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Probiotics and the Microbiome

Probiotic is derived from the Greek ‘pro bios,’ meaning, ‘for life.’ Humans beings have consumed foods since they accidentally discovered that food fermentation is a useful method of food preservation. Fermented milk products and pickled vegetables of all kinds have been consumed in many different cultures for millennia (Bagchi, 2014). Some anthropologists believe that mankind from nomadic wanderers into farmers specifically to grow barley to make beer in roughly 10,000 BC; not only was beer nutritious, the alcohol was divine, and it was treated as a gift from the gods (Nummer, 2002).

Fermentation was used for simple food preservation and to make less desirable ingredients into more palatable food. Microorganisms responsible for fermentations can also produce beneficial vitamins as they ferment. This produces a more nutritious end product from the ingredients (Nummer, 2002). Examples of fermented, probiotic-rich foods that have been traditionally consumed around the world include Kefir (Russia), Calpis (Japan), Tofu (Southeast Asia), Kimchi (Korea), and Kaymak (Turkey) (Bagchi, 2014).

The Microbiome in You

The word “microbiome” brings to mind images of a tiny encapsulated world and, essentially, that is what the human body is. In the mid-1800s, Hungarian physician Ignaz Semmelweis discovered the benefit of hygiene and hand-washing. Sadly, he subsequently went insane because no one would believe him, and ironically he died of sepsis in an insane asylum at the age of 47 (Davis, 2015). Even more ironically, the profession later embraced Semmelweis’s concept of hand-washing. In the quest to eradicate disease and infection, the only appropriate term for the subsequent reaction would be the word “overkill.”

While probiotics were identified and named around the time of Louis Pasteur, the concept was neglected during the 20th century and throughout the “golden age” of antibiotics and vaccines. It was the rise in the number of multidrug resistant diseases, and the recognition of the role that the human microbiota plays in health and disease, that caused interest in probiotics to expand (Hseih & Versalovic, 2008). The microbiome is now recognized to play a vital role in the dynamic process of health and disease prevention, and the NIH began a Roadmap Initiative in 2007 called the Human Microbiome Project (HMP) in order to “generate resources enabling comprehensive characterization of the human microbiota and analysis of its role in human health and disease” (NIH, 2018).

Human bodies are large, mobile containers of a vast and diverse universe. Demodex mites inhabit the follicles of eyelashes and feed on skin cells. Single-celled microorganisms, including viruses and microbes/bacteria, inhabit the skin, alimentary, and genitourinary tracts. By some estimates, 100 trillion microbes live within each human individual (Hsieh & versalovic, 2008). Researchers have been aware that bacteria in the gut contribute to vitamin production and absorption, metabolism of proteins and bile acids, fermentation of dietary starches, and prevention of pathogen overgrowth for over 30 years (Rolfe, 1984).

The Evidence for Health Benefit

Hippocrates declared, “death sits in the bowels” and added that “bad digestion is the root of all evil.” In fact, probiotics research suggests that this statement describes the role of probiotics in health maintenance and disease prevention.

At the beginning of 1900s Elie Metchnikoff, a Russian scientist working at the Pasteur Institute in Paris, attributed the exceptional long life of Bulgarian peasants to their consumption of large quantities of ‘sour milk’ containing Lactobacillus bulgaricus. Back in the early 1900s Metchnikoff was ahead of his time when he suggested that lactobacilli might counteract the putrefactive effects of gastrointestinal metabolism that contributed to illness and aging. Fecal microbiota transplantation documentation dates as far back as a fourth-century Chinese handbook for food poisoning or severe diarrhea. Fecal transplant remains the only cure for Clostridium difficile infections that prevents recurrence, with more efficacy than the antibiotic vancomycin. (Gasbarrini, Bonvicini & Gramenzi, 2016).

The study of probiotics and the effect on health was once ignored by the medical establishment. However, 13 years after the term probiotics was first officially recognized by the scientific community in 2001, an expert panel convened in Europe, and an expert consensus document was finally published on the scope and appropriate use of the term probiotic. It stated, “live microorganisms which when administered in adequate amounts confer a health benefit on the host” (Hill et al, 2014).

Canada and Italy were two of the countries that had already established guidelines for use based on the emerging research on probiotics. Health Canada has accepted the following bacterial species: Bifidobacterium (adolescentis, animalis, bifidum, breve and longum) and Lactobacillus (acidophilus, casei, fermentum, gasseri, johnsonii, paracasei, plantarum, rhamnosus and salivarius) (Hill et al, 2014).

Disorders and Diseases and the Research on Probiotic Therapies

Does oral probiotic supplementation work, or does your stomach acid kill off the beneficial bacteria? The research shows that deliberate and sustained remodeling of the gastrointestinal microbiome was demonstrated in multiple studies deploying different probiotics formulations by oral administration (Hemarajata & Versalovic, 2013; Hill et al, 2014; Hseih & Versalovic, 2008). It should be mentioned that some of these formulations also included prebiotics, which are carbohydrates that are not digestible by the human body but are beneficial nutrients for probiotic organisms.

Most probiotics fall into the group of organisms known as lactic acid-producing bacteria. Some of the beneficial effects of lactic acid bacteria consumption include:

  • improving intestinal tract health;
  • enhancing the immune system, synthesizing and enhancing the bioavailability of nutrients;
  • reducing symptoms of lactose intolerance, decreasing the prevalence of allergy in susceptible individuals;
  • reducing risk of certain cancers.

