Sanesco Blog

Inflammation and the Microbiome


Inflammation of the gut: what are the consequences? With a population of over 100 trillion cells, our bodies’ microbiome outnumbers the cells that make up each of us and play a crucial role in our health and well-being. An increasing amount of research connects gut microbiota to behavior, immunity, and inflammatory diseases, such as auto-immune diseases, allergies, inflammatory bowel disease (IBD), cancer, and cardiovascular disorders.[1],[2] The microbial ecosystem within us is often referred to as a “super organ,” because of its connections to several body systems.[3] This complex system has evolved alongside our immune system and the two function in tandem to combat pathogens and keep us alive and healthy.[4] Our gut microbiota is comprised of trillions of commensal species of bacteria that protect our bodies from pathogens, support digestion, and aid in absorbing essential vitamins and minerals.[5] Although our microbiome is densest in our guts (as opposed to our skin or mouths) it is sensitive to the substances we consume, environmental toxins, and psychological stress. These factors can cause dysbiosis in the gut, when detrimental bacteria or yeast outnumber beneficial microorganisms.[6],[7] Understanding the role symbiotic bacteria play in our immunity and knowing how to re-balance the gut in the event of dysbiosis are keys to alleviating inflammatory disease symptoms.

Microbiota, Inflammation, and Immunity

It is imperative that there be a balance between commensal bacteria and pathogenic bacteria. Dysbiosis can lead to inflammation, local infection, and disruption of gut epithelium.[8],[9] Microbial dysbiosis has been linked to several inflammatory diseases afflicting millions of people in one form or another. A common feature of autoimmune disorders is the increased permeability of the patient’s intestinal tract caused by a loosening of the tight junctions between the cells of gut epithelium.[10],[11] The phenomenon of increased intestinal permeability is known as leaky gut syndrome (LGS).[12] In the past, the pathology and origin of autoimmunity and allergies has had little more than genetic attribution. However, the idea that LGS leads to nonself antigens presenting to the immune system is providing new insight into the pathology of autoimmunity and allergies. Nonself antigens can upregulate the immune system, inducing an inflammatory response to non-pathogenic substances, such as peanuts or pancreatic beta-cells, in the case of Type I Diabetes.[13],[14] Common autoimmune diseases include Type I Diabetes, celiac disease, Hashimoto’s hypothyroidism, and rheumatoid arthritis.[15],[16] In a healthy gut, commensal microbiota support intestinal wall integrity, provide resistance to pathogenic bacteria, and aid in balanced immunity.[17],[18] However, dysbiosis causing a shift in the ratio of commensal to pathogenic microbiota can lead to impaired gut function and immune responses. In fact, a study found that patients with Crohn’s disease had a lower concentration of Faecalibacterium prausnitzi in their intestines. This bacterium is known to play a role in anti-inflammatory responses.[19] It’s been discovered that bacterial species such as Salmonella enterica and Citrobacter rodentium are responsible for initiating immune responses that cause dysbiosis, allowing pathogenic bacteria to take hold of the gut and drive inflammation.[20]

Prevention and Rebalance

Our microbiome is established during gestation and continues to proliferate as we age, which is why it is important to ensure that a resilient and robust population is established from day one.[21],[22] Dr. Janet Teodori, a pediatric neurologist, believes that a mother’s microbial profile heavily influences the microbiome of a developing fetus. Inflammatory conditions, such as obesity and chronic stress, in addition to psychological stress afflict many women of childbearing age. These factors cause disturbances in maternal gut microbiota and can be transmitted during pregnancy. Therefore, it’s crucial for women to take pre-natal actions to build a healthy microbiome and lower inflammation in their own bodies before becoming pregnant.[23]

Dysbiosis can also develop later in life. Evidence suggests that antibiotic use, chronic stress, and consumption of pathogens can disrupt gut microbiota.[24],[25],[26],[27] However, there are therapies to rebalance the gut in the event of dysbiosis. Case studies presented by Vojdani et al. found that administering probiotic supplements along with natural anti-inflammatory compounds, such as vitamin D and boswellic acid, reduced inflammation and alleviated symptoms in patients with multiple sclerosis and celiac disease.[28] In extreme cases of dysbiosis (e.g. C. difficile overgrowth) fecal transplants whereby pathogenic bacteria are removed and a new microbiome from a healthy donor is introduced to the patient have been seen to reduce inflammation and mediate gut balance.[29] Probiotics such as Bifidobacterium infantis 35624, B. longum, and Lactobacillus acidophilus have been found to improve symptoms of irritable bowel syndrome, reduce inflammation, and improve immune function in humans.[30],[31]  Several types of probiotics are available over the counter and ought to be considered when treating a patient with gut dysbiosis and chronic inflammation.


