Module 5: Acupuncture for the Treatment of Intestinal Permeability/ Gut Dysbiosis in Autoimmunity

Evidence is increasingly supporting Hippocrates’ two thousand year old claim that ‘all disease begins in the gut.’ In recent years, research has uncovered novel insights into the relationship between the gut and health, elucidating mechanisms by which the microorganisms that inhabit the gut interact with the immune system, exerting helpful or harmful effects on our health and wellbeing. Two primary components of gut health – the microbiota, or microbial composition of the gut, and gut barrier integrity, the loss of which is termed ‘intestinal permeability’ or more colloquially, ‘leaky gut’ – are of particular interest in the realm of autoimmunity.

The Microbiome

The gut microbiota is home to the largest repository of bacteria in the body, and its inhabitants outnumber human cells 10:1.56,57 Under healthy conditions, the gut is largely populated by commensal bacteria58 – microorganisms which derive benefit from the host without directly affecting it – and as we will see below, is equipped with numerous mechanisms, both mechanical and biochemical, that fortify it from pathogenic invasion. Alterations in gut flora composition and function, often referred to as ‘gut dysbiosis,’ have been associated with numerous disease states, including metabolic syndrome, obesity, diabetes, malignancy, and allergic conditions.56,59 Gut dysbiosis has also been implicated in autoimmune disease, perhaps unsurprisingly, given that the microbiota serves as an important hub for immune system development and maintenance. The microbiota directly impacts the immune system, and therefore can influence the rest of the body in a profound way – so profound that the transfer of unhealthy microbes to a healthy host has been shown to transfer susceptibility to autoimmune disease!56,59 Specifically, the microbiota play a critical role in bacterial recognition as well as in differentiation of Th cell subsets, therefore influencing the production and proliferation of inflammatory and anti-inflammatory Th cells and their cytokines.59 For instance, pathogenic gut bacteria have been shown to promote the differentiation of Th cells into the inflammatory Th17 type over the anti-inflammatory, immune suppressing Treg type; Th17 cells produce IL-17, which has been associated with the development of numerous animal models of autoimmune disease, namely Collagen Induced Arthritis (proxy for Rheumatoid Arthritis), Experimental Autoimmune Encephalitis (proxy for Multiple Sclerosis), and Non Obese Diabetes (proxy for T1DM).59  When the connection between the gut microbiota and immune system is disrupted, the ensuing inflammatory cascade and break in the immune system’s tolerance of the microbes that comprise the gut flora can contribute to the onset of autoimmunity.56 


Gut dysbiosis can develop in several ways. The previously-mentioned hygiene hypothesis attributes the lightened infectious disease burden and concomitant increase in autoimmune and allergic diseases in recent decades to improved sanitation practices that have accompanied ongoing westernization. The microbiome is highly influenced by lifestyle factors, not the least of which is hygiene, and studies of germ free (GF) animals have borne out this connection. Studies have repeatedly and reliably demonstrated that animals raised in GF conditions (or rendered germ free through dietary and pharmacological interventions) have impaired immune system development; of relevance to autoimmunity, GF animals display altered antibody production and T cell differentiation, potentiating the production of aberrant immune cell development and proliferation.8,59 Supporting this observation is the increased prevalence of Type 1 Diabetes (T1DM) in countries with enhanced hygiene and sanitation practices, relative to less westernized neighboring nations.58 Interestingly, the implantation of GF mice with a single species of commensal bacteria has been shown to stimulate the production of Tregs, which produced IgE that yielded a protective effect from inflammatory colitis.59 Though not pertaining to an outright disease state, the transfer of gut flora from both obese and lean hosts to GF mice has been to shown to lead to obesity among mice receiving microbes from obese volunteers, while mice receiving microbes from lean volunteers remained lean.56,57,58 Furthermore, the microbiome has been shown to be influenced by stress and to itself influence behavior, as an animal model of chronic unpredictable stress demonstrated reductions in lactobacillus that induced despair behavior and was reversed by the administration of a lactobacillus-containing probiotic.60 Taken together, these findings illustrate the extent to which gut microbes can influence health and disease.


