Probiotics: More than expensive poop?

Probiotics are one of the most intriguing natural medicine therapeutics. A probiotic is a live microorganism (usually bacteria) that is taken orally, topically, or rectally in an effort to influence and shift biochemical, microbial, and physiologic state of some system in the body. Since humans are born with a relatively sterile digestive tract and in the first few days it rapidly accumulates flora from mom via breast milk, skin contact, and the environment; we innately understand the pivotal role that gut microbes have on our digestion, nutrient absorption, and survival. And since much of the microbiome research from the American Gut Project pointed that gut microbiota diversity is a key in health and longevity; we have seen a growing interest in figuring out the best way to shift the microbiome. The use of probiotics is rampant with the sales of probiotics globally projected to reach 65.87 billion by the year 2024. We can assume that a fair percentage of people taking probiotics are experiencing noticeable benefit and some may not be benefiting at all from taking probiotics. The illusion that we can take a probiotic and make it grow in our gut has since been dismantled and now we are trying to conceptualize why and how probiotics work and which specific strains are most beneficial for certain diseases. In my practice, I use probiotics for all types of digestive disorders, skin disorders, allergy disorders, and mental health concerns. However, they are chosen artfully and used at specific times and status of a patient’s health status. I have posted on various issues with probiotics as well including the fact that some times probiotics may make people feel worse. I also have growing interest in therapeutic prebiotic use. See, prebiotics are non-digestible fiber components that support our microbiome. Also, an interest in the direction of fecal microbial transplant for more long-term microbiome shifts. Recently I invited an esteemed colleague Dr. Jason Hawrelak (The probiotic advisor) on my podcast.

Below I am sharing a summary of that conversation. To listen to full episode click here

Jason Hawrelak, PhD, ND , the probiotic advisor on Probiotics

About our guest:

Jason Hawrelak, PhD, is a research scientist, educator, naturopath and Western herbalist with nearly 20 years’ clinical experience. Jason practices at Goulds Natural Medicine, a 138-year-old natural medicine apothecary and clinic located in central Hobart in Tasmania, Austrailia. Dr Hawrelak did his Honours and PhD degrees in the areas of the gastrointestinal microbiota, the causes of dysbiosis, and the clinical applications of pre- and probiotics. He has written extensively in the medical literature on these topics – including 16 textbook chapters – and his research has been cited nearly 1000 times.

Dr Hawrelak has taught health professionals at both the undergraduate and postgraduate level for the past 18 years. He currently coordinates and teaches the Evidence-based Complementary Medicine Programs in the College of Health & Medicine at the University of Tasmania (Hobart, Australia) and teaches natural approaches to Gastroenterology within the University of Western States Master of Science in Human Nutrition and Functional Medicine program (Portland, Oregon). He is also a Visiting Research Fellow at the Australian Research Centre for Complementary and Integrative Medicine (ARCCIM) at the University of Technology Sydney (Sydney, Australia).

Jason is on the Medical Nutrition Council of the American Society for Nutrition and is a Fellow of both the American College of Nutrition and the Naturopaths and Herbalists Association of Australia. He is also Chief Research Officer at, which offers a searchable database that enables easy, evidence-based prescribing of probiotic products and online resources for clinicians, and health-conscious members of the public, to learn more about the human microbiome and how they can positively influence these ecosystems.

Background and interest in probiotics:

Dr. Hawrelak’s interest in probiotic began in his final year of Naturopathic training and he attended 1999 lecture on microbiome and it drew his interest. He was at a research institution and did a research project on a prebiotic, probiotic, herbal combination. He went on to do a PhD with emphasis on this topic and in 2000 did his honor thesis on probiotics. 20 years later is still passionate about his PhD topic.

Definitions of Probiotics:

The strict definition and criteria determining if something qualifies as a probiotic of probiotics is as follows;

○ It must consist of live microbes, when administered in adequate amounts, that have demonstrated therapeutic effects in humans. Human clinical studies done with the exact human strain used in the product.

