Benefits of Spore-Forming Probiotics
By Thomas G. Guilliams, PhD

In the past two decades, there have been few areas of research that have expanded as greatly as that which explores the importance of the human microbiome(s), especially the nuanced relationship between the bacteria in the GI tract and their human host. It is not uncommon to see papers published, weekly, showing the potential connection between metabolic activity within the gut microbiome and some important human pathophysiology.

For the clinician, this research is welcome news, confirming years of intuition and clinical experience. At the same time, it is equally overwhelming to realize that there isn’t an agreed upon definition of an “ideal” gut microbiota and there are limited therapies to help a person create an “ideal” gut microbiota.

Dietary changes, especially the increase in diversity of plant species, is likely the greatest lever in changing the microbiome, but the use of prebiotics and probiotics are also part of a helpful therapeutic strategy for many patients (as is the avoidance of unnecessary antibiotics). However, since commercially available probiotics represent a very small subset of GI organisms, the more recent availability of spore-forming probiotics offers the clinician additional therapeutic options for GI and other conditions.

While the vast majority of probiotic research has focused on Lactobacilli, Bifidobacterium, and even the yeast probiotic Saccharomyces boulardii; there has been a growing interest in the use and research of the spore-forming Bacilli species (i.e., B. coagulans, B. clausii, B. subtilis, B. indicus). Bacillus species are ubiquitous in nature (almost all are isolated from the soil, water, dust and air) and have a wide range of characteristics, secondary metabolites and enzymatic activities.

For instance, the B. subtilis strain natto is used in the fermentation of soybeans to make the Japanese food natto. Vegetative cells of this strain produce a serine protease, nattokinase, which is used as a dietary supplement for reducing blood clotting via fibrinolysis. In addition, Bacilli produce many structurally heterogeneous secondary metabolites (e.g., antibiotics, lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, lipoamides, isocoumarins, etc.) that have diverse physiological effects. Some Bacillus species (e.g., B. indicus, B. firmus, etc.) have even been shown to produce carotenoids which are likely to absorb in humans.

As with the more commonly studied probiotics, research into Bacilli spp. supplementation has been evaluated for a number of therapeutic uses, primarily GI-related dysfunctions. Limited, but promising, results have been published for outcomes such as gut microbiome alterations, irritable bowel syndrome (IBS), diarrhea (idiopathic, IBS-related), bowel discomfort, constipation, a range of functional bowel disorders, as well as a number of non-GI conditions. Again, while some of these studies are limited and preliminary, they are consistent with many of the published evidence of many other “established” probiotics.

As the pantheon of available organism which function as probiotics grow, including the addition of spore-forming Bacilli, it is important to remember that each species shouldn’t be viewed as “better” than another. In many cases, different species perform similar roles in the GI tract (when consumed as a supplement) and each may also have unique biological activities.

Research suggests that each individual may benefit differently to particular supplemented strains, depending on their baseline microbiota. Therefore, while we are glad to welcome spore-forming probiotics into the fold of microbiome therapies, though it is important to remember that they help to expand a wide-range of effective therapies, most of which are already well established.

More on this topic and access to the studies mentioned in this blog post can be found in Dr. Guilliams’ monograph, “The Role of Probiotics as Effective Therapies for Dysbiosis and GI Dysfunction.” Now available for free download!


Thomas G. Guilliams, PHD Headshot
Thomas G. Guilliams, PhD

Thomas G. Guilliams Ph.D. (Tom) earned his doctorate in molecular immunology from the Medical College of Wisconsin in Milwaukee. For the past two decades, he has spent his time investigating the mechanisms and actions of lifestyle and nutrient-based therapies, and is an expert in the therapeutic uses of dietary supplements. Tom serves as an adjunct assistant professor at the University of Wisconsin- School of Pharmacy and was the VP of Science for Ortho Molecular Products for 24 year (he now serves them as a consultant). Since 2014 he has been writing a series of teaching manuals (Road maps) that outline and evaluate the evidence for the principles and protocols that are fundamental to the functional and integrative medical community.  He is the founder and director of the Point Institute, an independent research and publishing organization that facilitates the distribution of his many publications. A frequent guest-speaker, Dr. Guilliams provides training to a variety of health care disciplines in the use of lifestyle and natural medicines.He lives in the woods outside of Stevens Point, Wisconsin with his wife and children.