Gut bacteria potential key to IBD and colon cancer prevention

Authors: Rabina Giri, Emily C. Hoedt, Shamsunnahar Khushi, Angela A. Salim, Anne-Sophie Bergot, Veronika Schreiber, Ranjeny Thomas, Michael A. McGuckin, Timothy H. Florin, Mark Morrison, Robert J. Capon, Páraic Ó Cuív, Jakob Begun

Link to research article: Secreted NF-κB suppressive microbial metabolites modulate gut inflammation: Cell Reports

Media Release:


Emerging evidence suggests that microbiome-host crosstalk regulates intestinal immune activity and predisposition to inflammatory bowel disease (IBD). NF-κB is a master regulator of immune function and a validated target for the treatment of IBD. Here, we identify five Clostridium strains that suppress immune-mediated NF-κB activation in epithelial cell lines, PBMCs, and gut epithelial organoids from healthy human subjects and patients with IBD. Cell-free culture supernatant from Clostridium bolteae AHG0001 strain, but not the reference C. bolteae BAA-613 strain, suppresses inflammatory responses and endoplasmic reticulum stress in gut epithelial organoids derived from Winnie mice. The in vivo responses to Clostridium bolteae AHG0001 and BAA-613 mirror the in vitro activity. Thus, using our in vitro screening of bacteria capable of suppressing NF-κB in the context of IBD and using an ex vivo organoid-based approach, we identify a strain capable of alleviating colitis in a relevant pre-clinical animal model of IBD.


The human gut is the largest immune organ of the body, and gut epithelial cells play a key role in the establishment and maintenance of gut homeostasis, as well as rapid responses to infection (Peterson and Artis, 2014). The gut is colonized by a diverse microbiota that has co-evolved with its host and forms a symbiotic relationship through its modulation of innate and adaptive immune responses (Geva-Zatorsky et al., 2017Kabat et al., 2014). However, with a few notable exceptions (Mazmanian et al., 2008Wlodarska et al., 2017), the microbes and microbial determinants of immune homeostasis remain cryptic.Inflammatory bowel diseases (IBDs) are composed of two predominant subtypes, Crohn disease (CD) and ulcerative colitis (UC), that are characterized by relapsing and remitting gut inflammation.

The nuclear factor-κB (NF-κB) family of transcription factors are master regulators of gut epithelial integrity and inflammation and activation of antigen-presenting cells and effector leukocytes. Upon activation, NF-κB dimers translocate to the nucleus, where they regulate transcription of a wide range of genes, including those involved in immune and inflammatory responses (Wullaert et al., 2011). In the healthy gut, NF-κB activation is tightly regulated (Renner and Schmitz, 2009), but several IBD genetic risk alleles, including NOD2TOLLIP, and A20, exert their pathogenic effects at least in part through dysregulated NF-κB signaling (Zaidi and Wine, 2018). Additionally, macrophages and epithelial cells isolated from the inflamed intestine of patients with IBD show increased activation, and nuclear localization of NF-κB-p65 (Rogler et al., 1998).

NF-κB signaling contributes significantly to multiple host responses underlying the pathogenesis of IBD.The gut microbiota is increasingly recognized as an important contributory risk factor for IBD development and activity, as healthy and IBD gut microbiota differ and are characterized by structure and function alterations (Costello et al., 2017Wilson et al., 2019). Several bacterial taxa are abundant in the healthy gut that can suppress inflammatory responses and alleviate inflammation in animal models of disease (Sokol et al., 2008Eeckhaut et al., 2012Takeshita et al., 2016). These “anti-inflammatory” properties are best characterized for the gut bacterium Faecalibacterium prausnitzii A2-165, which produces secreted peptides derived from the Mam protein that suppress NF-κB in vitro and in vivo via stabilization of the IKK complex (Quevrain et al., 2016).

However, although Firmicutes-affiliated Clostridia are among the most abundant and functionally diverse gut bacteria, Mam expression is largely restricted to members of Faecalibacterium spp., and much remains to be discovered about the immunomodulatory capacities inherent to other Firmicutes.Here, we identified five new Firmicutes isolates that are comparable or superior to F. prausnitzii A2-165 in their NF-κB suppressive activity and whose activities are characterized by strain-specific differences.

Notably, these bacteria suppressed cytokine-mediated IL-8 secretion in CD and UC gut-derived organoid cultures and peripheral blood mononuclear cells (PBMCs). On the basis of these observations, we demonstrated using two Clostridium bolteae strains and ex vivo assays that ex vivo activity in organoids predicts immunomodulatory bioactivity in vivo using the Winnie murine model of spontaneous colitis. Furthermore, using an activity-guided high-performance liquid chromatography (HPLC) purification method, we have shown that non-polar and hydrophobic bacterial supernatant derived fractions from Clostridium bolteae can suppress both cytokine and lipopolysaccharide (LPS)-driven chemokine/cytokine expression on human organoids and PBMCs, as well as non-canonical NF-κB in vitro and in vivo. These data demonstrate the potential of bioprospecting the human microbiome for novel therapeutic leads targeting immunologically relevant pathways for treating gut inflammation.


Firmicutes-affiliated bacteria are among the most abundant gut microbes, and these taxa are widely recognized to possess immunomodulatory capacities (Atarashi et al., 2011Atarashi et al., 2013Sokol et al., 2008). However, they are poorly represented in culture collections, and their ability to modulate immune responses remains largely undefined. In this study, we identified five gut bacterial strains affiliated with Clostridium clusters IV, XIVa, and XV that have NF-κB suppressive activity comparable or superior to the well-characterized F. prausnitzii A2-165 strain. The NF-κB suppressive bioactivities were characterized by significant biochemical and intraspecies variations suggesting that NF-κB suppressive capacity may be more prevalent than previously appreciated and not adequately captured in existing genetic-based studies of the gut microbiome.

This is consistent with Geva-Zatorsky et al. (Geva-Zatorsky et al., 2017), who determined that as few as 53 isolates were associated with more than 24,000 immune phenotypes that include functionalities relevant to IBD such as Treg induction. Modulating host immune responses may support the ability of gut bacteria to colonize and persist in the gut environment. Furthermore, the ability of the microbiota to act as an extrinsic regulator of host immunity may underpin immune homeostasis, and therefore alterations in the gut microbial composition may contribute to disease risk in genetically susceptible individuals.IBD is characterized by a dysregulated immune response with select genetic susceptibilities affecting therapeutic responsiveness (Niess et al., 2012Barber et al., 2016).

Given this variability in IBD, we used patient-derived gut epithelial organoids and immune cells to confirm bacterial capability to suppress cytokine-mediated inflammatory responses. The heat- and Proteinase K-resilient bioactives showed strong suppression of IL-8 secretion in organoids and immune cells from non-IBD, CD, and UC subjects. Interestingly, the proteinase sensitive bioactives produced by F. prausnitzii A2-165 and C. aldenense AHG0011 appeared less suppressive in UC-derived organoids and PBMCs, and in CD organoids, compared with organoids derived from non-IBD controls, which may be reflective of the increased endogenous protease activity observed in IBD (Vergnolle, 2016). Our in vitro and ex vivo data also suggested that functional capacity rather than phylogeny may be the key determinant of biologic effects. To explore this hypothesis, we capitalized on the C. bolteae intraspecies differences in activity and demonstrated that ex vivo effects observed in Winnie organoids, where CS from C. bolteae AHG0001 but not ATCC BAA-613 suppressed immune responses, predicted in vivo efficacy in ameliorating established colitis in Winnie mice.

Notably, treatment with C. bolteae AHG0001 CS was associated with a rapid onset of action with improvement in diarrhea, alleviation of inflammation and ER stress, as well as restoration of mucin production. Mucosal and histologic healing are among the best predictors of long-term outcomes in IBD (Turner et al., 2021) and taken together, our data suggest a precision medicine approach using ex vivo patient-derived organoids could be applied to select effective microbiome derived IBD treatments.The NF-κB suppressive strains we have identified carry multiple BGCs, many of whose products remain cryptic, underlining the inherent challenges in applying genomic-based approaches to map genotype with phenotype.

In addition, the biosynthesis of bioactives by gut bacteria may be driven principally through modest modifications of common primary metabolites that are underpinned by small BGCs (Cohen et al., 2015Cohen et al., 2017). As the medium dependent effects on NF-κB suppression may affect the therapeutic efficacy of live biotherapeutics for IBD, we used a bioassay-guided ethyl acetate extraction coupled with reversed-phase analytical high-performance liquid chromatography fractionation to further characterize low-molecular weight non-polar bioactive associated with the NF-κB suppressive activity of C. bolteae AHG0001. Consistent with other microbial bioactives, the C. bolteae AHG0001 bioactive acts independently of the bacterial cell and suppresses the inflammatory response in animals. In summary, our functional approach provides new opportunities to rationally bioprospect the gut microbiota for precision live biotherapeutic strains and/or bioactives that could be used to expedite the development of safer and more efficacious therapeutics in IBD.

Limitations of the study

In this study, we showed that Clostridium species isolated from a single individual have NF-κB suppressive ability, but the immunomodulatory properties are likely not limited to Clostridium. Although we identified multiple strains with secreted immunomodulatory activity, it remains undetermined if the immunomodulatory properties of Clostridium can be generalized to other species of bacteria. Similarly, we used one mouse model of colitis to validate the in vitro activity of culture supernatants, although the activity was validated in multiple cell lines as well as patient-derived organoids. Future studies should use other models of murine colitis.

Nerve stimulation promotes resolution of inflammation

Authors: April S. Caravaca Alessandro L. Gallina Laura Tarnawski Vladimir S. Shavva Romain A. Colas Jesmond Dalli  Stephen G. Malin  Henrik Hult  Hildur Arnardottir Peder S. Olofsson

Media Release: Nerve stimulation promotes resolution of inflammation | Karolinska Institutet Nyheter (

Link to full research report: Vagus nerve stimulation promotes resolution of inflammation by a mechanism that involves Alox15 and requires the α7nAChR subunit | PNAS

Inflammation is essential for an effective antimicrobial defense and response to tissue injury, but it must be well regulated and ultimately resolved to avoid excessive tissue damage and development of inflammatory disease. An important mechanism to restore homeostasis is the active resolution of inflammation. Defective resolution may result in nonresolving inflammation, which underlies many chronic inflammatory diseases (12). Key processes in the resolution of inflammation include the cessation of neutrophil infiltration and the promotion of macrophage reparative functions, including clearance of apoptotic cells from affected tissues by efferocytosis (34). However, the mechanisms that regulate resolution of inflammation are not yet fully understood, and specific therapeutic options to actively promote inflammation resolution are lacking (56).It is becoming increasingly clear that the onset and intensity of inflammation are regulated by homeostatic neural reflexes, such as the “inflammatory reflex,” in which the vagus nerve plays a key role (78).