Another lifestyle factor which directly and profoundly influences the composition and function gut flora is diet. Though the virtues of vegetable rich diets have long been extolled by health-conscious eaters, a mouse study highlights just how impactful vegetables – or lack thereof – can be on the gut flora, and by extension, the health of the immune system. In this model, mice that switched from a standard animal feed diet to a synthetic one bereft of vegetable matter had reduced lymphocyte counts in endothelial tissue, heightened susceptibility to endothelial damage and increased intestinal levels of colitis-inducing bacteroidetes.58  In another nod to vegetables, plants are the preferred energy substrate of beneficial bacteria in the gut; a plant-rich diet not only promotes the survival and proliferation of beneficial bacteria but also promotes resistance to harmful bacteria.8 Short chain fatty acids (SCFA’s), which are produced through intestinal microbes’ fermentation of dietary fiber, have been shown to impact immune function.56,58 Inadequate amounts of SCFA’s are associated with altered immune responses, and the onset of inflammatory bowel disease (Crohn’s and Ulcerative Colitis). Butyrate, a SCFA, is particularly pertinent to immune function, as it regulates macrophages and induces differentiation of Tregs.56 Other foods with demonstrated correlations to autoimmune disease include cow’s milk and T1DM, iodine and Hashimoto’s Thyroiditis, and high fat/sugar intakes and Crohn’s and Ulcerative Colitis.56 Furthermore, dietary emulsifiers and artificial sweeteners have been shown to shift the microbiota of GF mice to that a profile resembling metabolic syndrome, itself a risk factor for a number of chronic inflammatory diseases.56


In light of the demonstrated affects of food on the gut flora, it should come as no surprise that medications are also capable of influencing the microbiota. In particular, antibiotics have been shown to alter the balance of microbes in the gut in such a way that reduces beneficial bacteria and renders the host vulnerable to infection.8 Antibiotics can encourage a shift in gut flora that favors highly inflammatory Th17 responses; Th17 profiles and the cytokine they produce, IL-17, are associated with numerous inflammatory and autoimmune conditions.8 Though undoubtedly a life-saving intervention when medically necessary, overzealous prescribing of antibiotics can also be problematic for a chronically-ill population, as their non-specific immune suppressing effects can lead to symptom exacerbation and increased vulnerability to pathogenic invasion, not to mention antibiotic resistance.56

Birth, Infancy, and Pregnancy

A perhaps less-appreciated but equally significant influence on gut flora is the period comprising delivery and early infancy. An infant’s first exposure to the world follows its emergence from the vaginal canal; it is then unsurprising that infant microbiomes are largely informed by the vaginal flora of their mothers, and that babies delivered via C-section are predisposed towards autoimmune disease more so than vaginally-delivered babies.59 C-section infants have 20-30% higher risk of developing autoimmune disease and obesity,56 and, along with formula-fed babies, have been shown to have skewed, disease-favoring ratios of beneficial to pathogenic bacteria.8 Illustrating this point, mice raised in non sterile environments had a 10% incidence rate of T1DM, while mice decontaminated at birth via C-section and raised in sterile conditions yielded strikingly higher incidence rates of T1DM – to the tune of 90% – within only one generation.59 Though the microbiota may be influenced by the above-discussed factors – diet, medication – throughout the lifetime, it is largely fixed as of the first week of life, and will revert to its baseline composition and function following periodic insults and provocations, underscoring the importance of this critical time in an infant’s life.59

No discussion of delivery and early infancy could be considered complete without acknowledging the importance of the mother during the gestational period. The shift in immune system profile towards Th2 dominance during pregnancy can have profound implications for autoimmune disease patients, with sufferers of Th1 conditions often experiencing symptom remission during pregnancy and symptom exacerbation following delivery, and sufferers of Th2 conditions enduring flares throughout gestation, each scenario posing implications for the inflammatory burden of the mother. With respect to the gut flora during pregnancy, variations in microbial composition are seen from trimester to trimester, with the third trimester representing the greatest threat, as certain species of bacteria associated with inflammatory diseases are elevated during this time.56 Moreover, increased levels of inflammatory cytokines such as IFN-γ, IL-2, IL-6, and TNF-α have been reported in the stool of 3rd trimester patients relative to women in their 1st trimester.56


Lastly, genetic factors can mediate the relationship between the gut flora and autoimmunity. ‘Genetic dysbiosis,’ the study of the effects of genes on the microbiome’s composition and function, has in recent years occupied a growing area of interest, as the scientific and medical communities increasingly acknowledge the influence of genetic variation on the immune system’s intersections with the microbiota. Single nucleotide polymorphisms – or SNP’s – are variations in DNA sequences that encode genes involved in the differentiation of B and T cells; associations have been made between certain SNP’s involved in immune system function and autoimmune disease, with mutations shown to be related to T1DM, RA, Lupus, and Crohn’s.56 While some genes associated with susceptibility to autoimmune disease have been shown to influence the composition of the microbiota, the relationship is bi-directional, as gut microbes have the capacity to alter and disrupt gene transcription and translation, as well as downstream metabolic processes,8 evidencing a ripple effect that can have profound implications for immune health and function.

