is in the function of the human body, I believe that almost any major disease or dysfunction is going to involve dysbiosis either as a cause (primary or one factor among many) or as a result of the disease.  If your health is “messed up,” you probably have a gut dysbiosis.

Second, gut dysbiosis manifests itself commonly as digestive symptoms, including (but not limited to) gas, bloating, heartburn /GERD, constipation, diarrhea, IBS (irritable bowel syndrome), and IBD (Crohn’s and ulcerative colitis, among others).

Where do probiotics come from? 

Probiotics are bacteria, and bacteria are on everything – so in a sense, our bacteria come from everywhere.  Most of our probiotics historically are coming from two places though: dirt and food.

First, hygiene wasn’t such a big issue back in the day – people ate a lot more dirt, and didn’t run around squirting Purell on every exposed surface, human or otherwise. Our ancestors had exposure to far more soil based sources of bacteria.

In addition, historically probiotics were a regular part of our daily diet.  Before refrigeration, fermenting foods was one key way we preserved them Most of the Neolithic “traditional” cuisines around the world served fermented foods daily, if not at every meal – so there’s our food based sources of probiotics.

Today, food-based sources of probiotics include anything fermented and not pasteurized, as pasteurization will kill the bacteria. These foods include sauerkraut, kimchi, lacto-fermented fruits and vegetables, non-pasteurized yogurt, kefir and cheese, non-pasteurized meats like salami and some sausages.

Nowadays we also have supplements of probiotics, in pill or powder form.

Does a Paleo diet typically reduce the need for probiotics? Does healing the gut help restore a healthy balance of gut flora and fauna?

Gut health and gut flora are a very chicken and egg type of thing.  Bad gut flora causes poor gut health.  Poor gut health causes poor gut flora.  Depending on how severe the dysfunction, sometimes we have to address both in order to get things working properly, sometimes not.

There are a variety of reasons that a gut can be messed up.  If the main reason is food-based (i.e., if the person is having food reactions), then a program like the Whole30® is superb for helping.  However, if the dysfunction includes a hefty gut flora component, I haven’t found a standard Paleo diet by itself (without specifically including food-based sources of probiotics) is enough to make the gut healthy.

However, a generally Paleo lifestyle (which includes such thing as adequate sleep, appropriate exercise, and stress management) along with fermented foods would reduce the need for probiotics.

Do you see any issues with the Paleo diet in terms of gut bacteria balance?

Yes. A general Paleo diet doesn’t emphasize probiotic sources like fermented foods or probiotic supplements, which I think is a problem.  Also, occasionally you’ll see people on a “Paleo” diet who aren’t eating much in the way of fruits and veggies. Not enough soluble fiber in the diet can also be detrimental to the gut flora.

How does someone know if they need probiotics, and what kind is the best?

I think everyone needs “probiotics” on a regular basis, but I’m super picky about my probiotic supplements.  With a lot of other supplements you can get good brands over the counter (OTC), but not so much with probiotics.  There hasn’t been a lot of testing that I’m aware of in this area, but what little I know of was pretty damning to the OTC probiotic market.  Most were contaminated with pathogenic bacteria (“bad” stuff), or did not meet their potency/strength claims, or failed to grow (were non-viable).  Meaning at best you wasted your money, at worst you hurt yourself more by taking the supplement.

In my practice, I use the high end stuff you get from the better supplement companies. Most aren’t easily available to the general public. Here are a couple of suggestions:

  • Don’t go to the bargain bin for your probiotics.  If you can buy 4 for $1, you’re getting what you paid for.
  • Use a reputable brand – I’ve seen good results with the Jarrow brand (which is available OTC), and one brand I use I’ve seen pretty available on the Internet is the Klaire Labs line.
  • Look for potency/strength. We’re not exactly sure how strong probiotics need to be, but in general stronger seems better.  An 8 billion/dose is the minimum I’ll use, and often I’m using stronger doses than that.  A lot of OTC brands are down in the 2 billion/dose range, which most of the time just isn’t going to cut it.  And if they don’t list the dose (some probiotics have secret proprietary formulas or some such) don’t bother with it.
  • Be suspicious of the kitchen sink. This isn’t as hard and fast a rule as the others, but I’ve seen a lot of crappy brands try and look impressive by putting a lot of strains in their formulas.  Most of the high grade probiotic supplements we use have around 1-6 strains in them.  Is that ideal?  Probably not, but if you see a brand with 10+ ( especially if it’s vague on the counts), there’s a reasonable chance they’re padding out the product to try and make it look more impressive than it is.

So what, specifically, can people look for in a probiotic supplement?

In general, right now, you’re looking for strains of Lactobacillus and Bifidobacterium.  Let’s illustrate this with the label off of the Jarrow product I linked to above.

