Background:Complementary and integrative medicine (CIM) modalities, particularly probiotics, prebiotics, and fermentable dietary fibers (PPF) use in IBD patients is common and increasing, particularly for symptom management. This study aimed to assess the prevalence of CIM and PPF use among IBD patients and to identify potential demographic and clinical factors associated with utilization. Methods:This was a cross-sectional study of adult IBD patients at a tertiary IBD centre in Western Canada. A self-administered questionnaire and chart review were performed, focusing on demographic and clinical characteristics, CIM and PPF use in the past year (current) and/or lifetime, and sources of awareness about PPF products. Results:A total of 267 patients were included, 182 with CD and 85 with UC. Overall, 89.9% of participants reported CIM use in the current year, while the current and lifetime prevalence of PPF use was 51 and 63%, respectively. UC diagnosis was associated with increased likelihood of current PPF use (OR: 1.91, 95% CI: 1.10-3.12). Holding a university degree was associated with increased likelihood of lifetime PPF use (OR: 2.21, 95% CI: 1.07-4.55). PPF awareness through gastroenterologists (OR: 3.19, 95% CI: 1.55-6.58) was significantly associated with lifetime PPF use. Conclusion:Use of CIM modalities such as PPF is common among IBD patients. This study found that lifetime PPF use was associated with higher level of education and awareness through gastroenterologists. Healthcare providers, and specifically gastroenterology specialists, should routinely inquire about PPF use and educate IBD patients. Further studies are required to determine the benefit derived from these products.

BACKGROUND & AIMS: Inflammatory bowel diseases (IBD) are affected by dietary factors, including nondigestible carbohydrates (fibers), which are fermented by colonic microbes. Fibers are overall beneficial, but not all fibers are alike, and some patients with IBD report intolerance to fiber consumption. Given repro-ducible evidence of reduced fiber-fermenting microbes in patients with IBD, we hypothesized that fibers remain intact in select pa-tients with reduced fiber-fermenting microbes and can then bind host cell receptors, subsequently promoting gut inflammation. METHODS: Colonic biopsies cultured ex vivo and cell lines in vitro were incubated with oligofructose (5 g/L), or fermentation su-pernatants (24-hour anaerobic fermentation) and immune re-sponses (cytokine secretion [enzyme-linked immunosorbent assay/meso scale discovery] and expression [quantitative poly-merase chain reaction]) were assessed. Influence of microbiota in mediating host response was examined and taxonomic classifi- cation of microbiota was conducted with Kraken2 and metabolic profiling by HUMAnN2, using R software. RESULTS: Unfermented dietary b-fructan fibers induced proinflammatory cytokines in a subset of IBD intestinal biopsies cultured ex vivo, and immune cells (including peripheral blood mononuclear cells). Results were validated in an adult IBD randomized controlled trial examining b- fructan supplementation. The proinflammatory response to intact b-fructan required activation of the NLRP3 and TLR2 pathways. Fermentation of b-fructans by human gut whole microbiota cul-tures reduced the proinflammatory response, but only when mi-crobes were collected from patients without IBD or patients with inactive IBD. Fiber-induced immune responses correlated with microbe functions, luminal metabolites, and dietary fiber avoidance. CONCLUSION: Although fibers are typically beneficial in individuals with normal microbial fermentative potential, some dietary fibers have detrimental effects in select patients with active IBD who lack fermentative microbe activities. The study is publicly accessible at the U.S. National Institutes of Health data-base (clinicaltrials.gov identification number NCT02865707).