○ It must have gastric acid stability (be able to survive the stomach pH)

The different types of probiotics include

  • Food sources of probiotics: typically a yogurt base with a probiotic integrated into the probiotic including Medicinal yogurts and Medicinal Kefir

  • Human origin strains (a lot of the lactobacillus and bifidobacterium strains found in probiotics are human origin)

  • Yeast based probiotics : Saccharomyces boulardii (from the skin of Lychee) also Saccharomyces cerevisiae.

  • Spore based probiotics : Bacillus clausii ( fromphylum firmicutues) .Bacillus clausii, has been found to produce antimicrobial substances that are active against gram positive bacteria including Staphylococcus aureus, Enterococcus faecium, and Clostridium difficile. Bacillus Coagulans which is originally from cow intestinal tracts. Also see Bacillus subtilis, an endospore, gram positive, bacteria found in soil and the gastrointestinal tract of ruminants and humans. Can survive in anaerobic environments. Bacilus subtilis is strongly antimicrobial.


Dr. Hawrelak states this is a class of agents poorly used by clinicians

● He points out that they do more then feed bacteria

● The definition of a prebiotic is as follows :

○ A substrate that is selectively used by host microbes conferring a health benefit.

○ Must be indigestible

○ They must be a selective substrate for 1 or more commensal bacteria primarily in the large intestine.

○ They shift the ecosystem to a healthier state

○ There is some benefit from the ecosystem shift

● Many fibers do not meet the definition of prebiotics

Most prebiotics will increase bifidobacteria, akkermansia, lactobacilli, faecalibacterium, and butyrate producing bacteria. (hence the importance of prebiotics in the diet)

See my handout on prebiotics here.

Myths and controversy of probiotics

● There is a long standing and hopefully squashed myth that probiotics permanently colonize the GI tract. 95% of the time there is no long-term colonization. Probiotics may stick around for 2 weeks at most and usually cannot be seen on stool testing after you discontinue taking.

● Yet, probiotics are still therapeutic even though probiotics are not inoculating the intestine

● The probiotics have an action while you are taking and you will benefit for that time and a number of days afterwards

● Some probiotics for example decrease cholesterol; they will only benefit you while you are taking the probiotic. Once you stop the benefit stops.

● For hyperlipidemia (high cholesterol) the following strains of lactobacillus probiotics (L. plantarum and L. reuteri) have been beneficial in reducing cholesterol

● The other often debated question.When should you take probiotics when on antibiotics? According to Dr. Hawrelak, take them spaced between antibiotic dosage. Don’t wait until after the course is done!

Researched indication for probiotics

● Traditional uses: Irritable bowel syndrome, Inflammatory Bowel Disease, and Antibiotic related gut issues

● Emerging indications: Alzheimer's disease, anxiety, asthma, rheumatoid arthritis, mastitis, chronic fatigue syndrome, cervical dysplasia, celiac disease.

● Endometriosis is being studied with a non-commercially available strain

● We will eventually have a probiotic materia medica to co-exist with herbal materia medica.

● Esschericia Coli Nissle 1917 has good evidence for IBD. Been available since 1920’s. N. America is cautionary because of E. Coli association.(ask me about patients of mine flying through Germany to stalk up on this one!)

● Strains are not available worldwide. This is slowly changing. Europe is leading the way in probiotics.

Shopping for probiotics, how to select a good strain?

● If generally healthy, Dr. Hawrelak says you are better off getting your probiotics from fermented foods such as sauerkraut, kimchi, and yogurt vs. taking probiotics.

● Even though yogurt bacteria will die in the small bowel; there can be some benefit to immunity/natural killer activation related to even dead probiotics.

● For specific use of probiotics, you need to work with a health practitioner.

● Don’t use label claims to make your decisions.