In this study, we found that VNS accelerated resolution of inflammation. Activation of the vagus nerve promoted efferocytosis and shifted the LM balance toward a more proresolving profile in wild-type mice with peritonitis. VNS-mediated acceleration of resolution was impaired in mice genetically deficient in either Alox15, a key enzyme in LM biosynthesis, or the ACh receptor subunit α7nAChR, which is commonly found on immune cells. Together, these observations demonstrate that the vagus nerve controls resolution of inflammation by cholinergic regulation of the inflammation microenvironment and SPM biosynthesis.Inflammation resolution is characterized by cessation of neutrophil infiltration and increased efferocytosis (36). Studies pioneered by the laboratory of Serhan and coworkers (2229) showed that mice that were vagotomized 7 d before initiation of peritonitis had higher peak neutrophil numbers and delayed resolution of inflammation compared with vagus nerve–intact mice, supporting a role for the vagus nerve in the regulation of peritoneal inflammation. In the present study, we observed that activation of the vagus nerve by electrical stimulation shortened resolution time compared with in sham-treated mice in zymosan-induced peritonitis. Importantly, this study shows that activation of the vagus nerve accelerated the resolution phase of inflammation and exerted cholinergic control of SPM biosynthesis and efferocytosis.VNS enhanced the production of specific DHA- and n-3 DPA–derived SPMs in peritoneal exudates during inflammation resolution in vivo. In particular, VNS enhanced biosynthesis of the RvD, PD, and MaR families, as demonstrated through identification of RvD2,17R-PD1, and MaR2 as well as their pathway markers 10S,17S-diHDHA (PDX) and 7S,14S-diHDHA, respectively, that are biosynthesized via double lipoxygenation (37). While many mechanistic details of SPM biology, such as their precise mode of action in different inflammatory contexts and the cognate receptors for some of the compounds, at present are incompletely defined, the activity of several compounds (for example, MaR1, RvD2, RvD3, RvD5, RvE1, PD1, and LxA4) was evidenced by the effect on resolution when administered in experimental inflammatory conditions (28303138). The VNS-dependent regulation of Alox15-dependent LMs reported here indicates that activation of signals in the vagus nerve can shift the balance of LMs during inflammation toward a more proresolving state.

This notion is evidenced by the up-regulation of MaR2, RvD2, 17R-PD1, and 10S,17S-diHDHA in the vagus nerve–stimulated mice. As part of their key characteristics, SPMs, including MaR2, RvD2, and PD1, are potent regulators of macrophage phagocytosis and neutrophil trafficking to sites of inflammation (3941). PD1, also termed neuroprotection D1, is neuroprotective (3740), and MaR1, in addition to its potent proresolving actions with immune cells, is also neuroprotective and enhances recovery from spinal cord injury (42). Furthermore, RvD2 and 17R-RvD3, which accelerate resolution of inflammation (42), were also associated with the separation of the VNS and sham clusters on the PLS-DA plot (Fig. 2A). These observations also infer that VNS accelerates inflammation resolution and enhances efferocytosis by activating the Alox15 biosynthetic pathways, a key enzyme in SPM biosynthesis (37). Of note, cyclooxygenase-derived PG and TX were not significantly altered by VNS in wild-type mice, indicating that the vagus nerve may specifically regulate lipoxygenase but not cyclooxygenase biosynthetic pathways, which resulted in an overall proresolving LM profile in exudates from wild-type mice. An imbalance in SPM to proinflammatory eicosanoids (PG, TX, and LT) has been connected with chronic disease progression, including impaired efferocytosis associated with advanced atherosclerotic lesions (2).

Additionally, the ratio of SPM to proinflammatory LT or PG is being proposed as a potential biomarker or measure of nonresolving cardiovascular inflammation (4345). Taken together, these results show that VNS can increase SPM production and accelerate resolution of inflammation in vivo, providing a potential means to activate resolution in chronic inflammatory conditions.VNS is known to regulate the release of proinflammatory cytokines in early stages of inflammation through an α7nAChR-dependent mechanism (9111314), and activation of α7nAChR attenuates inflammation in experimental models of chronic disease (4648). In the present study, the α7nAChR was also required for the VNS-mediated effect on resolution of inflammation in peritonitis (Fig. 4) (1315). As expected from studies of acute inflammation, levels of IL-1β and IL-6 were decreased in exudates of VNS-treated wild-type mice compared with sham 12 h after zymosan-induced peritonitis. We did not observe any significant effect by VNS treatment on TNF levels at 12 h after zymosan administration, likely because TNF levels are known to peak early in this model and are considerably reduced toward baseline at 12 h (4950).

Furthermore, there were no significant differences in the levels of measured cytokines 24 h after zymosan injection. The lack of significant difference between VNS- and sham-treated wild-type mice on levels of the neutrophil chemoattractant, CXCL1, suggests that neutrophil egress and efferocytosis play a role in the reduction of resolution time (Ri) and the increase in inflammation decay (Id) by VNS. These observations together support the notion that SPMs that rely on biosynthesis by Alox15 are important mediators of resolution of inflammation regulated by cholinergic signals elicited by the vagus nerve in this model.ACh is a key neurotransmitter in the inflammatory reflex, and VNS increases ACh in the spleen (71314). ACh also up-regulates the Alox15 biosynthetic pathway in both human and mouse cells (29). Congruently, ACh up-regulates the RvD and PD biosynthetic pathway marker 17-HDHA in innate lymphoid cells group 3 (29). Interestingly, the peritoneum in rodents is innervated by the vagus nerve (51), and peritoneal ACh levels are reduced in peritonitis after vagotomy (22).

It is possible that peritoneal ACh levels regulated by the vagus nerve control resolution of peritoneal inflammation through activation of α7nAChR on innate immune cells (111315). Our findings here (that the VNS treatment on α7nAChR-deficient mice failed to reduce neutrophil numbers and levels of proinflammatory cytokines during the resolution phase of zymosan-induced peritonitis) further support that cholinergic signaling is important for the effective resolution of inflammation and depends, at least partly, on the α7nAChR. Of note, injection of a set of synthetic SPMs into α7nAChR-deficient mice reduced neutrophil numbers in peritoneal exudates after zymosan injection, demonstrating that while the α7nAChR is essential for neural regulation of SPM biosynthesis, it is not required for the effect of SPMs.The use of mathematical modeling of the dynamic changes in local neutrophil numbers here facilitated analysis of the inflammation resolution phase. Our analysis of data from previous studies of neutrophil counts over the course of an episode of peritonitis revealed that the change in neutrophil counts over time showed exponential decay (SI Appendix, Fig. S3). In addition to conventional determination of resolution indices (SI Appendix, Fig. S2B), the model of exponential decay permits calculation of key indices of inflammation resolution without precise knowledge of the peak time or peak numbers of neutrophil infiltration, points that are challenging to experimentally determine and compare. Accordingly, we add to the indices of resolution the rate of “inflammation decay,” Id, as a measure of the speed with which inflammation resolves.

Three genetically different mouse models were used in this study. A limitation is that the genetic modifications in question have important effects on the immune system. Alox15-deficient mice are known to show lower intensity of the immune response, particularly neutrophil infiltration (5253), precluding direct comparisons of the absolute values of neutrophil numbers with the other two models. The α7nAChR-deficient mice have impaired regulation of inflammation with significantly increased cytokine release in proinflammatory events (13), and in the long-term, α7nAChR deficiency may increase the propensity to develop inflammatory diseases. For example, ablation of α7nAChR in hematopoietic cells promotes vascular inflammation and atherosclerosis (54). Therefore, it must be considered that the baseline status of the immune systems in the three models is dissimilar and that direct comparisons between the genotypes are challenging.

While there was no significant difference in the inflammation decay between VNS- and sham-treated Alox15-deficient mice, we did note a difference in the mean numbers of peritoneal exudate neutrophils, with lower numbers and higher mean Id in the VNS-treated group than in the sham, but the observations were not statistically significant. Of note, VNS treatment did have a significant effect on levels of several non–Alox15-dependent LMs in both Alox15-deficient and α7nAChR-deficient mice, although the relative effect on LMs was opposite between the strains, the mechanism of which is yet not known. It is conceivable that the effects by VNS on resolution of inflammation are not restricted to regulation of Alox15-dependent mediators. In support of this notion, the relative differences in the mean numbers of peritoneal exudate neutrophils were much smaller between VNS- and sham-treated animals in the α7nAChR-deficient mice, and there was less separation between VNS- and sham-treated animals by PLS-DA in α7nAChR-deficient mice compared with both Alox15-deficient and wild-type mice. The observations in the three different mouse strains together suggest that the α7nAChR is essential for VNS-mediated regulation of the inflammation decay in this model, and while likely not alone responsible for the entire effect, Alox15 is a component of this regulation.Together, these observations demonstrate that VNS promotes resolution of inflammation in vivo through a mechanism that involves SPM biosynthesis and requires cholinergic signaling. The findings encourage further exploration of neural regulation in resolution of inflammation.

Experimental studies over the past decades have demonstrated that vagus nerve stimulation (VNS) reduces the release of proinflammatory cytokines in acute inflammation (911). Rodents subjected to minutes-long VNS treatment show reduced proinflammatory cytokine release for ≥24 h (1012); activation of this cholinergic anti-inflammatory pathway attenuates inflammation in experimental models of inflammatory diseases (71315), and VNS reduced levels of proinflammatory cytokines in clinical settings (1617). Consistent with these findings, 3 d after disruption of vagus nerve signaling by vagotomy, release of proinflammatory cytokines is increased in inflammation (18). Hence, animals subjected to prolonged disruption of vagus nerve signals by vagotomy respond more strongly to proinflammatory stimuli and show increased propensity for inflammation and higher inflammation-associated mortality (1920). This may potentially be explained by the loss of the homeostatic inhibition of inflammation that is normally conferred by the intact vagus nerve (721). Interestingly, 1 wk after disruption of vagus nerve signaling by unilateral surgical vagotomy, peak numbers of neutrophils in zymosan-induced peritonitis are higher and the duration of neutrophil clearance is longer than in sham-treated mice (22). Consistent with these observations, levels of specialized proresolving mediators (SPMs), a class of potent bioactive lipid mediators (LMs) that actively regulate inflammation resolution, are significantly lower in vagotomized mice compared with sham (22). While it has been recently reported that stimulation of human and mouse vagus nerve ex vivo can enhance SPM production from the vagus nerve tissue itself (23), whether activation of the vagus nerve promotes resolution of inflammation and regulates proresolution mechanisms in inflammation in vivo remains to be determined. Here, we postulated that electrical VNS promotes resolution of inflammation in vivo.