[1] Teodori, J. (2016). Microbiome and fetus: A relationship for life. Journal of Prenatal & Perinatal Psychology & Health, 30(3), 145-167.

[2] Bourzac, K. (2014). The bacterial tightrope. Nature, 516(7529), S14-S16.

[3] Op. cit. Teodori, J.

[4] Brown, E. M., Sadarangani, M., & Finlay, B. B. (2013). The role of the immune system in governing host-microbe interactions in the intestine. Nature Immunology, 14(7), 660-7.

[5] Op. cit. Teodori.

[6] Op. cit. Bourzac, K.

[7] Maranduba, C. M., Castro, S. B., Souza, G. T., Rossato, C., Guia, F. C., Valente, M. A., . . . Silva, F. D. (2015). Intestinal Microbiota as Modulators of the Immune System and Neuroimmune System: Impact on the Host Health and Homeostasis. Journal of Immunology Research, 2015, 1-14.

[8] Op. cit. Brown et al.

[9] Op. cit. Maranduba et al.

[10] Fasano, A. (2012). Leaky gut and autoimmune diseases. Clinical Reviews in Allergy & Immunology, 42(1), 71-8.

[11] Vojdani, A., & Bautista, J. (2012). Intestinal and blood-brain barrier: Interface between health and diseases. Functional Neurology, Rehabilitation, and Ergonomics, 2(3), 277-297.

[12] Op. cit. Fasano, A.

[13] Op. cit. Fasano, A.

[14] Janeway CA Jr, Travers P, Walport M, et al. (2001) Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; Autoimmune responses are directed against self antigens.

[15] Lin, L., & Zhang, J. (2017). Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunology, 18

[16] Op. cit. Vojdani et al.

[17] Hand, T. W. (2016). The role of the microbiota in shaping infectious immunity. Trends in Immunology, 37(10), 647-658.

[18] Op. cit. Lin et al.

[19] Op. cit. Lin et al.

[20] Op. cit. Brown et al.

[21] Op. cit. Brown et al.

[22] Chan, Y. K., Estaki, M., & Gibson, D. L. (2013). Clinical consequences of diet-induced dysbiosis. Annals of Nutrition & Metabolism, 63, 28-40.

[23] Op. cit. Teodori.

[24] Op. cit. Lin et al.

[25] Op. cit. Vojdani et al.

[26] Op. cit. Brown et al.

[27] Op. cit. Teodori, J.

[28] Op. cit. Vojdani et al.

[29] Op. cit. Chan et al.

[30] Op. cit. Lin et al.

[31] Op. cit. Chan et al.


Clinical Contributor

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Disclaimer: The information provided is only intended to be general educational information to the public. It does not constitute medical advice. If you have specific questions about any medical matter or if you are suffering from any medical condition, you should consult your doctor or other professional healthcare provider.


Connie Shoemaker, ND

Connie Shoemaker, ND

“Educating Sanesco’s clients is the culmination of a life’s work.” Beginning when she left the hospital environment to manage a functional laboratory, Genova Diagnostics (formerly Great Smokies Laboratories) in 1987, Dr. Connie Shoemaker has continued to increase her knowledge of herbs and biochemistry as a journey of love. With her bachelor’s in science from Western Carolina University, she had worked in hospital laboratories for the first twelve years of her career. Then, personal health challenges led her to discover a new approach to her health and a determination to share it with others. In 1991, she began teaching and educating innovative practitioners in the U.S. and internationally as a manager of marketing, sales, and customer service.

The addition of her Doctor of Naturopathy degree to her existing knowledge base expanded her knowledge and her respect for a more natural approach to healing through balance. At Sanesco, she initially served to oversee technical development of products and services.

Now, she educates Sanesco’s clients on application of the CSM™ model for their specific patients and how to integrate the CSM™ model with other modalities they offer in their practice. In her personal life, Connie educates private clients on various health topics.

Disclaimer: The information provided is only intended to be general educational information to the public. It does not constitute medical advice. If you have specific questions about any medical matter or if you are suffering from any medical condition, you should consult your doctor or other professional healthcare provider.

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