Persistent inflammation can trigger altered epigenetic, inflammatory, and bioenergetic states. Inflammatory bowel disease (IBD) is an idiopathic disease characterized by chronic inflammation of the gastrointestinal tract, with evidence of subsequent metabolic syndrome disorder. Studies have demonstrated that as many as 42% of patients with ulcerative colitis (UC) who are found to have high-grade dysplasia, either already had colorectal cancer (CRC) or develop it within a short time. The presence of low-grade dysplasia is also predictive of CRC. Many signaling pathways are shared among IBD and CRC, including cell survival, cell proliferation, angiogenesis, and inflammatory signaling pathways. Current IBD therapeutics target a small subset of molecular drivers of IBD, with many focused on the inflammatory aspect of the pathways. Thus, there is a great need to identify biomarkers of both IBD and CRC, that can be predictive of therapeutic efficacy, disease severity, and predisposition to CRC. In this study, we explored the changes in biomarkers specific for inflammatory, metabolic, and proliferative pathways, to help determine the relevance to both IBD and CRC. Our analysis demonstrated, for the first time in IBD, the loss of the tumor suppressor protein Ras associated family protein 1A (RASSF1A), via epigenetic changes, the hyperactivation of the obligate kinase of the NOD2 pathogen recognition receptor (receptor interacting protein kinase 2 [RIPK2]), the loss of activation of the metabolic kinase, AMP activated protein kinase (AMPKα1), and, lastly, the activation of the transcription factor and kinase Yes associated protein (YAP) kinase, that is involved in proliferation of cells. The expression and activation status of these four elements are mirrored in IBD, CRC, and IBD-CRC patients and, importantly, in matched blood and biopsy samples. The latter would suggest that biomarker analysis can be performed non-invasively, to understand IBD and CRC, without the need for invasive and costly endoscopic analysis. This study, for the first time, illustrates the need to understand IBD or CRC beyond an inflammatory perspective and the value of therapeutics directed to reset altered proliferative and metabolic states within the colon. The use of such therapeutics may truly drive patients into remission.

A relationship between ulcerative colitis (UC) and diet has been shown in epidemiological and experimental studies. In a 6-month, open-label, randomized, placebo-controlled trial, adult UC patients in clinical remission were randomized to either an “Anti-inflammatory Diet (AID)” or “Canada’s Food Guide (CFG)”. Menu plans in the AID were designed to increase the dietary intake of dietary fiber, probiotics, antioxidants, and omega-3 fatty acids and to decrease the intake of red meat, processed meat, and added sugar. Stool was collected for fecal calprotectin (FCP) and microbial analysis. Metabolomic analysis was performed on urine, serum, and stool samples at the baseline and study endpoint. In this study, 53 patients were randomized. Five (19.2%) patients in the AID and 8 (29.6%) patients in the CFG experienced a clinical relapse. The subclinical response to the intervention (defined as FCP < 150 µg/g at the endpoint) was significantly higher in the AID group (69.2 vs. 37.0%, p = 0.02). The patients in the AID group had an increased intake of zinc, phosphorus, selenium, yogurt, and seafood versus the control group. Adherence to the AID was associated with significant changes in the metabolome, with decreased fecal acetone and xanthine levels along with increased fecal taurine and urinary carnosine and p-hydroxybenzoic acid levels. The AID subjects also had increases in fecal Bifidobacteriaceae, Lachnospiraceae, and Ruminococcaceae. In this study, we found thatdietary modifications involving the increased intake of anti-inflammatory foods combined with a decreased intake of pro-inflammatory foods were associated with metabolic and microbial changes in UC patients in clinical remission and were effective in preventing subclinical inflammation.