Good bacteria showing promise for the treatment of Crohn’s disease, ulcerative colitis

‘Good’ bacteria show promise for clinical treatment of Crohn’s disease, ulcerative colitis — ScienceDaily

“A new study published in Nature Communications demonstrates that a consortium of bacteria designed to complement missing or underrepresented functions in the imbalanced microbiome of inflammatory bowel disease (IBD) patients, prevented and treated chronic immune-mediated colitis in humanized mouse models”. The study’s senior author, Balfour Sartor, MD, Midget Distinguished Professor of Medicine, Microbiology and Immunology, Co-Director of the UNC Multidisciplinary IBD Center, said the results are encouraging for future use in treating Crohn’s disease and ulcerative colitis patients.

“The idea with this treatment is to restore the normal function of the protective bacteria in the gut, targeting the source of IBD, instead of treating its symptoms with traditional immunosuppressants that can cause side effects like infections or tumors,” Sartor said.


Chronic intestinal inflammation can be induced by multiple exogenous and endogenous signals and is mediated by immune and nonimmune cells in genetically susceptible hosts with defects in epithelial barrier function, immunoregulation, or bacterial killing. Exogenous substances including dietary products, pathogenic microorganisms, xenobiotics including antibiotics, or various combinations thereof, can trigger initial mucosal injury and/or dysbiosis to initiate acute intestinal inflammation that is perpetuated by the antigenic activities of a subset of resident microbiota1,2. Examples of these conditions are inflammatory bowel diseases (IBD), which encompass two main clinical disorders: Crohn’s disease and ulcerative colitis. Current IBD treatments primarily control inflammation through anti-inflammatory and immunosuppressive mechanisms. Some of the most successful drugs for treating IBD include infliximab, adalimumab, vedolizumab, ustekinumab, and tofacitinib, which target specific immune components to control the inflammatory process. However, these and other immune modulating drugs induce sustained, steroid-free remission in only a small subset of patients and can have multiple serious side effects, including an increased risk for serious and potentially life-threatening infections and neoplasia. In addition, these drugs do not correct upstream conditions that contribute to the chronic inflammatory mechanisms, including the leaky mucosal barrier, a pro-inflammatory gut microbiome and immunoregulatory defects.

As an alternative to anti-inflammatory and immunosuppressive therapies, microbiome-inspired live biotherapeutic products (LBPs) are being developed to treat conditions linked to chronic intestinal inflammation and increased permeability. The traditional approach for LBP discovery has been to compare the microbiomes of healthy subjects and patients suffering from a specific condition, such as IBD, to identify microorganisms that are lacking or under-represented in large databases, such as the HMP2 project3. This information, further enforced by the results from microbial association studies, is used to propose a therapeutic formulation to replenish the microorganisms that are lacking or under-represented2,4. In the case of IBD, early efforts have focused on the use of strains belonging to the Clostridium clusters IV and XIVa, which were found to successfully decrease inflammation in rodent IBD models5,6,7. Using germ-free (GF) mice inoculated with healthy human fecal material pretreated with chloroform to enrich for spore-forming bacteria, a stable 17-strain consortium was enriched from a single donor based on their ability to induce colonic regulatory T cells (Tregs)7,8. This consortium was comprised of spore-forming Clostridium cluster IV, XIVa, and XVIII strains that produced butyrate and decreased the severity of several colitis models7.

Open label application of Fecal Microbiome Transplants and enrichment-based approaches have several disadvantages. The outcome is defined by the stool sample used for the enrichment, with different samples representing different consortia with variable efficacy;9 undesirable strains/functions associated with safety risks including virulence factors and transferable antibiotic resistance functions might be present, such as the presence of enteropathogenic and Shigatoxin-producing Escherichia coli strains10 and antibiotic-resistant E. coli strains11 in FMTs, or the presence of transferable vancomycin resistance elements as found in the genome of the VE202 consortium strain Blautia coccoides VE202-06 (GenBank Accession Number Accession: PRJDB525). Furthermore, consortium modeling, as presented in this study, shows that other bacterial species besides spore-forming Clostridium bacteria provide metabolic support and additional therapeutic functions required for optimal engraftment and therapeutic performance of live biotherapeutic products in the hostile gut environment of patients with intestinal inflammation. These shortcomings can be addressed by a bottom-up rational consortium design approach that is rigorously informed by mechanistic modeling and insights from microbiome ecology and disease pathogenesis. We used this approach to combine well-characterized strains isolated from many healthy human stool samples into a consortium of metabolically interdependent strains with a variety of therapeutic functionalities being distributed in a redundant way between strains. Initially a 17-strain consortium, GUT-103, was designed around publicly available strains. GUT-103 rapidly colonized mice, restored normal function to the inflamed colon, and prevented and reversed established experimental colitis in gnotobiotic mice. Based on these proof of concept studies, a refined 11-member consortium, GUT-108, was designed around a panel of proprietary human bacterial strains that strongly engrafted and provided similar redundant protective functions. Therapeutically applied GUT-108 corrected functional dysbiosis of the inflamed gut microbiome and treated established colitis in a humanized mouse colitis model while decreasing opportunistic pathogenic bacteria, increasing resident protective bacterial groups, and restoring immunologic and metabolic homeostasis.


Resident bacterial strains of the GUT-103 and GUT-108 consortia, designed to interdependently restore normal function to the inflamed colon, rapidly colonized gnotobiotic mice as well as ex-germ-free humanized mice that had developed a pro-inflammatory gut microbiome. These GUT-103 and 108-colonized mice exhibited the desired functional properties consistent with the rational design of the two consortia.

The two separate rationally designed consortia of intestinal bacterial strains with redundant functionalities that were previously found to be under-represented in the gut microbiome of IBD patients with active disease3 were shown to promote homeostatic immune functions and bacterial metabolism and prevent onset or progression of intestinal inflammation. We believe that this approach has the potential to maintain long term remission in a physiologic and safe manner, which should be tested in a Phase 1 clinical trial.

Testing GUT-103 against EER-induced colitis in gnotobiotic Il10−/− mice is clinically relevant to human Crohn’s disease because adherent-invasive Escherichia coli and Ruminococcus gnavus are increased in active Crohn’s disease3,31,32 and the adherent-invasive E. coli strain used was isolated from the ileum of a Crohn’s disease patient33. GUT-108 showed therapeutic efficacy to reverse established colitis in Il10−/− humanized mice by intervening 2 weeks after onset of moderate-severe intestinal inflammation, supporting a potential role for GUT-108 to treat active IBD. Moreover, the Il10−/− model of chronic pathobiont-driven T-cell-mediated chronic inflammation is more predictive of therapeutic responses in IBD patients than acute epithelial injury models such as dextran sodium sulfate2.

GUT-103 and GUT-108 were designed based on human data showing that protective functions provided by commensal bacteria are under-represented in the gut microbiome of IBD patients. These functions include the synthesis of SCFAs, indole and its derivatives, bile acid deconjugation and conversion, and competition for the critical nutrient iron and the synthesis of antagonistic molecules to control opportunistic pathogens3,34. Several animal studies have highlighted the role for SCFAs, especially propionate and butyrate, in regulatory T cell recruitment and function8,12,13,34,35,36. The recruitment in the colon and extrathymic conditioning of regulatory T cell response by SCFA make these molecules an important link in the crosstalk between the gut microbiome and the immune system. Therefore, commensal bacteria identified to produce propionate and butyrate were selected in the rational design of GUT-103 (Table 1) and GUT-108 (Table 2).

Several studies have shown the role of indole, a metabolite produced from tryptophan, and its metabolites in reducing attachment of pathogenic E. coli to epithelial cells37, strengthening the mucosal barrier and mucin stimulating production38. Therefore, commensal bacteria identified to produce indole and its derivatives were selected in the rational design of GUT-103 (Table 1) and GUT-108 (Table 2).

An inflammatory gut microbiota can result in the inefficient microbial conversion of bile salts into their primary and secondary bile acids3. IBD patients with an unbalanced gut microbiome due to inflammation have lower fecal and circulating concentrations of secondary bile acids and higher conjugated fecal bile acid concentrations than do healthy subjects39. Thus, activities essential for the conversion of primary bile acids, specifically the conversion of CA and TCDCA acid via a multistep process that includes 7-alpha-dehydroxylation by 7-alpha dehydratase (7-α-DH) or 7-alpha-hydroxy steroid dehydrogenase (7-α-HSD) activity15, are included in the strain selection for GUT-103 (Table 1) and GUT-108 (Table 2).

Competition for iron helps drive the competitiveness and establishment of microorganisms40. Therefore, GUT-103 (Table 1) and GUT-108 (Table 2) include several strains that synthesize one or more siderophores under iron-limiting conditions. Ideally, these siderophores are insensitive to inhibition by Lipocalin-2, a peptide that inhibits specific siderophores and their uptake, and is a major colonic defense system triggered by bacterial infections. Lipocalin-2 levels were increased after induction of inflammation in Il10−/− mice colonized with the EER consortium (Fig. 1c) or human fecal microbiota (Fig. 4c).

Bacteriocins, of which lantibiotics are considered a specific class, have shown great promise as new antibiotics for therapeutic application, as reviewed by Field et al.41. Thus, bacteriocin synthesis was included as a key functionality in strain selection as part the rational design process of GUT-103 (Table 1) and GUT-108 (Table 2).

The optimized 11-strain GUT-108 consortium was rationally designed to build on the proof-of-concept results obtained with GUT-103. GUT-108 went beyond members of the Clostridium clusters IV and XIVa strains, including Bacteroides and Akkermansia species. Furthermore, based on their genome analysis, strains with undesirable properties including the presence of transferable antibiotic resistances or putative virulence factors were excluded. We also omitted species that are fastidiously anaerobic, such as Faecalibacterium prausnitzii, from the GUT-108 consortium. Compared to GUT-103, GUT-108 strains provide additional redundancy for the synthesis of the protective secondary bile acids LCA and DCA, plus multiple mechanisms to compete with opportunistic pathogenic Enterobacteriaceae including synthesis of the siderophore yersiniabactin, and lantibiotics. In the inflammatory gut environment of humanized Il10−/− mice, beneficial Lachnospiraceae and Ruminococcaceae family members are decreased while opportunistic Enterobacteriaceae are increased42, as reported for Crohn’s disease patients32,43. Therapeutic application of GUT-108 reduced levels of colitogenic Enterobacteriaceae and increased beneficial resident Clostridium (Clusters IV and XIVa) species, especially Lachnospiraceae including Dorea species and Lachnoclostridium species that are not GUT-108 constituents (Fig. 4b). This altered community composition increased cecal luminal propionate concentrations, but not butyrate levels (Fig. 4f). Previous studies demonstrated that butyrate levels are not necessarily an indicator of a healthy gut microbiome, as butyrate synthesis from fermentation of amino acids such as lysine can contribute to inflammation under conditions associated with mucosal permeability44.

GUT-108 increased expression of Gpr41 and showed an upward trend for Gpr43 in Il10−/− mice humanized with a fecal transplant (Supplementary Fig. 5). As previously reported, SCFA produced by gut bacteria stimulate Tregs8 with propionate’s effect mediated through GPR4336. SCFA also mediate the function of GPR41, a key regulator that controls host energy balance45.