The teeth, tongue, cheek, and gums within the oral cavity are colonised by distinct microbial communities, playing a vital role in digestion and the immune system as the gateway to the human body (Dewhirst et al, 2010). Some researchers suggest that the oral microbiome influences the development of cavities and dental decay. There is a publicly-accessible and expanding database dedicated just to the human oral microbiome that can be found here: http://www.homd.org/

A large and well-documented body of research shows that probiotic therapy benefits a diversity of diseases and disease-symptoms (Hemarajata & Versalovic, 2013; Hill et al, 2014):

  • infectious and antibiotic-associated diarrhea;
  • gut transit;
  • Irritable Bowel Syndrome (IBS);
  • abdominal pain and bloating;
  • ulcerative colitis;
  • necrotizing enterocolitis, a fatal disease that causes severe inflammation and destroys the bowels of newborns and premature infants;
  • may restore the composition of the gut microbiome and introduce beneficial functions to gut microbial communities, resulting in amelioration or prevention of gut inflammation.

Probiotics also may have the ability to treat obesity, and this possibility is gaining attention due to evidence of the gut microbiota’s role in energy homeostasis and fat accumulation. Probiotics interact with existing bacterial residents in the gut by altering their properties, which may also affect metabolic pathways involved in fat metabolism regulation (Arora, Singh & Sharma, 2013).

The gut-brain axis is a term used to describe the closely interconnected physiological systems of the enteric nervous system in the digestive tract and the central nervous system. The axis enables two-way communication between the two, linking the brain’s emotional and cognitive centers with peripheral functions in the intestines (Saulnier, 2013). More recent evidence suggests that the gut–brain axis functions to support neuron development and neurological system maintenance, while gut dysbiosis, or imbalance in the microbiome, manifests in neurological disease (Westfall et al, 2017).

Frontiers in Nutritional Psychiatry

The field of psychiatry is transforming. This is due to the explosion of data supporting the beneficial effects of probiotic therapies in health conditions related to digestion and inflammation. The current revolution comes from the wave of the rapidly accumulating knowledge of how inflammation, microbiome imbalance (gut dysbiosis), oxidative stress, and impaired cellular mitochondrial output can affect brain function (Kaplan, Rucklidge, Romijn & McLeod, 2015).

Clinical studies using animal models indicate that the administration of beneficial microbes, via supplementation and/or fecal microbial transplant, can influence mood state, brain function, and mental outlook (specifically depression and anxiety). Benton, Williams and Brown (2007) found that initially depressed participants experienced improved mood from drinking a probiotic-containing milk beverage for three weeks. An unrelated pilot study of chronic fatigue syndrome patients who were administered an oral Lactobacillus casei probiotic for 8 weeks found a significant improvement in anxiety (but no depression improvement).

Using a variety of validated anxiety, stress, and depression scales, French researchers reported significant improvements in daily depression, anger, anxiety, and lower levels of the stress hormone cortisol among otherwise healthy adults taking a daily Lactobacillus helveticus and Bifidobacterium longum combination probiotic supplement (Messaoudi, 2011). Thus, specific probiotic strains may have specific ranges of effect on mood that are similar to those observed with SSRI medications. Soon enough, we may receive a prescription for a probiotic rather than an SSRI when we seek psychiatric help.

Probiotics for Disbiosis

Probiotics have been neglected in the past due to a lack of rigorous research methods. Due to the mapping of the microbiome, research methods have improved. Epidemiological studies demonstrate increased risk of depressive symptoms in healthy adults with blood chemistry that indicates insulin resistance. Intestinal microbiota, via a number of mechanisms, play a role in mediating the mood-related effects of diet.

The development of antibiotic-resistant infections, in an era where chronic disease processes are the leading causes of disease and death, demonstrates the necessity of exploring treatment options available through probiotic therapies. Probiotics are now recognized as a necessary part of treatment, especially following a course of antibiotic therapy. Please consult your healthcare provider for guidance if you have questions or concerns.


Arora, T., Singh, S., & Sharma, R. K. (2013). Probiotics: interaction with gut microbiome and antiobesity potential. Nutrition, 29(4), 591-596. http://www.nutritionjrnl.com/article/S0899-9007(12)00321-8/abstract

Bagchi, T. (2014). Traditional food & modern lifestyle: Impact of probiotics. The Indian Journal of Medical Research, 140(3), 333–335. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248377/

Benton, D., Williams, C., & Brown, A. (2007). Impact of consuming a milk drink containing a probiotic on mood and cognition. European journal of clinical nutrition, 61(3), 355. https://www.ncbi.nlm.nih.gov/pubmed/17151594?dopt=Abstract

Bested, A. C., Logan, A. C., & Selhub, E. M. (2013). Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: part III–convergence toward clinical trials. Gut Pathogens, 5(1), 4. https://gutpathogens.biomedcentral.com/articles/10.1186/1757-4749-5-4

Davis, R. (2015). The Doctor Who Championed Hand-Washing And Briefly Saved Lives. https://www.npr.org/sections/health-shots/2015/01/12/375663920/the-doctor-who-championed-hand-washing-and-saved-women-s-lives

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