Crohn's disease (CD) is an inflammatory bowel disease (IBD) sub-type characterized by transmural chronic inflammation of the gastrointestinal tract. Research indicates a complex CD etiology involving genetic predisposition and immune dysregulation in response to environmental triggers. The chronic mucosal inflammation has been associated with a dysregulated state, or dysbiosis, of the gut microbiome (bacteria), mycobiome (fungi), virome (bacteriophages and viruses), and archeaome (archaea) further affecting the interkingdom syntrophic relationships and host metabolism. Microbiota dysbiosis in CD is largely described by an increase in facultative anaerobic pathobionts at the expense of strict anaerobic Firmicutes, such as Faecalibacterium prausnitzii. In the mycobiome, reduced fungal diversity and fungal-bacteria interactions, along with a significantly increased abundance of Candida spp. and a decrease in Saccharomyces cerevisiae are well documented. Virome analysis also indicates a significant decrease in phage diversity, but an overall increase in phages infecting bacterial groups associated with intestinal inflammation. Finally, an increase in methanogenic archaea such as Methanosphaera stadtmanae exhibits high immunogenic potential and is associated with CD etiology. Common anti-inflammatory medications used in CD management (amino-salicylates, immunomodulators, and biologics) could also directly or indirectly affect the gut microbiome in CD. Other medications often used concomitantly in IBD, such as antibiotics, antidepressants, oral contraceptives, opioids, and proton pump inhibitors, have shown to alter the gut microbiota and account for increased susceptibility to disease onset or worsening of disease progression. In contrast, some environmental modifications through alternative therapies including fecal microbiota transplant (FMT), diet and dietary supplements with prebiotics, probiotics, and synbiotics have shown potential protective effects by reversing microbiota dysbiosis or by directly promoting beneficial microbes, together with minimal long-term adverse effects. In this review, we discuss the different approaches to modulating the global consortium of bacteria, fungi, viruses, and archaea in patients with CD through therapies that include antibiotics, probiotics, prebiotics, synbiotics, personalized diets, and FMT. We hope to provide evidence to encourage clinicians and researchers to incorporate these therapies into CD treatment options, along with making them aware of the limitations of these therapies, and indicate where more research is needed.

Abstract Background Dietary fibers are not digested in the bowel; they are fermented by microbes, typically promoting gut health. However, IBD patients experience sensitivity to consumption of fibers. Our previous findings offered the first mechanistic evidence demonstrating that unfermented dietary β-fructans (inulin and FOS) can induce pro-inflammatory cytokines in a subset of pediatric IBD colonic biopsies cultured ex vivo, and in the SYNERGY-1 (β-fructan) clinical study of adult remission UC patients. Incubating FOS with whole-microbiota intestinal washes from non-IBD or remission IBD patients improved fermentation and reduced pro-inflammatory responses, but not from patients with active disease. Fibre-induced immune responses correlated with microbe functions, luminal metabolites, and fibre avoidance. Aims Here we aimed to expand on our findings and define the role of microbial functions in mediating host response to β-fructans. Methods Colonic biopsies cultured ex vivo and cell lines in vitro were incubated with FOS (5g/L), or fermentation supernatants (24hr anaerobic fermentation). Immune responses (cytokine secretion [ELISA/MSD] and expression [qPCR]) were assessed. Taxonomic classification of microbial fermentation cultures was conducted with Kraken2 and metabolic profiling by HUMAnN2. HPLC and gas chromatography volatile fatty acid (CG-VFA) analysis were used to identify concentrations of remaining fibre and SCFAs following anaerobic fermentation. Results 7 microbial enzymes were identified to be predictive of cytokine (IL-1β, IL23, IL-5, IL-8, MIP-1α) secretion in ex vivo colonic biopsies from pediatric Crohn disease (CD; n=38), ulcerative colitis (UC; n=20), and non-IBD (n=21) patients, in response to β-fructans; their use as biomarkers of response was determined in patient stool from the SYNERGY-1 clinical study cohort. Fermentation of FOS by whole-microbe intestinal washes from only non-IBD or remission IBD patients reduced cytokine secretion, and our findings demonstrate that this was due to a combination of reduction of β-fructan present and production of a precise combination of anti-inflammatory SCFAs. Conclusions Our findings suggest that intolerance and avoidance of fibers in select IBD patients is associated with the inability to ferment these fibers, mediated by altered microbial functions (enzymes), leading to worsened inflammation. Data indicate that gut microbial function, not composition, predicts patient pro-inflammatory response to β-fructans, supporting our hypothesis that overall community function impacts fibre fermentation and affects associated pro-inflammatory effects. Our work highlights select disease state scenarios in which administration of fermentable fibers should be avoided and tailored dietary interventions considered. Funding Agencies CIHRWeston Foundation, Mitacs