With its functional redundancy and metabolically interdependent auxotrophies, GUT-108 is designed to engraft and perform under a wide range of conditions. When applied to Il10−/− mice humanized with a fecal transplant, all GUT-108 strains except Clostridium scindens GGCC_0168 were established for at least 2 weeks. Clostridium scindens has been previously described as one of the essential strains necessary to convert primary bile acids into LCA and DCA. However, despite the absence of this strain, the established functional multi-strain network produced secondary bile acids, with Extibacter sp. GGCC_0201 providing the 7α-dehydratase activity required to convert CA and CDCA into the therapeutic secondary bile acids DCA and LCA, respectively. Normalizing the intestinal bile acid profile can restore intestinal epithelial stem cell function46, and increase colonic RORγ+ Treg cell counts that ameliorate host susceptibility to colitis47, while LCA stimulates Treg differentiation and inhibits Th17 cells48 consistent with GUT-108’s ability to restore secondary bile acid metabolism (Fig. 4f) and activate inducible IL-10+ RORγ FoxP3+ CD4+ Treg cells (Fig. 3f). GUT-108 stimulated regulatory (protective) immunity by increasing numbers of colonic LP IL-10-producing CD4+ T cells, B cells and DC and numbers and percentages of regulatory T cells, including inducible Tregs (IL-10+ RORγT+ FoxP3+ CD4+ cells) and IL-10+ Tregs (Fig. 3f). We further documented the anti-inflammatory effects of therapeutic GUT-108 in Il10−/− mice humanized with a fecal transplant by demonstrating that GUT-108 decreased IFN-ɣ+, IL-17α+, and IFN-ɣ+ IL-17α+ synthesizing colonic LP CD4+ TH1 and TH17 cells (Fig. 5a) and reduced expression levels of innate and Th1 and Th17 pathway cytokines, including IL-1β, IL-12p40, IL-13, IL-17α, IFNγ, and TNFα (Fig. 5b). Interestingly, GUT-108 treatment increased expression of IL-15 mRNA, a homeostatic cytokine that controls T cell inflammatory responses. Exogenous IL-15 treatment decreases IL-17α expression by Th17 cells in vitro through STAT5 enrichment at the IL-17 locus49, consistent with the ability of GUT-108 therapy to increase IL-15 gene expression and decrease IL-17α mRNA expression in colonic LP cells (Fig. 5b).

Increased intestinal bacterial metabolism of tryptophan, especially indole and its derivatives IAA and IPA, activates the Ahr pathway. AHR acts as a sensor of the microbiota community and, through its established role of modulating immune functions, maintains host-microbe homeostasis50. IPA is also a pregnane X receptor (PXR) agonist mediating its responses through TLR451. GUT-108 therapy increased both IAA and IPA levels in stool (Fig. 4f) and colonic Ahr gene expression (Fig. 5c). AHR is a critical mediator of anti-inflammatory responses to infection by bacterial pathogens and of the differentiation and function of immune cells including T cells, innate lymphoid cells, macrophages and DC28. AHR promotes the expression of the anti-inflammatory cytokine IL-10 and inhibits macrophage apoptosis, decreases the expression of inflammatory cytokines (IL-6 and TNF-α) and inhibits activation of NF-κB. Therefore, the Ahr pathway is critical to protect from excessive inflammatory cytokine expression and septic shock. In addition, Ahr pathway activation protects the mucosa during inflammation52.

Efficacy of GUT-108 in Il10−/− mice is mediated by IL-10-independent mechanisms. Further insights into these possible protective mechanisms include increased expression of metabolite sensors and mediators (Gpr41, Gpr43, Fxr, Pxr, Pparg, Fgf15, Fgf21) and pathways mediating differentiation of immune cells including Treg and Breg cells (cMaf, Il5, April, Aid, Bcl6) (Supplementary Fig. 5). For example, intestinal epithelial FGF15 is activated by bile acids serving as ligands for the nuclear receptor farnesoid X receptor (FXR). FXR/FGF15 signaling regulates bile acid homeostasis and protects against experimental colitis53. APRIL impacts immune regulatory T cells by stimulating their proliferation and survival, and directly contributing to their immune suppression54. Bcl6 induces IL-10 and follicular T helper cells and regulates the balance of innate lymphoid cells subsets55. Decreased expression of Nos2 (Supplementary Fig. 5), a part of the Ace2 -Nos2-IFNɣ biosynthesis gene cascade56, could lead to lower levels of ACE2, a key regulator to control intestinal inflammation induced by epithelial damage57. Certain viruses, including the coronaviruses SARS-CoV-1 and SARS-CoV-2, use the ACE2 protein for infecting respiratory and intestinal epithelial58. Therefore, chronic gut inflammation, as seen in type-2 diabetes and obesity59 might trigger elevated gut epithelial ACE2 levels, and therefore patients suffering from these conditions could be more sensitive for Coronavirus infection and at higher risk for complications, highlighting the importance of therapeutically targeting the pro-inflammatory gut microbiome as the underlying cause of chronic inflammation60.

In addition to analyzing fecal material, we measured cecal microbiota and in some cases cecal luminal metabolites to represent bacterial communities and function within the cecum/colon, since the cecum is one of the sites of most active inflammation (Fig. 4d). Previous rodent studies have shown broadly similar microbial patterns in cecal luminal and fecal samples61. Furthermore, we demonstrate similar cecal (Fig. 2) and fecal (Fig. 4f) secondary bile acid (LCA and DCA) responses to GUT-103 and GUT-108, respectively.

Although no animal model completely replicates all clinical features of human Crohn’s disease or ulcerative colitis, we believe that our use of a human fecal transplant in germ-free mice to initiate chronic TH1/TH17-mediated colitis and our treatment protocol of administering GUT-103 and 108 to mice with established mild to moderate inflammation replicates IBD as closely as feasible for preclinical studies. Proof of efficacy in human IBD will have to await a clinical trial.

GUT-103 and GUT-108 combine multiple modes of action to treat the upstream causes of inflammation by correcting the abnormal microbiome environment, activating various IL-10 synthesizing immune cells, lowering inflammatory responses, and restoring bacterial metabolic profiles to levels found in stool samples of healthy individuals. These overlapping protective mechanisms are predicted to maintain long term remission of IBD in a physiologic and safe manner, in contrast to most biologicals, which block downstream immune effector responses by neutralizing a single cytokine or molecule and induce immunosuppression that can be associated with increased infection and neoplasms. These integrated protective mechanisms make GUT-108 a promising novel therapy to treat a range of conditions whose pathogenesis is characterized by dysbiosis-mediated chronic intestinal inflammation and increased mucosal permeability. Besides IBD this could include graft versus host disease, hepatic encephalopathy, alcoholic liver disease, atherosclerosis, hypertension, obesity, metabolic syndrome, and type-2 diabetes mellitus.

Reference: van der Lelie, D., Oka, A., Taghavi, S. et al. Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis. Nat Commun 12, 3105 (2021).

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A study has linked psychological stress to Crohn’s disease flare-ups

McMaster-led study links stress to Crohn’s disease flare-ups “The main takeaway is that psychological stress impedes the body’s ability to fight off gut bacteria that may be implicated in Crohn’s disease. Innate immunity is designed to protect us from microbes that do not belong in the gut, like harmful bacteria,” said senior author Brian Coombes, professor and chair of biochemistry and biomedical sciences at McMaster.

“When our innate immune system functions properly, it prevents harmful bacteria from colonizing us, but when it breaks down, it leaves an opening for pathogens to colonize locations they normally cannot and cause illness.”

Below is the introduction and discussion of the study.


Crohn’s disease (CD) is an inflammatory disorder of the gastrointestinal tract triggered by microbial and environmental insults1,2,3. The global burden of disease associated with CD is rising, particularly in developed countries where an upward trend in incident cases has occurred for decades. Emergent disease is now appearing in Asia, Africa, and South America4. Current standards of care, including immunomodulatory biologics, are expensive and have high rates of primary and secondary non-responsiveness. Thus, there is an urgent unmet clinical need to better understand the microbial and environmental triggers of CD that will underpin new preventions and therapies.

The CD-associated microbiome has been intensely scrutinized as a source of inflammation in the gut5,6,7. General microbial features in CD include decreased community diversity, reduced levels of Clostridiales, and increased abundance of Proteobacteria7,8,9. Clinical observations consistently show bacteria in close association with the mucosal epithelium in Crohn’s patients, particularly members of the Enterobacteriaceae that are enriched in virulence and secretion pathways10,11,12. Adherent-invasive Escherichia coli (AIEC) is an abundant pathobiont at inflamed sites in the gut13,14. Numerous studies have confirmed that AIEC are enriched in humans with CD compared to healthy subjects and are often the dominant bacterial species present15,16. AIEC have a multiphasic lifestyle and can grow as extracellular planktonic cells, in biofilms, and intracellularly in epithelial cells and macrophages, where they induce host inflammatory pathways17,18,19,20. Thus, understanding the colonisation dynamics of AIEC is expected to yield insights into the progression of CD and may inform therapeutic intervention.

Several components of mucosal immunity are disrupted in CD. These include epithelial barrier integrity, mucous production and cell turnover, the production of antimicrobial peptides and proteins (AMPs), and the release of metal ion scavengers that contribute to nutritional immunity21,22,23. Nutritional immunity functions to limit bacterial growth by sequestering essential nutrients and metals required for bacterial replication22. Collectively, these elements of mucosal immunity work to spatially restrict bacteria largely to the gut lumen and to reduce the overgrowth of pathogens24. Interleukin (IL)-22 is a cytokine that regulates several aspects of mucosal immunity in the gut, including the production of AMPs and the activation of nutritional immunity25,26 Some enteric pathogens including Salmonella and Citrobacter can overcome IL-22-dependent host defenses through AMP resistance and metal acquisition systems that bypass the host defense proteins lipocalin (Lcn2) and calprotectin27,28. Similarly, IL-22 has been implicated in the induction of other iron scavengers, including hemopexin and haptoglobin, that can control the enteric pathogen Citrobacter rodentium29. The role of IL-22 in host control of CD-associated pathobionts has not been explored.

Disease expression in CD patients follows a relapsing and remitting course, where relatively asymptomatic periods are followed by heightened inflammation and disease activity30,31. A considerable body of clinical literature establishes psychological stress as a disease modifier in CD32,33,34,35,36. Episodes of acute psychological stress are associated with flares, relapse, and increased inflammatory markers in both the serum and mucosa of patients with CD and ulcerative colitis33,34,37. Rodent models of stress have extended these findings, demonstrating increased inflammation38, barrier disruption38,39,40, reactivation of disease induced by chemical exposure38,41, and increased susceptibility to enteric infection42. A previous study demonstrated that chronic stress coupled with DSS-induced colitis resulted in a modest alteration in inflammation and microbiome composition in the cecum and colon43. However, the mechanisms driving the mucosal and microbiological dysfunction associated with psychological stress remain unknown, particularly in the ileum.