Intestinal Permeability

Previously, we’ve discussed numerous instances in which a body under healthy, physiological circumstances is equipped to withstand infection or injury but chronic illness, autoimmunity in particular, disrupts the normal protective mechanisms that would maintain homeostasis, leading to downstream effects such as unchecked inflammatory and stress hormone cascades. Intestinal permeability is yet another mechanism that illustrates this point. Intestinal permeability denotes a breach of the wall that separates the gut from the rest of the body; when the epithelial tissue lining the gut suffers a loss of integrity and becomes permeable, food proteins travel into the bloodstream where the immune system may recognize them as foreign antigens and activate an immune response.57,60 Antigens circulating in the body are typically prohibited from reaching the gut by the intestinal epithelial wall; a healthy intestinal barrier prohibits all but a fraction of one percent of the body’s antigens from reaching the inner layers of the gut lining. Those antigens that do manage to breach the intestinal barrier have the potential to stimulate systemic immune responses;57 to that end, the more permeable the gut lining, the greater the potential for immune activation and heightened immune responses, possibly contributing to autoimmunity. Intestinal permeability has been linked to numerous autoimmune diseases,57,60 including ulcerative colitis, Crohn’s disease, celiac disease, ankylosing spondylitis, juvenile onset arthritis, psoriatic arthritis, primary biliary cirrhosis, and Type 1 Diabetes Mellitus.61 An interesting observation and potential explanation for the tendency of autoimmune diseases to cluster in families is the increased incidence of intestinal permeability in not only T1DM patients but also among their first degree relatives, relative to healthy controls.57

The integrity of the gut barrier is regulated by a class of proteins called Tight Junction Proteins (TJP’s), which open and close the junctions between the cells of the epithelial wall, and mucins, proteins secreted by epithelial cells, forming a protective layer that shields the gut from outside antigens.57 Whereas commensal intestinal bacteria have been shown to promote intestinal barrier health through colonization resistance, the presence of unhealthy gut flora can predispose a host to intestinal permeability; for instance, T1DM patients have been shown to have decreased levels of certain types of bacteria that produce mucin, therefore rendering them vulnerable to antigenic exposure.57 Other contributors to intestinal permeability include parasites, inflammatory cytokines, industrial food additives, dietary peptides and lectins, enzymes, neurotransmitters, free radicals and malfunctioning Tregs.61 As was the case for microbiota composition and function, the role of diet is not to be understated here; the virtuous short chain fatty acids (SCFA’s) mentioned previously also partake in the preservation of intestinal barrier integrity, with butyrate in particular playing a beneficial role through mucin synthesis, strengthening of TJP’s and reducing transport of bacteria across the epithelial lining.74

Serving as yet another example of the interconnectedness between the gut, and the immune and nervous systems is the enteric nervous system (ENS), which operates as a branch of the nervous system living within the gut that regulates gastrointestinal function. The ENS is comprised of enteric neurons and enteric glial cells (EGC’s), the latter of which are of interest owing to their capacity for regulating blood flow, gastrointestinal motility, nutrient absorption and secretion, and most importantly, modulating immune and inflammatory processes within the gut.62 While research on EGC’s as it relates to autoimmunity has thus far focused on the autoimmune gastrointestinal disorders Ulcerative Colitis and Crohn’s Disease, it would not be unreasonable to suspect some involvement of EGC’s in other autoimmune conditions, particularly those in which intestinal permeability and gut dysbiosis have been implicated, as EGC’s have been shown to strengthen tight junction proteins and intestinal epithelial cells, and preserve intestinal barrier integrity by inhibiting a major transcription factor involved with gut barrier dysfunction, NF-kappa-B.36


While the role of acupuncture in treating functional gastrointestinal disorders is well supported by research demonstrating its capacity for promoting gastrointestinal motility and alleviating visceral pain,55 research on acupuncture in the realm of the microbiota and intestinal permeability is still in a nascent stage. That said, a number of animal research models have illustrated the protective effect of acupuncture on various components of microbiome composition and function, as well as gut barrier integrity; their results are described below.


Several studies in which hemorrhagic shock was induced to simulate disruption of the gut barrier have shown acupuncture to be effective in the reduction of both intestinal and systemic inflammation that follows a breach in the gut barrier.29,32,36,62 Specifically, acupuncture was able to reduce IL-6, an inflammatory cytokine believed to be critical for the development of gut barrier dysfunction.29 In both animal and human studies, acupuncture reduced inflammatory marker TNF-α,32,36 and among Crohn’s Disease patients decreased levels of IL-12, an inflammatory cytokine that stimulates the secretion of IFN-γ and TNF-α, which collectively alter gut barrier function and promote intestinal permeability.32 In human studies of Inflammatory Bowel Disease (IBD) Crohn’s Disease and Ulcerative Colitis, both patient populations indicated significant inflammation in affected areas of the intestinal tract which was markedly reduced following acupuncture treatment.32,62 These demonstrated anti-inflammatory effects of acupuncture are particularly salient as they represent a means of disrupting the vicious cycle of gut barrier dysfunction provoking an immune response, which stimulates production of inflammatory cytokines that further stimulate immune reactivity and cause intestinal epithelial damage.32 Results illustrated by a mouse model of endotoxemia, in which acupuncture reduced elevations in TNF-α and IL-8 in the intestines as well as the lungs, liver, and blood,37 further support the inclusion of acupuncture in the treatment of patients with chronic inflammatory and autoimmune disorders, as it attenuates not only local but also systemic inflammation. This poses an important implication for such patients, as in many cases they do not receive acupuncture in the early stages of disease at which point inflammation may be more localized and responsive to treatment, instead seeking acupuncture treatment once disease has progressed to the point of having significant and widespread inflammation.