BackgroundUlcerative colitis (UC) is associated with altered intestinal microbiome (‘dysbiosis’), most significantly, reduced strict butyrate-producing anaerobes and increased facultative anaerobes. Inulin-type prebiotics appear to reduce and prevent colitis in preclinical studies and small clinical trials. However, these results need to be validated in randomized controlled clinical trial (RCT) studies.AimsThe aim of this RCT study was to assess the efficacy of β-fructans (oligofructose and inulin) in preventing relapses in UC patients in clinical remission as well as identify potential mechanisms of activity.MethodsAdult UC patients in clinical remission (total Mayo score ≤ 2) were randomized to supplement their diet with 15g/d of either β-fructans (oligofructose and inulin; Synergy1/Prebiotin) or placebo (maltodextrin) for 6 months. Partial Mayo scores, medications, adverse events and intervention compliance were monitored monthly. Fecal specimens were collected throughout the study to measure fecal calprotectin (FCP), along with stool metabolites.ResultsEighty-nine UC patients in clinical remission were randomized to β-fructans (n=43) or placebo (n=46). Of those, 11 participants never started, 2 were withdrawn, and 76 were included in the study population (β-fructans n=35; placebo n=41). Although there was no difference in symptomatic clinical flare (β-fructans n=11 flare; placebo n=10 flare, P=0.60), patients randomized to oligofructose and inulin showed only a 3-fold median FCP increase versus 17-fold in the placebo group (P=0.038). Interestingly, antibiotics and serotonin reuptake inhibitors significantly increased the relative risk (RR) of flare (RR 3.321, 95% Cl 2.005 to 5.344, P < 0.0001). β-Fructan intake significantly increased anti-inflammatory fecal metabolites (arabinose, L-arabitol, 5-oxo-D-proline).ConclusionsAlthough oligofructose and inulin did not prevent symptomatic relapses in UC patients, their oral administration significantly reduced the severity of biochemical relapse compared to placebo which was further associated with increased anti-inflammatory metabolites.

: The worldwide incidence of paediatric inflammatory bowel diseases (pIBD) is increasing, especially in the Western world, but the pathophysiology of these diseases remains poorly understood. Genetic susceptibility, an aberrant immune response, alterations in the intestinal microbiome, and a patient's environment, including diet, have been found to contribute to disease development. Diet is of particular interest as this modifiable factor provides a unique opportunity to amend the interaction between gut microbes, host metabolism, and immunity. Certain dietary factors, such as fibres, are fermented by gut microbes, resulting in key regulators of the host gut environment, including short-chain fatty acids (SCFA) and other metabolites. Several SCFA-producing commensal bacteria, including Roseburia and Faecalibacteria, are reduced in pIBD, further illustrated by lower SCFA levels. SCFAs are thought to improve barrier integrity and regulate immune tolerance, two areas shown to be deficient in active pIBD. An altered host-microbe relationship, partly mediated by microbial metabolites (e.g., SCFAs), is evident and often varies with disease activity. Despite these insights into diet's relationship with IBD pathogenesis, nutritional interventions remain underutilised and most current IBD therapies focus mainly on suppressing the immune system, exposing patients to potential risks and side effects. Novel and established nutritional therapies, capable of modifying these host-microbe relationships, are becoming increasingly available for clinical use. Here we provide an overview of the pathogenesis of pIBD and then discuss the evidence suggesting that modification of these host-microbe relationships via diet or other therapies is linked to therapy effectiveness in IBD, ultimately ameliorating gut inflammation and restoring intestinal homeostasis.