Here we show in a pre-clinical model, designed to investigate the comorbid effects of psychological stress on microbial composition and immune pathways in the gut, that stress induces a multidimensional loss of host protection, provoking a dysbiotic shift in the ileal microbiome dominated by AIEC and other Enterobacteriaceae, with attendant immunological and barrier defects. These mucosal deficits are traced back to an apoptotic depletion of CD45+CD90+ cells resulting in the loss of protective IL-22 signaling that blunts AMP responses and barrier repair. The combined effects of nutritional immunity and stress-induced impairment of protective IL-22 responses create a favorable niche for AIEC expansion. These deficiencies are correctable using either exogenous IL-22, or by blocking stress-induced glucocorticoid signaling, which restores mucosal immunity and averts ileal dysbiosis including the expansion of AIEC. These data indicate that immunomodulation can normalize the dysbiotic shifts associated with CD in response to psychological stress, providing avenues for therapeutic interventions.


CD patients experiencing psychological stress are more likely to relapse and have increased disease activity, yet the mechanisms underlying this remain obscure33,65,66,67. Likewise, despite a higher frequency of AIEC colonization in CD patients, the host factors that influence the fluctuation of AIEC load in patients are not understood68. Current evidence indicates that AIEC is a pathobiont in the human gut and takes advantage of inflammatory niches derived from host insults, such as antibiotic use69, secondary enteric infections20, western diet70, and/or genetic predisposition71. In this study, we determined that psychological stress is associated with impaired IL-22-dependent mucosal antimicrobial defenses that result in profound small intestinal dysbiosis dominated by AIEC expansion.

Previous studies have demonstrated a link between intestinal dysbiosis and inflammation in mice47,72,73 and in IBD patients7. In our study, exposure to acute psychological stress resulted in a profound dysbiosis dominated by outgrowth of Enterobacteriaceae family members and genera commonly found to be enriched in CD patients7,8,9. For instance, an enrichment of Enterococcus faecalis is strongly associated with disease severity in CD patients74, and this species was also enriched following exposure to psychological stress. Bifidobacterium, which are commonly associated with intestinal health and generally have decreased abundance in CD, were also decreased following overnight stress.

Psychological stress has traditionally been considered anti-inflammatory in nature, owing to the production of glucocorticoids50,75,76. Our findings, in line with a recent publication43, demonstrate that stress induces a mixed inflammatory response. In our model of psychological stress, the pro-inflammatory features appear to play a dominant role in shaping the microenvironment that favors the expansion of AIEC. For example, mice exposed to stress had reduced expression of genes associated with barrier function, including tight junctions and mucins. The encroachment of AIEC towards the epithelium and dissemination to systemic sites that we observed following stress is likely facilitated by these weakened physical barriers, which further provokes the host inflammatory response. Indeed, we observed more pronounced barrier defects, increased pro-inflammatory cytokine expression, and dysbiosis in AIEC-colonized mice exposed to psychological stress compared to AIEC-naive mice exposed to the same stressor. Thus, the combination of inflammation-tolerant bacteria like AIEC, and the mucosal defects brought about by stress, appear to create a tipping point in gut homeostatic balance that favors inflammation.

Interestingly, while nutritional immunity was necessary, it was not sufficient to phenocopy the ileal dysbiosis induced by stress. Indeed, psychological stress independently impaired IL-22-driven protective mucosal immunity against AIEC. A pivotal role for IL-22 was revealed using IL-22 depletion and administration of IL-22-Fc to probe the functional consequences of this pathway during stress. Administration of IL-22-Fc functionally restored the expression of genes downstream of IL-22 signaling including fut2 and antimicrobial proteins which appeared to have a functional effect in preventing stress-induced AIEC expansion and in correcting the ileal dysbiosis that occurred following stress. Interestingly, recent clinical studies are evaluating the use of IL-22 in the treatment of IBD patients (Clinical Trial: NCT03558152, NCT02749630). When ileal explants taken from mice exposed to stress were stimulated with IL-23, these tissues failed to produce IL-22 whereas ileal tissues from unstressed mice showed a robust IL-22 signature, suggesting that the IL-22 producing cell population was depleted following psychological stress. Indeed, the gut of mice exposed to psychological stress had a significant reduction in the number of CD45+CD90+ cells in the small intestine following psychological stress, which we directly linked to stress because this cell population was restored by blocking glucocorticoid signaling.

Although psychological stress impaired IL-22-dependent host protection, nutritional immunity appeared to remain intact, and in fact was required for AIEC expansion. The host protein calprotectin sequesters zinc, manganese, calcium, and iron under states of inflammation59,77. In response to host nutritional immune pressure, some Enterobacteriaceae have evolved mechanisms to exploit nutrient limitation to outcompete commensal microbes27,28,78. For example, Salmonella expresses a high-affinity zinc transporter, ZnuABC, and can thrive in the presence of calprotectin-mediated nutritional immunity77. Interestingly, AIEC appears to also thrive in inflammatory environments13,14 and has acquired the ZnuABC transporter, likely providing a fitness advantage in states of nutritional immunity. Given the essentiality of iron for bacterial replication, the host has multiple mechanisms to limit the availability of iron in its various forms. Iron is typically transported complexed with heme and is a common target of bacterial species79,80. As such, the host sequesters free-heme in pathophysiological settings22,29. Accordingly, we found that both HPX and haptoglobin were upregulated during psychological stress exposure, potentially limiting iron availability to bacterial species22,29,81. Enhanced recruitment of neutrophil-like CD11b+Gr1+ cells in our model was accompanied by robust induction of neutrophil-derived Lcn2 following stress. The host releases Lcn2 to limit the acquisition of iron-bound enterobactin, preventing its reuptake by commensal strains of E. coli23. Unlike most commensal strains, many AIEC encode the biosynthetic and secretion machinery for salmochelin, a glycosylated variant of enterobactin that evades Lcn2 sequestration27,60,82 and provides a competitive advantage to Salmonella27,82. Indeed, AIEC derived a salmochelin-dependent competitive advantage in stressed mice, but not in unstressed mice, indicating that psychological stress creates a competitive gut environment that appears to benefit microbes that have evolved mechanisms to evade nutritional immunity. Interestingly, we found that neither LPS-mediated induction of iron limitation, nor CD90 depletion, in isolation, was sufficient to phenocopy the AIEC expansion seen during stress. Instead, our data are consistent with a combinatorial effect of psychological stress whereby the combined activation of nutritional immunity and immune cell attrition support the intestinal dysbiosis seen following psychological stress.

Overall, our study shows that psychological stress creates a beneficial environment for AIEC, a CD-associated pathobiont in the gut. Given that the pathological changes observed following psychological stress are augmented in the presence of AIEC, this work establishes a rationale for future studies to dissect the relative contributions of the microbiome and psychological stress on the gut environment. In our current study, AIEC appears to derive this benefit by evading host nutritional immunity while taking advantage of an impaired induction of IL-22-mediated host defenses that rely on antimicrobial proteins and barrier maintenance. Thus, in the presence of pathobionts that efficiently evade nutritional immunity, this aberrant stress-induced host response provides a promiscuous niche for their unregulated expansion. The ability of IL-22 treatment to correct both mucosal host defenses and prevent E. coli-dominated ileal dysbiosis provides compelling rationale for continued investigation of this intervention. This work reveals insight into the role that psychological stress plays in disease expression of CD. Uncovering the interactions between microbes, the host immune system, and epithelial host defenses will lay the biological underpinnings that guide preventions and therapies that address unmet clinical needs for CD management.

Reference: Shaler, C.R., Parco, A.A., Elhenawy, W. et al. Psychological stress impairs IL22-driven protective gut mucosal immunity against colonising pathobionts. Nat Commun 12, 6664 (2021).

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Stress and Inflammatory Bowel Disease: Clear Mind, Happy Colon

The Authors

Joaquim Francisco Maria De Sousa, Smit Paghdar, Taheseen M. Khan, Nishant P. Patel, Savitri Chandrasekaran, Nicholas Tsouklidis


Inflammatory bowel disease (IBD) is a condition whose prevalence in the general population worldwide is increasing at an exponential pace. Many risk factors affect the incidence, progression, and overall outcome of IBD, one of them being psychological stress. This study examined the relationship between psychological stress and inflammatory bowel disease.

A search for relevant studies was conducted using PubMed, Google Scholar, ResearchGate, and SCOPUS. A systematic review was conducted on the relevant articles after critical appraisal.

This article mainly focused on studies that evaluated the presence of inflammatory markers observed in individuals who have been diagnosed with IBD and have high levels of psychological stress. It also assessed if lowering an individual’s psychological stress could help improve the outcomes of IBD.

Psychological stress can have a detrimental effect on individuals diagnosed with IBD. There is a need to conduct studies that can further confirm the association between psychological stressors, mental health conditions, and IBD. We should also encourage medical practitioners to educate patients who have been diagnosed with IBD regarding the benefits of stress reduction.

Introduction & Background

Inflammatory bowel disease (IBD) is an umbrella term that encompasses a group of inflammatory conditions that affect the small intestine and the colon. Crohn’s disease (CD) and ulcerative colitis (UC) are the two main subtypes of IBD [1].

UC is a chronic, inflammatory condition often limited to the colon and the rectum [2]. Patients with UC typically present with bloody diarrhea, tenesmus, and abdominal pain [3]. This was the first subtype of IBD to be discovered and serves as a starting point in the history of IBD. However, it is highly likely that the other forms were also present but not fully understood yet [4]. UC was first described in 1875 by two English physicians, Wilks and Moxon, who helped differentiate it from other diarrheal diseases caused by infectious agents [5]. In the following decades, the overall understanding of UC grew tremendously. Its role in causing cancer was better understood, and multiple treatment modalities followed soon after that.

CD is defined as “a chronic transmural inflammatory bowel disease, with skip lesions that may involve any part of the GI tract from the mouth to anus” [6]. Giovanni Battista Morgagni first described this condition. One of his case reports discussed a 20-year-old male patient who died following a prolonged spell of illness, including fever, abdominal pain, and bloody diarrhea. An autopsy was later performed, revealing perforations and transmural inflammation with ulceration, which extended from the terminal ileum to the colon. The report also suggested the presence of mesenteric lymphadenopathy and splenomegaly. Though Morgagni’s work was essential to introducing CD, it was an article written by Burrill B. Crohn, Leon Ginzburg, and Gordon D. Oppenheimer published in the Journal of the American Medical Association that gave us a better understanding of CD. The authors described a condition that affected the terminal part of the ileum. Its pathology included the presence of granulomas along with chronic necrotizing and cicatrizing inflammation in the ileum. There was also the presence of ulceration in the intestinal mucosa and connective tissue reactions, which repeatedly occurred, resulting in the obstruction of the intestinal lumen leading to the formation of fistulas. CD was recognized as a separate entity from UC in 1932 by Crohn et al. [4].

