Everything you wanted to know about probiotics
By Dr. Debby Hamilton, MD, MPH
By Dr. Debby Hamilton, MD, MPH
The microbiome is the ecosystem of microorganisms living within the body. While there are different microbiomes in different areas of the body, the most well-studied is the microbiome in the digestive tract. More probiotic, beneficial bacteria inhabit this microbiome than we have cells in our entire body, which means the gut microbiome is incredibly complex and vital to our overall health and wellness.
The beneficial bacteria in our gut microbiome are essential to a balanced immune system, digestion, regulation of the gastrointestinal system, and regulation of gut inflammation. By occupying space and producing vitamins and natural antimicrobial compounds, they protect the body against pathogens, infections, and dysbiosis.
Because the American diet has increased intake of processed foods, along with the over-prescription of antibiotics, many people discover they have a disruption in their microbiome, leading to a decrease in essential beneficial bacteria. A decrease in probiotic bacteria can result in dysbiosis, a concomitant increase in pathogenic bacteria, and an overgrowth of yeast. Dysbiosis can lead to an imbalance of the immune system, with a decrease in immune tolerance and an increase in the risk for autoimmune disease. Dysbiosis is also an inflammatory state, which is known to contribute to the development of autoimmune diseases and chronic digestive issues.
As we discover more about the importance of the microbiome, research continues to indicate the value of probiotics.
Because of the challenges of our diet and environment, it is essential to supplement these beneficial probiotic bacteria to maintain a healthy microbiome. Fermented foods and yogurts are a viable option. However, these natural sources may not provide enough probiotics for people with more severe health complications such as chronic digestive issues. Therefore, it is important to understand the various benefits offered by probiotics so that patients can adequately supplement based on their needs.
There are two types of probiotics available: food-based probiotics and spore or soil-based probiotics.
Spore-based probiotics are primarily of the Bacillus family. Spore-based bacteria are named for their hard outer shell, the spore, which helps them survive in harsher environments, such as soil. The spore protects against water, heat, as well as other microbes.
When protection from the environment is not needed, the bacteria shed the spore and behave like any other bacteria. When spore-based probiotics are ingested, the spore protects the bacteria from both the stomach acid and the bile acid so that they can easily pass into the intestine, where they can colonize. Once in the intestines, these bacteria lose their spore form and colonize.
Spore-based probiotic bacteria play many roles in supporting the health of the gut. While a relatively recent addition to probiotic supplements, spore-forming probiotics have always been familiar residents of a healthy microbiome. Two of the most well-known and researched spore-based probiotic bacteria are Bacillus coagulans and Bacillus subtilis. Bacillus subtilis, for example, was discovered in 1915 and was used as therapy for gastrointestinal and urinary tract illnesses prior to the discovery of antibiotics. Bacillus subtilis has been found to produce 66 anti-bacterial compounds. Multiple studies have shown that by colonizing the GI tract, soil-based probiotics may support digestive issues such as irritable bowel syndrome, diarrhea, and constipation.,,Once spore-based probiotics colonize the intestine, they compete for space and crowd out harmful pathogenic bacteria. In addition to physically crowding out other microorganisms, they produce lactic acid, which is anti-bacterial and inhibits harmful bacteria from increasing. They are also known to promote the growth of other beneficial bacteria, such as lactobacillus and bifidobacterium.3
Spore-based probiotics have been found to support many functions, such as positive changes in microbiome and metabolism, support for metabolic blood sugar issues, and support for immune function.,
Food-based probiotics are primarily of the Lactobacillus and Bifidobacterium family. Occasionally, Streptococcus species (such as Streptococcus thermophilus from yogurt cultures or Streptococcus salivarius) are utilized in supplements. Both Lactobacillus and Bifidobacteria species are non-spore forming, gram-positive bacteria that are a stable component of the microbiome. Colonization of the microbiome by both species occurs during vaginal birth. They are also present in fermented foods and dairy products, which is why they are referred to as “food-based” or “dairy-based” probiotics. An imbalance of either of these groups of bacteria can lead to dysbiosis, which is associated with multiple health conditions, ranging from digestive disorders to immune complications such as autoimmunity.
Fermented foods have been part of many cultures’ diets because they contain natural probiotics and offer many health benefits. With modern diets decreasing consumption of fermented foods, increasing consumption of processed foods, and over-utilizing antibiotics, many people have lower levels of beneficial bacteria. As with soil-based probiotic bacteria, Lactobacillus and Bifidobacteria produce beneficial compounds that support the microbiome. Lactobacillus, as the name suggests, excretes lactic acid by fermenting sugars. Bifidobacteria produce short-chain fatty acids, which are essential for maintaining the balance in the microbiome.