Intestinal Injury

The autoimmune Inflammatory Bowel Diseases Crohn’s Disease and Ulcerative Colitis are characterized by not only inflammation, but also damage to the layers of tissue lining the gut. Whereas tissue damage is generally relegated to the large intestine in Ulcerative Colitis, Crohn’s Disease can feature damage at any point along the digestive tract, from the mouth to the anus. Two studies referenced above with regard to inflammation also looked at the effects of acupuncture on intestinal injury among Crohn’s Disease patients and rats with Ulcerative Colitis, finding that acupuncture combined with moxibustion, an adjunctive treatment involving the burning of a therapeutic herb on or near an inserted needle, decreased intestinal injury by blunting morphological changes significantly relative to untreated controls.32,62 All study subjects prior to treatment displayed moderate to severe morphological disturbance in intestinal tissue; acupuncture improved tissue structure and texture, reduced edema, congestion, and erosion, and in the case of Ulcerative Colitis, induced growth of epithelial cells over ulcers, promoting ulcer recovery.32,62 In the above mentioned mouse model of endotoxemia, acupuncture attenuated intestinal injury resulting from endotoxin-induced ischemia, indicating only minimal histological changes to intestinal tissue, significantly less than that of sham and untreated controls.37

Intestinal Permeability

More broadly relevant to the wider spectrum of autoimmune is the demonstrated capacity for acupuncture to promote gut barrier integrity and reduce intestinal permeability. Acupuncture preserves gut barrier integrity in two primary ways: by mediating expression and function of both tight junction proteins (TJP’s) and enteric glial cells (EGC’s).29,36,37,62 Specifically, acupuncture has been shown to increase levels of TJ’s zonulin (ZO-1), occludin, and claudin, enhance mRNA expression of TJP’s, preserve the structure and distribution of existing TJP’s, and attenuate further loss and redistribution of TJP’s owing to disease progression.29,36,37,62 With regard to EGC’s, acupuncture, in a mouse model of hemorrhagic shock, indicated greater activation of EGC’s relative to sham and untreated controls, along with greater mRNA expression of glial fibrillary acidic protein (GFAP), a protein responsible for EGC activation, relative to sham and untreated controls.36

Gut Dysbiosis

Research studies elucidating the influence of acupuncture on intestinal inflammation and permeability have also recently begun to shed light on its potential for modulating the gut flora. It is not uncommon for sufferers of Ulcerative Colitis to have decreased levels of bifidobacteria and lactobacillus,32 a rat model of Ulcerative Colitis demonstrated exactly that, along with increased levels of harmful B. fragilis and E. coli, relative to healthy controls. Following acupuncture treatment, the Ulcerative Colitis rats display increased levels of bifidobacteria and lactobacillus strains, and decreased levels of B. fragilis and E. coli.32 Acupuncture effectively modulated gut flora in such a way that restored balance to previously dysbiotic gut profiles, therefore attenuating the progression of pathology in the gut.32 A study examining the effects of acupuncture on obesity looked at gut flora as a secondary measure, finding that acupuncture significantly increased levels of bifidobacteria and lactobacillus among thirty obese women.63 Aside from achieving marked reductions in BMI and improving deficiencies in gut flora composition relative to controls, acupuncture reduced levels of pathogenic bacteroides, thought to promote obesity by causing the body to absorb and store more calories from food.63 Given that alterations in bacteroides have been shown in T1DM, Ulcerative Colitis and Crohn’s Disease32,58,62 these preliminary findings represent a novel application for acupuncture in the treatment of autoimmune disease.


Taken together, the weight of the evidence suggests a role for acupuncture in addressing  intestinal inflammation and permeability and gut dysbiosis recognized as contributing factors in autoimmune pathogenesis and disease progression. While the research studies that informed this discussion have been largely short-term interventions, knowledge of acupuncture’s long term effects on gut and immune health is insufficient to recommend it categorically; rather these examples serve to illustrate the potential for acupuncture to support a comprehensive approach to autoimmune disease management, including stress management practices, conscious diet and lifestyle practices, often aided by pharmacological therapy.