Due to the increasing number of newly diagnosed cases, there has also been a new interest in deciphering the risk factors that might be responsible for causing this disease [7]. Major risk factors such as high-fat diet, smoking (a risk factor for CD and a protective factor for UC), psychological stress, and appendectomy (a protective factor for UC and a risk factor for CD) have all been attributed to increasing the chances of being diagnosed with IBD in the future [8].

The relationship between the immune system, nervous system, and psychological processes is being established and has always been an area of considerable interest [9]. There is mounting evidence that associations between these systems play an essential role in IBD [10,11]. Psychological stressors affect the gut through various mechanisms, such as increased production of pro-inflammatory cytokines, activation of macrophages, and tumor necrosis factor through the hypothalamus-pituitary-adrenal axis [12].

IBD and psychological disorders share multiple pro-inflammatory pathways, such as the clinical expression of activated immune-inflammatory, oxidative, and nitrosative stress (IO&NS) pathways, including tryptophan catabolite (TRYCAT), autoimmune, and gut-brain pathways. These shared pathways are involved in the pathogenesis of IBD and psychological disorders, which can explain the concomitant flare-up of IBD in patients with depression as well as the worsening treatment outcomes of IBD patients who are diagnosed with psychological disorders [13].

In addition to the above-mentioned shared inflammatory pathways, the gut-brain axis has also been mentioned as one of the shared pathways between IBD and psychological disorders. This pathway involves bidirectional communication between the gut and the central nervous system. The principal component of this is the autonomic nervous system, of which the vagus nerve forms the core component. Stress is known to inhibit vagal nerve stimulation, which has anti-inflammatory properties, resulting in deleterious effects on the gastrointestinal tract. Early recognition and efforts to lower stress levels should help [14]. Figure 1 demonstrates the pathogenesis of IBD through the gut-brain axis.

Figure 1: Pathogenesis of IBD through the gut-brain axis.

IBD: inflammatory bowel disease

The United States had the highest age-standardized prevalence rate (464.5 [438.6-490.9]) per 100,000 population), followed by the United Kingdom (449.6 [420.6-481.6] per 100,000) [15]. As with any highly prevalent disease, there is a need to know the factors that trigger this condition. Psychological stress was a risk factor in many of these patients. It was also found that psychological stress caused a worsening of the quality of life in some IBD patients, and reducing stress levels in IBD patients helped in their remission [16]. Psychological stress is a risk factor that can be decreased if detected. Over time, various methods have been shown to help reduce stress, ranging from coping strategies to medications and lifestyle changes. Hence, gaining a better understanding of how psychological stress impacts the incidence and the outcomes of IBD has become paramount.

This review aims to explore the relationship between psychological stress on the incidence and outcomes of IBD. Further, this article aims to evaluate if reducing stress can help improve the chances of remission of IBD.

This article was previously presented as a poster at the International Virtual Medical Conference (IVMC): Spring Conference on April 23, 2022.


Effect of Psychological Stress on the Onset of IBD

Psychological stress can have a detrimental effect on our mental health and harm our physical well-being. In a study conducted in 2003 by Tuglu et al., 43 participants were chosen [17]. In total, 26 patients were diagnosed with major depressive disorder, and the remaining 17 were control subjects. This study aimed to examine the relationship between a psychological stressor such as major depressive disorder and an increase in pro-inflammatory cells such as IL-1, IL-6, and TNF-alpha. The measurement of these inflammatory markers was done at the start of the study and after six weeks of anti-depressant treatment. This study confirmed that psychological stressors have a role in increasing inflammatory markers as they were significantly higher in patients with major depressive disorders than in the control, and the levels of inflammatory markers markedly reduced after six weeks of anti-depressive treatment.

Another study by Mawdsley et al. aimed to study the rectal mucosa’s inflammatory response to psychological stress [18]. To assess this, serum IL-6 and IL-13 concentrations, TNF-alpha, and IL-6 production by lipopolysaccharide (LPS)-stimulated whole blood, leukocyte count, NK cell numbers, platelet activation, platelet-leukocyte aggregate (PLA) formation, substance P release, reactive oxygen metabolite (ROM) production, mucosal blood flow (RMBF), and histology were all actively measured in two groups of patients. One group underwent a stress test in which participants were asked to complete a 60-minute intelligent quotient (IQ) test in 50 minutes with music playing in the background and being repeatedly reminded to increase their efforts in completing the test. The second group underwent a control procedure and was asked to complete the same IQ test in 50 minutes but with background music of their choice. The inflammatory markers were measured before and after the process. This study also confirmed the presence of inflammatory response in individuals who experienced psychological stressors, which resulted in their relapses, further confirming that psychological stressors can cause an increase in inflammatory markers, which are seen in IBD.

Effect of Psychological Stress on the Disease Progression in IBD

Being diagnosed with IBD can be a traumatic experience for individuals from a physical and psychological standpoint. Patients diagnosed with IBD can present with various symptoms, such as abdominal pain, recurring bloody diarrhea, weight loss, and extreme tiredness. Many of these patients suffer from psychological stress due to being diagnosed with a chronic condition and from the symptoms they suffer. A few studies have shown that by reducing psychological stress, a patient’s quality of life is improved as a result of minimizing their psychological stress. One such study by Kuo et al. aimed to investigate the effect of stress reduction techniques on patients diagnosed with IBS and irritable bowel syndrome (IBS) [19]. This study enrolled 19 patients diagnosed with IBS and 29 IBD patients in a nine-week relaxation exercise called relaxation response-based mind-body group intervention (RR-MBI). A questionnaire regarding patients’ symptoms and inflammatory markers was used in a pre-post intervention study and after a short-term follow-up. This study showed that the patients’ pain scores and overall quality of life improved after the relaxation exercise.

Finally, a study by Gerbarg et al. evaluated the effect of a breath-body-mind workshop (a type of relaxation exercise) on various aspects of a patient who was diagnosed with IBD, such as their physical symptoms, inflammatory markers, and their psychological well-being [20]. In total, 29 patients diagnosed with IBD and enrolled in the Jill Roberts IBD centre were chosen and were randomly allocated to a group that would participate in the breath-body-mind workshop or an educational seminar. The IBD questionnaire, fecal calprotectin, C-reactive protein, perceived stress questionnaire, perceived disability scale, Beck anxiety inventory, and Beck depression inventory measures were obtained at baseline to measure the study outcomes and at weeks six and twenty-six. This study showed that patients enrolled in the breath-body-mind workshop were associated with significant improvements in their overall physical symptoms and psychological well-being and showed a drop in their C-reactive protein level. The studies mentioned above showed that stress reduction could benefit patients who have been diagnosed with IBD regarding their physical symptoms and psychological well-being and help improve their overall quality of life.

Effect of Psychological Stress and Mental Health Conditions on the Outcomes of IBD

Psychological stress and mental health conditions can also affect the disease outcomes, as described in a study by Persoons et al. in Belgium, whose aim was to study the effect of major depressive disorder on the outcomes of patients who were taking infliximab for luminal CD [21]. Major depressive disorder was diagnosed using the Patient Health Questionnaire. A total of 100 consecutive unselected patients were chosen for this prospective study. The patients were assessed at baseline and at four weeks after being treated with infliximab. Assessments included the patients’ clinical, psychosocial, and demographical disease-related biological parameters. The patients were then followed up clinically for the next nine months or had a flare-up. This study pointed out major depressive disorder as a risk factor for treatment failure with patients on infliximab and was responsible for earlier relapses in patients with CD.

A study by Bitton et al. aimed to identify if psychosocial, biological, and clinical parameters could predict relapse in inactive CD [22]. A total of 101 patients were recruited for this study, of whom 14 patients withdrew. Serum cytokines, anti-Saccharomyces cerevisiae antibodies, C-reactive protein, erythrocyte sedimentation rate, and intestinal permeability were measured every three months. Psychological distress was measured every month for a year. This study pointed out that patients under low stress or who did not engage in social diversion were less likely to relapse.

A large study conducted by Bernstein et al. aimed to study if stress, infections, antibiotics, or non-steroidal anti-inflammatory drugs trigger symptomatic flares in patients diagnosed with IBD [23]. A flare-up of the disease was identified using the Manitoba Inflammatory Bowel disease index. In total, 704 participants completed a baseline survey. These participants were selected from a population-based IBD register. They were followed up every three months for a year. This survey tracked the use of non-steroidal anti-inflammatory drugs, antibiotics, infections, major life events, and any forms of stressors faced by the participants. This study pointed out that stress was responsible for most symptomatic flare-ups in IBD.

Lastly, a study by Boye et al. aimed to test the theory that psychotherapy helped improve the overall disease progression and prevent relapses in patients diagnosed with IBD [24]. In total, 58 patients with UC and 56 patients with CD were selected and randomized to either receive treatment with standard medical management in one group or receive medical management and psychotherapy in the second group and were assessed at baseline, three, six, twelve, and eighteen months using the Inflammatory Bowel Disease Questionnaire to measure the outcomes. The study concluded that psychotherapy did not help improve the disease progression in patients diagnosed with IBD, nor did it reduce the chances of preventing relapse of the disease. Some of the studies mentioned above highlight that psychological stress and mental health conditions can contribute to relapses and symptomatic flare-ups in patients who have been diagnosed with IBD. Although some above-mentioned studies contradict this fact, this is an area that should be further investigated in the future. It can aid clinicians in formulating a follow-up plan that can help prevent relapses in patients diagnosed with IBD.

Limitations and future recommendations

Several studies and clinical trials did not have a large enough sample size. To better understand the relationship between psychological stress and IBD, much larger sample sizes would be needed in the future. Moreover, a few of the trials that were used are more than 15 years old. We need more studies in the future to confirm the extent to which psychological stress influences the disease course in IBD.

Recommendations for the future include allocating more resources toward further studying the link between IBD and psychological stressors and incorporating stress reduction techniques in the management plan for patients diagnosed with IBD.


While many risk factors can affect the overall course of disease for a patient who is yet to be diagnosed or has already been diagnosed with IBD, studies have found that stress and mental health conditions can increase inflammatory markers, thus increasing the probability of being diagnosed with IBD in the future. Studies have reported that stress can cause earlier relapses in patients with inactive IBD. In addition to affecting the incidence of IBD, stress reduction can reduce symptoms in patients who have already been diagnosed with IBD, hence improving the quality of their lives. We believe this article can further incite interest in investigating the relationship between IBD and psychological stressors. It can encourage medical practitioners to gauge stress levels in patients diagnosed with IBD during their consultation or with the help of questionnaires. They can then advise these patients of the benefits of stress reduction and recommend ways to do this using techniques such as mindfulness-based interventions, cognitive behavioral therapy, and similar stress alleviating processes.