You can see this product contains six strains.  The three on the left and top one on the right are labeled “L. something” are the Lactobacillus strains.  The two on the right labeled “B. something” are the Bifidobacterium strains.

You can tell this is a good product by the letters and numbers after the names.  For example, “L. acidophilus LA-02”: the LA-02 is the pedigree of this strain.  This strain of acidophilus has been purified, genetically characterized and then registered.  The company (Jarrow) then bought the right to use that strain, took a pure sample and grew it to put in this product.  Do you have to have those numbers to have a good product? No.  But the presence of those letters is the sign of a quality product, as the company spent the extra dollars to get a pure, genetically characterized strain.

Anything else you think would be helpful for our community?

Probiotics are critically important, and the data just keeps piling up.  I honestly think our understanding of gut flora is going to revolutionize our understanding of health and disease, and you’re just going to see it growing in importance over the next few years.

I believe everyone needs a baseline probiotic intake.  If you’re healthy and you make or buy non-pasteurized fermented foods and eat them at least a few times a week, I doubt you need probiotic supplements.  If you’re sick, you’re probably going to need to do a lot more than just that.

One last thing.  If you think you’re very dysbiotic – you have a very disordered gut, or serious health problems – you’re going to want to start slowly with this stuff.  Taking tons of probiotics or gobbling up tons of fermented foods is probably going to make you feel bad, bad, bad.  The changing gut ecology brought on by an “overdose” of probiotics is going to send your system topsy-turvy and can lead to many issues, including diarrhea or constipation, fatigue and/or brain fog, body aches and flu like symptoms, skin “stuff” including rashes, and possibly a worsening of the symptoms you already have.  So start slow.  If using fermented foods, start with a teaspoon once a day and build up from there.  If using probiotics, go with one of the lower potency probiotics to start with, possibly as low as 1-2 billion/dose, and gradually increase from there.  (And, as always, it’s best if you can work with a naturopath or a functional medicine practitioner.)

tim gerstmarDr. Tim Gerstmar is a Seattle-based Naturopath who specializes in treating complex chronic diseases – those issues that leave most other doctors stumped. His area of expertise is in digestive health. He uses clinical nutrition (primarily Paleo, Weston A. Price and GAPS) and lifestyle counseling, botanical medicine (herbs), functional medicine, homeopathy in his practice. You can learn more about Dr. Gerstmar and Aspire Natural Health at, or contact him via Facebook ( or Twitter, @DrTimGerstmarND.

Subscribe to the Whole9 Newsletter



  1. Steve says

    Hello Dr,

    Is taking two tablets with 20 billion live probiotic cultures the same as taking one tablet with 40 billion probiotic cultures? (assuming all other variables are the same, brand, strains etc.?)

    Thank You

  2. Jo says

    Can you tell me if Garden of Life PRIMAL DEFENSE ULTRA is w30 compliant? I just noticed it contains rice maltodextrin and it says “cultured in dairy, which is generally consumed during the fermentation process”
    Will this hinder our results? We are on day 10 but just started on the probiotics.

  3. laura says

    Hello doctor in starting on probiotic 20 billion first time ..
    my question is if my 9 year old daughter can also take the pill ..

    probiotic blen 20 billion CFU’s
    lactobacillus axidophilus
    bifidonacterium lactis..
    daily. Value (dv) not established

  4. Amy says

    I have BioImmersion Beta-Glucan. I wonder if USDA Patented Oat Bran is ok to taking during my Whole 30 since we’re not supposed to have any grains. Thanks!

  5. Norellen pickell says

    L in types of food you suggest/ i have diverticulosis ,ulcers, and large hiatel hernia.

  6. De Ann Hawkes says

    I lost most of my stomach five yrs ago. Now the nightmare gas, bowel losage (small amt) but one tab 3 or 4 times a day. Have to wear pads.
    Had procto. Am ok. He wanted to put me on very expensive Rx of pobiatics. Gave me samples. My system went went nuts. So pains, gas, more bowel problems. Called Dr said take anyway that can be normalnwill wear off. My gut would not do that. I can not drink milk. But I feel better with fresh made parmason or any cheese. Drink Soy milk.
    Make shakes to get enough protien with yogart, fruit, protein powder.
    Stomach size of egg. Always fighting to hang on to weight. Lost stomach to undiagosed whooping cough at 65 yrs old. Full of ulcers. Dr built new stomach. Had an infection. Got that cleared up three yrs ago, but left with this. Varies in how much problems. Biggest is litttle bit of bowel lossage through day and also at night. Thank you
    De Ann p.s. At beginning after surgery did great except would throw up milk or ice cream.