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. The full transcript of this podcast is at the end of the post.

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?