Reference: De Sousa J, Paghdar S, Khan T M, et al. (May 15, 2022) Stress and Inflammatory Bowel Disease: Clear Mind, Happy Colon. Cureus 14(5): e25006. doi:10.7759/cureus.25006

Link to website: Cureus | Stress and Inflammatory Bowel Disease: Clear Mind, Happy Colon

A very strong field of 15 candidates applied for two $75,000 CCA IBD PhD Scholarships, offered over 3 years.

CCA congratulates the two successful candidates:

  • Jessica Fitzpatrick
    A dietitian from Monash University and Alfred Health for her study ‘The role of a low emulsifier diet in treating Crohn’s disease’.
    Dietary emulsifiers are a category of food additives that are found readily available in the food supply. In animal models, emulsifiers cause inflammation in the gut, similar to that seen in Crohn’s disease. This project aims at investigating if removing emulsifiers from the diet of people with Crohn’s disease induces disease remission.
  • Dr Ralley Prentice:
    From Monash University/Monash Health/Hudson Institute of Medical Research/St Vincent’s Hospital Melbourne will undertake the Pregnancy in Crohn’s and Colitis: Observations, Levels and Outcomes Extension study.
    Also known as the PICCOLO-X study, it is a multicentre study with observational and scientific aims. It is investigating how to accurately predict IBD activity in pregnancy and subsequently any changes to the foetal/neonatal immune system and brain development. The study will define how thiopurine metabolite, vedolizumab and ustekinumab levels vary through pregnancy, how much drug crosses the placenta, how quickly the baby clears the drug and finally, how this may affect the immune system of both mum and baby.

The Crohn’s Disease Exclusion Diet – a promising new therapy

By Dr Emma P. Halmos

About the Author

Accredited Practising Dietitian, Department of Gastroenterology, The Alfred Hospital & Monash University, Melbourne VIC 3004

Historically, diet was always dismissed as a therapy for Crohn’s disease, until the emergence of exclusive enteral nutrition (EEN), a six-week diet comprising only of liquid nutritional supplements. EEN has been proven many times to induce remission in up to 80% of patients with Crohn’s disease and launched a pivotal change to our view of diet. No longer could it be argued that diet had no bearing on disease activity, but replacing food with a synthetic meal replacement gave no clues as to what food components would drive or alleviate intestinal inflammation. Furthermore, living on nothing but supplements for six weeks is an extremely “unfriendly” treatment, so adherence is generally poor, particularly amongst adults. 

While our understanding about the specific food components and how they affect IBD is being investigated, one priority is to offer a better dietary treatment than EEN. So, the race was on to find a more attractive alternative to EEN and to prove its benefit in a human trial.  The first such diet was developed by a paediatric group in Israel, called the Crohn’s Disease Exclusion Diet (CDED) and the results of their first trial were published last year. 

Phases one and two were assessed in a trial of children with mildly active Crohn’s disease in comparison to EEN and showed to be equivalent in treating mild Crohn’s disease on both symptoms and markers of inflammation. This study showed promise for another dietary option to EEN that may be easier to adhere to, albeit still a difficult dietary treatment with rigid rules. 

The CDED has not yet been formally investigated in adults, as a stand-alone therapy without PEN or for moderate to severe disease, so caution must be taken in applying it in these circumstances. Furthermore, its impact on nutritional markers are unknown, so EEN may still be more suitable in some situations, such as in those who have planned surgery, where EEN can reduce disease activity as well as improve surgical recovery.

Since publication of the CDED, gastroenterologists and dietitians have been using it with our Crohn’s disease patients and have developed a feel for the practical pros and cons of the diet.  Unlike EEN, the CDED is better equipped to satisfy hunger, gives the feeling of being adequately full and does not seem to cause constipation, which is a common side effect of EEN. 

Conversely, the limited foods allowed on the CDED can cause difficulties, particularly for families, who may have to cook and eat two different meals. The CDED may also not be an option in someone who already restricts foods that are allowed on the CDED as the use of substitutions have not been assessed. As with any dietary treatment, discussion between patient, gastroenterologist and dietitian of CDED is necessary to ensure careful assessment, application and monitoring of health outcomes.

We know that holistic care can have a huge and positive impact on people living with and managing their Crohn’s disease or ulcerative colitis. However, research shows that access to allied health professionals is low, with fewer than 1 in 3 patients having a dietitian as part of their treatment team*.

The Solution

GutSmart – designed to educate and inform A new and exciting online education platform designed to further educate health professionals on Crohn’s disease and ulcerative colitis to better target the care of IBD patients.

Research links gut fungi to intestinal inflammation in Crohn’s disease

Results of a new study by researchers at Case Western Reserve University represent a step toward improving our understanding of Crohn’s disease and the factors that cause its intestinal inflammation.

Crohn’s disease is a type of inflammatory bowel disease that can lead to chronic inflammation of the entire digestive tract. Symptoms include diarrhea, pain and cramping, fatigue, weight loss and more. There is no cure for Crohn’s disease, but patients can alleviate symptoms with current treatment options.  

 New treatment options for Crohn’s disease patients may be on the horizon thanks to the research linking a common fungal pathogen to inflammatory bowel disease.

The study recently appeared in Cellular and Molecular Gastroenterology and Hepatology.

This new research from the Case Western Reserve School of Medicine focuses on the role of the fungus, Candida tropicalis (C. tropicalis), in triggering chronic inflammation within the gut microbiome. The gut microbiome is a complex ecosystem of fungus and bacteria found within the digestive tract.

Researchers introduced the fungus into animal models and induced colitis (inflammation of only the large intestine) through a chemical compound. The models infected with C. tropicalis showed severe inflammation and significant imbalance of the gut microbiome with changes in bacteria levels.

Researchers say the findings show that this imbalance of fungi and bacteria can create a predisposition to inflammatory bowel disease. Past studies have shown that people with Crohn’s disease have higher levels of C. tropicalis when compared to healthy individuals. 

Understanding the impact of C. tropicalis on a person’s health will play a role in developing treatments for Crohn’s disease.

“Our findings provide a scientific rationale for eliminating C. tropicalis fungal infection of the gut,” said Fabio Cominelli, professor of medicine and pathology and associate dean for program development at the Case Western Reserve School of Medicine. “The next step in our research is to study other fungal organisms within the gut and then antifungal therapies in patients with this devastating condition. Remission is very difficult to obtain in Crohn’s disease patients.”

Original source here.

First structure of human protein complex with ‘licence to kill’

A team of WEHI researchers has for the first time visualised a human cell death complex linked to autoimmune and inflammatory conditions, such as inflammatory bowel disease, and injuries associated with excessive cell death.

Using the Australian Synchrotron, the team solved the structure of the human cell death proteins MLKL and RIPK3 bound to each other, as well as human RIPK3 alone. When RIPK3 activates MLKL, it triggers a type of inflammatory cell death called necroptosis that kills the cell and alerts the immune system that it is under attack. However, when uncontrolled, necroptosis has been linked to human inflammatory diseases.

The findings will help scientists discover drugs that can target and suppress cell death by necroptosis, which could lead to new treatments for a range of autoimmune and inflammatory diseases including inflammatory bowel disease, renal injury and diabetes.

The research, published in Nature Communications, was led by WEHI researchers Yanxiang Meng, Dr Katherine Davies, Associate Professor Peter Czabotar and Associate Professor James Murphy. The discovery is the latest in an almost 15-year-long journey to understand necroptosis for treating disease.

At a glance

‘The cell death pathway’

Necroptosis is a type of inflammatory cell death process that helps protect the body against infection. Most often triggered when a cell is infected by a virus or bacteria, the cell is instructed to die and send inflammatory signals to warn the immune system of foreign invaders. However, when necroptosis is uncontrolled or excessive, the inflammatory response can trigger disease.

PhD student Yanxiang Meng said that MLKL and RIPK3 are bound in an inert state in all cells of the body, waiting to be activated.

“MLKL and RIPK3 form an inert complex, with RIPK3 ‘holding’ MLKL in an inactive state to prevent necroptotic cell death,” he said.

“When the cell is infected, RIPK3 chemically modifies MLKL then detaches, giving it a ‘licence to kill’ the infected or damaged cell for the greater good,” he said.

He said the Australian Synchrotron and Collaborative Crystallisation Centre (C3) facility at CSIRO were crucial to visualise the structure of human forms of RIPK3 bound to human MLKL for the first time.

“The necroptotic cell death proteins are conserved across different organisms, however there are differences between the proteins’ structures in different animals and how they bind to each other.

“We showed that the human versions of these proteins bind differently to what we have seen in other species. This is something the scientific community has been waiting many years for.”

New targets for drug discovery

Dr Davies said the team hoped this structural information would, in the future, lead to new treatment options for patients suffering from diseases linked to excessive necroptosis. 

“We now have a picture of how two key proteins in this death pathway are maintained in their dormant state. It would be interesting to know how this is regulated and leads to disease and whether this could be targeted with small molecule drugs,” she said.

The research was supported by ACRF, Australian Government National Health and Medical Research Council and Department of Education, Skills and Employment, Australian Institute of Nuclear Science and Engineering (AINSE) Postgraduate Research Award, Melbourne Research Scholarship, Wendy Dowsett Scholarship, and the Victorian Government. 

Original source here.

COVID-19 vaccine and IBD

Patients with inflammatory bowel disease (IBD) are frequently treated with immunosuppressive medications.

By Associate Professor Britt Christensen 

Key Messages

Prior to COVID-19 vaccine access, most recommendations and publications reported on preventing COVID-19 infection in immunocompromised patients by encouraging social exclusion. 

It was evident early in the pandemic that immune-compromised patients would be faced with additional concerns and consequences regarding both infection with SARS-CoV-2 and vaccination against COVID-19. It has therefore become a priority of my research activities to help address these concerns. 

As a researcher at the University of Melbourne and The Royal Melbourne Hospital, I lead a team of clinician scientists looking at multiple facets of IBD including the pathogenesis of IBD, monitoring and optimisation techniques and the development of new treatment strategies. 

Our team realised early on that there was a need for ongoing, updated information around SARS-CoV-2 infection and prevention in immunocompromised individuals for both patients and clinicians. This led to our review article published in Alimentary Pharmacology and Therapeutics early last year summarising the issues around prevention, diagnosis and management of COVID-19 infection in patients with IBD and highlighted that patients with IBD were unlikely to be at increased risk of being infected with SARS-CoV-2 or developing serious COVID-19. 

The exception to this was patients on high dose corticosteroids who may be more likely to develop serious complications from COVID-19. We therefore recommended that patients stay on maintenance medical therapy with the aim to reduce flares, prevent the need for corticosteroids and prevent inpatient admission where patients may be more likely to be exposed. These conclusions have since been confirmed in prospective studies around the world. Our research group published a further review article on COVID-19 vaccination and IBD which highlighted that COVID-19 vaccination is safe in IBD patients and is recommended early. We also concluded that high dose corticosteroids may reduce the immune response to COVID-19 vaccination and therefore in areas of low community transmission, it may be prudent to withhold vaccination in patients on high dose corticosteroids until they are on equivalent doses of prednisolone <20mg per day. 