● High CFU and most species/multiple strain does not equal a good selection of a probiotic. For example: Antibiotic associated diarrhea. 60 billion CFU multi strain (4 strains) Vs. 1 strain Lactobacillus reuteri ATCC 55730 200 million strain, single strain . The 200 million did help reduce diarrhea rates and c.difficile rates but the larger multi-strain probiotic did not. See study here on Lactobacillus reuteri

Evaluating microbiome for probiotic selection

● Dr. Harwelak uses lactulose/mannitol for checking intestinal permeability. Arguably the most validated test for gut leakiness. Tells you how severe. (authors note: there are others including stool or serum Zonulin and also panels looking at Actomyosin IgA, Occludin/Zonulin IgG, Occludin/Zonulin IgA, Occludin/Zonulin IgM ,Lipopolysaccharides (LPS) IgGm Lipopolysaccharides (LPS) IgAm and Lipopolysaccharides (LPS) IgM)

● Healing intestinal permeability can be a 3-12-month process.

● Example Chronic Fatigue Syndrome patient. Had intestinal permeability. Was 80% improved after 12 months of gut healing protocol. This was consistent with his improvement in the lactulose/mannitol testing.

He also uses microbiome testing. American Gut Project, Thyrve[1], 16srRNA testing. Is a game changer. He has found that the overall diversity score and number of species on these tests is very helpful. Only $100 follow up testing. Gauges changes and dietary compliance. Example Bilophila wadsworthia (a gram-negative, obligatorily anaerobic, bile resistant bacteria) will be high if someone is on a high fat diet. It only feeds off bile. Bliophila wadsworthia produces hydrogen sulfide gas which is something we want to be careful with it. (authors note Hydrogen Sulfide production has been linked with intestinal inflammation ) Follow up testing helps with motivation and understanding how well treatment recommendations are working. These are now essential tools that have improved the results.

Dangers, contraindications, and warnings in probiotics

● Systematic studies say to be careful with yeast-based probiotics specifically like saccharomyces boulardii in hospitalized immuno-suppressed patients.

Future work and take-home messages from Dr. Hawrelak

● Looking at research for natural agents that will not harm our commensals. He is concerned that some of the herbal medicines we use for sibo and dysbiosis that are being used for long term use may actually harm the microbiome.

● He is continuing to build the Probiotic advisor data base.

● He states to choose probiotic tools wisely. Based on evidence. Not on manufacturer information.

● Prebiotics are undervalued and are the best at shifting microbiome

○ Used for obesity and metabolic issue as well

○ Prebiotics and prebiotic supplements taste good!


One of my favorite articles on prebiotics by Lauren Glucina, a New Zealand based Naturopath, Medical Herbalist and Nutritionist

Addition comments on the topic...

Plethora of possible mechanisms of Probiotics.

Probiotics have taken a big hit in scientific and lay person circles. Mainly because people think that we are just making expensive “poop” and that since probiotics do not necessarily permanently grow in the gut then they are a waste. Well many research models have continued to show some of the beneficial shifts that might happen while on probiotics. I think the graph below really highlights a few. Probiotics are best viewed like a medicine and once you stop then the benefits will likely taper down. Prebiotics might be looked however more of a longer-term move. For now these are some of the benefits of probiotics proposed.

(Hill et al., 2014)

Courtesy of Hill, et. al. 2014

When I think of this list as a clinician, I would rank the following as most noticeably:

  • Regulation of intestinal transit (better stool consistency and frequency)

  • Neurological effects (I will often see less anxiety and depression)

  • Reduced intestinal permeability ( probiotics help in some cases improve mucus lining, and helps reduce endotoxin levels)

  • I typically see less gas and bloating

However, do note, in my practice we focus on really specific strains and not mega volume, multi-species probiotics. Also, probiotics are usually introduced at a later stage of health stability in my patients. Hence, the body is usually in a better state to integrate this microbiome shift.

Future directions of probiotics will likely be further exploration of the long-term benefits of spore-based probiotics. I am personally interested in the spore-based probiotic Bacillus subtilis (HU-58) as its ability to live in anaerobic environment and release antimicrobial elements that may be effective in warding of pathobionts make it an attractive option. Also developing a flexible and prebiotic-centric diet

If you are generally well and want increase prebiotics in your diet you may start with something like a prebiotic smoothie bowl. Warning : if you currently on unstable digestively adding prebiotics rapidly like this may lead to more GI-distress temporarily. For the recipe ; Check it out below

Recipe courtesy of

[1] "Thryve Personalize." Accessed 29 Oct. 2019.

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