Lactobacillus Rhamnosus GG is one of the most studied probiotics, with over 800 published studies, including approximately 200 clinical studies. It has a higher survival rate through the gastric juice compared to some other Lactobacillus and Bifidobacterium species. While in the intestine, it has good adhesion to intestinal epithelial cells and increases the secretion of protective mucins. L. Rhamnosus GG supports the immune system, and research indicates it can support the reduction of eczema and allergies. Multiple studies have also shown L. Rhamnosus GG to improve digestive symptoms ranging from abdominal pain to diarrhea., Lactobacillus Salivarius has also been found to have immunomodulating properties, specifically supporting regulatory T cells (Treg) and IL-10, which help improve immune tolerance.
Bifidobacteria strains are some of the first strains that inhabit the digestive tract for infants and help establish a healthy microbiome. As with Lactobacillus, Bifidobacteria strains have shown efficacy in supporting immune and digestive function.,  Bifidobacteria Lactis specifically is known as one of the strongest for immune support.17 It has also been studied for supporting the intestinal microbiota during antibiotic therapy.
The importance of the microbiome and its impact on our immune system, our response to infections, our digestion, and even our mental health is well researched. Because our diet and environmental exposures often harm our microbiome, it is crucial to ensure proper supplemental support with a broad range of probiotic bacteria.
 Hyronimus B. et al. Acid and bile tolerance of spore-forming lactic acid bacteria. In J Food Microbiol 2000.
 Novelli A. et al. Bacillus subtilis spores as a natural pro-host oral agent. Preliminary data in children Chemioterapia. 1984; 3:152–155.
 Awais Et al . Production of antimicrobial metabolites by Bacillus Subtilis immobilized in polyacrylamide gel. J Zool. 2010 42(3): pp 267-275.
 Mu Y, Cong Y. Bacillus coagulans and its applications in medicine. Benef Microbes. 2019. 10(6):679-688.
 Hun, L. Bacillus coagulans significantly improved abdominal pain and bloating in patients with IBS. Postgrad Med. 2009.121:119-124.
 Majeed M. et al. Bacillus coagulans MTCC 5856 supplementation in the management of diarrhea predominant Irritable Bowel Syndrome: a double blind randomized placebo controlled pilot clinical study. Nutr J. 2016 Feb 27; 15:21. doi: 10.1186/s12937-016-0140-6.
 Labellarte, GM. et al Tolerance and Efficacy of the Probiotic DE-111™ Delivered in Capsule Form.. Department of Biology, University of Wisconsin- La Crosse.
 Sudha, R.M. et al. Effect of supplementation of Bacillus coagulans Unique IS-2(ATCC pat-11748) on hypercholesterolemic subjects: a clinical study.. Inter. J. Probiotics Prebiotics. 2011. 6(2):89-94.
 Gerritsen J. et al.Intestinal microbiota in human health and disease: the impact of probiotics. Genes Nutr. 2011 Aug; 6(3):209-40.
 Well JM. Immunomodulatory mechanisms of lactobacilli. Microb Cell Fact. 2011 Aug 30; 10 Suppl 1():S17.
 Tojo R. et al.Intestinal microbiota in health and disease: role of bifidobacteria in gut homeostasis. World J Gastroenterol. 2014 Nov 7; 20(41):15163-76.
 Kalliomaki M. et al., (2003), ‘Probiotics and prevention of atopic disease: 4-year follow-up of a randomised placebo-controlled trial’. Lancet, 361:1869-71.
 Arvola T. et al., (1990), ‘Prophylactic Lactobacillus GG reduces antibiotic-associated diarrhea in children with respiratory infections: a randomized study’. Pediatrics, 104(5):e64.
 Gawroska A. et al., (2007), ‘A randomized double-blind placebo-controlled trial of Lactobacillus GG for abdominal pain disorders in children’. Aliment Pharmacol. Therapy, 25: 177-84.
 Petersen ER, Claesson MH, Schmidt EG, Jensen SS, Ravn P, Olsen J, Ouwehand AC, Kristensen NN. Consumption of probiotics increases the effect of regulatory T cells in transfer colitis. Inflamm Bowel Dis. 2012 Jan;18(1):131-42. doi: 10.1002/ibd.21709. Epub 2011 Apr 14. PMID: 21495121.
 Lee JH, O’Sullivan DJ. Genomic insights into bifidobacteria. Microbiol Mol Biol Rev. 2010;74(3):378-416. doi:10.1128/MMBR.00004-10.
 Paineau D., et al., (2008). ‘Effects of seven potential probiotic strains on specific immune responses in healthy adults: a double-blind, randomized, controlled trial’. FEMS Immunology & Medical Microbiology, 53 (1):107–113.
 Ringel Y. et al., (2008). ‘Probiotic bacteria Lactobacillus acidophilus NCFM® and Bifidobacterium lactis Bi-07 improve symptoms of bloating in patients with function bowel disorders (FBD)’. J. Clin. Gastroenterology,45(6):518–525.
 Engelbrekston, AL, et al (2009) ‘A randomized, double blind, controlled trial of probiotics to minimize the disruption of fecal microbiota in healthy subjects undergoing antibiotic therapy’. Journal of Medical Microbiology, 58:663-670.