Undergoing the process of this vaccine review highlighted to our team the knowledge gap regarding immune responses to COVID-19 vaccination in patients with autoimmune conditions on a range of immunosuppressive medications.

Remarkably, within 18 months of the beginning of the pandemic, nine COVID-19 vaccines worldwide have been approved. However, clinical trials for these vaccines have excluded patients who are immunocompromised or been exposed to immunosuppressive medications within 3-6 months of vaccine administration. Therefore, the efficacy and safety of COVID-19 vaccines in these patient cohorts remains to be determined. 

This led our research team to Professor Katherine Kedzierska’s incredible lab at The Doherty Institute. Together with my fellow Eva Zhang, Dr Katherine Bond Head of Microbiology at The Royal Melbourne Hospital and Oahn Nguyen an NHRMC Fellow at The Doherty Institute, we have set up the exciting collaborative research study, Immune Responses to COVID-19 Vaccination in Immunocompromised Hosts (IRVAX).

This single site prospective observational cohort study aims to characterise the immune responses to COVID-19 vaccines in patients with autoimmune conditions including inflammatory bowel disease, rheumatological and dermatological diseases who are taking immunosuppressant medications including biological agents. 

107 patients have been recruited and serial blood tests before and after their first, second and, where applicable, third (both primary and booster) COVID-19 vaccine are being collected. We are analysing antibody and T cell response at these various time-points and differences in the immune response in this immunosuppressed group will be compared to healthy controls. We will also evaluate immune responses stratified by immunosuppressive medication regimen, autoimmune condition and type of vaccine received. 

This study will be one of the first to characterise the T cell response in addition to B cell response to COVID-19 vaccination in patients with autoimmune conditions on a range of immunosuppressants. It will also be the first study to describe the immune response to third dose primary vaccination and booster vaccination in an immunocompromised cohort with autoimmune diseases and one of the first to be able to compare these results to healthy controls. This study will allow us to accurately determine whether and to what degree immunosuppressive medications have an impact on the immune response to vaccination. This will be practice changing and provide the evidence required to develop accurate guidelines regarding vaccine timing, dosing and protection in this vulnerable group. 


  1. Rubin DT, Abreu MT, Siegel CA et al. Management of patients with Crohn’s disease and ulcerative colitis during the coronavirus disease-2019 pandemic: results of an international meeting. Gastroenterology. 2020 (In Press) (part of international meeting)
  2. Al-Ani A… Christensen B. Review Article: Prevention, diagnosis and management of COVID-19 in the inflammatory bowel disease patient. Aliment Pharmacol Ther. 2020 Jul;52(1):54-72. doi: 10.1111/apt.15779.Epub 2020 May 26
  3. Al-Ani A… Christensen B. Practical management of inflammatory bowel disease patients during the COVID-19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty. Intern Med J. 2020 July. Doi: 10.1111/imj/14889
  4. Garg M… Christensen B. Low Population MortalityFrom COVID-19 in Countries South of Latitude 35 Degrees North-supports Vitamin D as a Factor Determining Severity. Authors’ Reply. Aliment Pharmacol Ther. 2020 Jun;51(12):1438-1439. doi: 10.1111/apt.15796.Epub 2020 May 12
  5. Garg M, Christensen B, et al. Gastrointestinal ACE2, COVID-19 and IBD–opportunity in the face of tragedy? 2020 doi: 10.1053/j.gastro.2020.04.051
  6. Al-Ani A… Christensen B. Authors’ Reply to Letter: IBD Nurse – Pivotal Role in the Time of the Pandemic. Aliment Pharcol Ther. In Press. 2020
  7. A-Ani A…. Christensen B. Authors Reply To Letter: Is Pneumococcal Vaccination Safe During Covid-19 Pandemic? Aliment Pharcol Ther. In Press. 2020
  8. Seigal C, Christensen B et al. Review Article: Guidance for Restarting Inflammatory Bowel Disease Therapy in Patients Who Withheld Immunosuppressant medications During COVID-19. J Crohn’s Colitis. In Press. 2020
  9. Prentice RE, Al-Ani A, Christensen B. Managing COVID-19 in patients with inflammatory bowel disease: navigating unprecedented challenges. Internal Medicine Journal. 2021 Feb 1;51(2).
  10. Prentice R, Rentsch C, Al-Ani AH, Zhang E, Johnson D, Halliday J, Bryant R, Begun J, Ward M,7 Lewinden PJ, Connor SJ, Ghaly S , Christensen B. Review Article: SARS-CoV-2 Vaccination in Patients with Inflammatory Bowel Disease. GastroHep 2021 Accepted. In Press
  11. Al-Ani AH, Prentice RE, Rentsch C, Christensen B. SARS-CoV-2 infection in two inflammatory bowel disease patients treated with dual targeted therapy-Authors’ reply. Aliment Pharmacol Ther. 2021:766-7.

Is Crohn’s disease considered an autoimmune disease?

Whether Crohn’s can be considered an autoimmune disease remains unclear.

By Jacquelyn Cafasso 

Crohn’s disease is a type of inflammatory bowel disease (IBD). People with Crohn’s disease experience inflammation in their gastrointestinal tract, most commonly in the small and large intestines. This causes symptoms such as diarrhea, stomach cramps, bloody stool, fever, and weight loss.

An autoimmune disease happens when your immune system attacks healthy cells in your body.

Some people hypothesize that in Crohn’s disease, the immune system is attacking healthy cells of the digestive tract or the bacteria naturally present in the digestive tract.

We’ll dive in and look at what the research shows and what additional data we need to answer this question.Is Crohn’s an autoimmune disease?

The immune system protects the body against foreign invaders, like viruses, bacteria, and parasites. When these harmful invaders enter the body, the immune system identifies them and launches an attack to eliminate the threat.

An autoimmune disorder is when the body’s immune system mistakenly attacks healthy cells of the body. This often results in inflammation.

Although the immune system is thought to be involved in Crohn’s, the disease isn’t classified as an autoimmune disorder. In fact, the exact cause of Crohn’s disease is still not completely understood.

The researchTrusted Source suggests that the immune system is launching some sort of inappropriate response in people with Crohn’s disease.

However, the current evidence isn’t strong enough to prove that the body is creating antibodies against itself. Crohn’s disease also fails to meet the current standard criteria for classification as an autoimmune disorder.

What causes Crohn’s disease?

Research suggests that the immune system, along with genetics and environmental factors, likely all play a role in the development of Crohn’s disease.

Older research showed that about 14 percentTrusted Source of the people with Crohn’s disease studied also have a first-degree relative — such as a parent, child, or sibling — with the disease. This suggests that genes do play a role.

In addition, several environmental factors and other risk factors have been identified that increase our chance of developing Crohn’s disease. These include:

Are any other autoimmune diseases connected to Crohn’s?

People with Crohn’s disease often have an increased risk of having an autoimmune disorder, which suggests there may be a connection.

2017 population-based registry study found that certain autoimmune diseases were significantly more common in people with IBD compared to the control group. The study included 47,325 people with Crohn’s disease or ulcerative colitis or both.

For people with Crohn’s, studies find that they’re at a higher risk of having another autoimmune disorder, such as:

This research suggests an overlap between Crohn’s disease and autoimmune conditions. There may also be certain genes that play a role in the development of several related conditions.

More research is needed to fully understand the reason behind this connection.

The bottom line

Crohn’s disease Is a complex disease. While it technically isn’t an autoimmune disease, a malfunctioning immune system likely does play a role in its cause.

Other factors, including genetics and environmental factors, likely also contribute to the development of Crohn’s disease.

If you have Crohn’s disease, you’re at an increased risk of also developing an autoimmune condition. This suggests some overlap in the process by which Crohn’s disease and autoimmune disorders develop in the body.

More research is needed to understand the role of the immune system in Crohn’s disease. Original source here.

Glial cells crucial to maintaining healthy gut immunity

Researchers at the Francis Crick Institute have uncovered a fundamental role of glial cells in the nervous system of the gut in maintaining a healthy intestine.

These cells have been found to coordinate the immune responses of the gut following pathogen invasion and could be key targets when exploring new treatments for inflammatory bowel conditions.

Maintaining a healthy intestine and repairing tissue after infection or other types of injury is a complex process, and if this goes wrong, it can lead to inflammatory bowel diseases, such as Crohn’s disease and colitis. While much previous research in this area has focused on the activity of different immune cells, a lot of mysteries about the mechanisms behind these diseases still remain unanswered, which suggests that other cells may play a critical role.

In their study, published in Nature today (20 October), researchers studied the role of enteric glial cells in response to tissue damage. These cells lie within the gut wall and form part of the enteric nervous system which governs the contractions of intestinal muscles and other aspects of digestive function.

They infected mice with a common roundworm parasite, Heligmosomoides polygyrus, and found that when the parasite invades the gut wall, a protein, called interferon gamma, is quickly released by immune cells. Although this protein so far was thought to target cells of the immune system, this new study found that one of its first targets are the nearby glial cells. The protein activates these cells which then release signals that attract other immune cells to the site of damage to fight the infection.

To identify if similar mechanisms occur in humans, the researchers analysed data previously collected by others of colon samples from people with ulcerative colitis, a long-term condition where the colon and rectum become inflamed, and which causes severe diarrhoea and stomach cramps. Similar to the mouse cells, genes associated with interferon gamma were also activated in the human glial cells. This suggests that glial cells in the human gut are also implicated in inflammatory conditions of this organ.

Fränze Progatzky, author and postdoctoral scientist in the Crick’s Development and Homeostasis of the Nervous System Lab, says: “Sadly, currently treatments for inflammatory bowel disease are often limited to alleviating the symptoms, rather than tackling the cause. Our insights into the importance of enteric glial cells in maintaining a healthy intestine open the door to further studies into how these cells work and interact with the immune system and in the future could help us develop potential new treatments for these conditions.”

The team also studied the role of glial cells in maintaining healthy intestinal gut tissues, in the absence of infection. To do this, they blocked the ability of enteric glial cells to be activated by interferon gamma and found that this led to tissue inflammation even in normal mice. This shows the cells are also important outside of disease or injury, in maintaining healthy intestinal tissue.

Vassilis Pachnis, author and group leader of the Development and Homeostasis of the Nervous System Lab at the Crick, says: “Glial cells are present in many organs, and so it’s possible they also play similar roles in maintaining healthy tissue and mounting appropriate responses to pathogens or toxins in other parts of the body. It will be exciting to explore this possibility further.”

This research was carried out in collaboration with the AhRimmunity Laboratory at the Crick, led by Gitta Stockinger, and is part of an ongoing collaboration between the labs to study the processes which influence health and disease in the gut. 

Original source here.