Abstract Background Inflammatory bowel disease (IBD) is characterized by altered intestinal microbiome (i.e. dysbiosis), described by reduced strict butyrate-producing anaerobes versus increased facultative anaerobes. Data from preclinical studies and clinical trials show prebiotic inulin-type fibers can prevent and reduce colitis. However, other dietary fibers (e.g. resistant starches, RS) are understudied and it is unknown if RS-induced microbial shifts are protective in experimental colitis. Aims Assess efficacy of isomaltodextrin (IMD), a novel RS, to reduce intestinal inflammation in HLA-B27 transgenic (TG) rat colitis model and identify protective mechanisms associated with gut microbial composition and function. Methods 4 week old HLA-B27 TG rats were fed standard chow supplemented with: 7.5% IMD (low dose, LD), 15% IMD (high dose, HD), negative control (15% cellulose, NC), or positive control (15% fructooligosaccharides, PC) for 12 weeks. Body weight and food intake were measured. Cecal and colonic inflammation assessed by weight/length ratio, macroscopic scoring and mucosal IL-1β secretion. Changes in microbial energy metabolism evaluated by measuring short chain fatty acid (SCFA) production in stool and cecal contents. Endpoint fecal and cecal microbiota composition differences assessed by 16S rRNA gene sequencing (Illumina MiSeq platform). Results IMD showed dose-dependent effect on cecal inflammation, measured by macroscopic tissue scoring, weight/length ratio and IL-1β secretion. HD rats had significantly lower cecum IL-1β concentration compared to NC (q=0.01), while LD showed only a trend (q=0.09). HD had significantly higher cecal amounts of Bacteroidaceae and Allobaculum spp. and lower amounts of Peptostreptococcaceae, Eubacterium and Barnesiella spp. versus the LD and NC. HD was associated with significantly higher total SCFA compared to NC (q<0.01) and showed a trend of higher total SCFA than LD (q=0.06). Analysis of SCFAs revealed propionate, isobutyrate and valerate ratios were significantly lower in HD than LD and NC. HD showed a trend of higher ratio of butyrate + acetate compared to NC. This suggests increased carbohydrate fermentation by acetate-producing and -converting microbial groups. Correlation analysis confirmed IL-1β concentrations were positively associated with isobutyrate (r=0.52, q<0.01), valerate (r=0.54, q<0.01), and propionate (r=0.48, q<0.01), suggesting their use as chronic inflammation markers in HLA-B27 models. Conclusions IMD was dose-dependently effective in reducing chronic cecal inflammation in experimental colitis. Benefits were associated with specific shifts in gut microbiome composition and SCFA production. Results from this preclinical study warrant future microbiota-altering intervention trials using IMD in clinical IBD. Funding Agencies Hayashibara Co., Ltd.

Abstract Background Dietary fibers pass through the bowel undigested and are fermented within the intestine by microbes, typically promoting gut health. However, many IBD patients describe experiencing sensitivity to fibers. β-glucan, found on the surface of fungal cells during fungal infection, has been shown to bind to fiber receptors, such as Dectin-1, on host immune cells, resulting in a pro-inflammatory response. These fungal fibres share properties with dietary fibers. Aims As an altered gut microbial composition has been associated with IBD, we hypothesized that the loss of fiber-fermenting microbes populating the gut in IBD could lead to dietary fibers not being efficiently broken down into their beneficial biproducts (e.g. short chain fatty acids; SCFA), resulting in binding of intact fibers to pro-inflammatory host cell receptors. Methods Immune and epithelial cell lines and colonic biopsies cultured ex vivo were incubated with oligofructose or inulin (5g/L), or pre-fermented fibers (24hr anaerobic fermentation). Immune responses were measured by cytokine secretion (ELISA), and expression (qPCR). Barrier integrity was measured by transepithelial resistance (TEER). Food frequency questionnaire (FFQ) data of patient fiber consumption were correlated with gut microbes (shotgun sequencing) and immune responses to fiber in patient biopsies. Results Unfermented oligofructose induced IL-1β secretion in leukocytes (macrophage, T cell, neutrophil) and in colon biopsies from pediatric Crohn disease (CD; n=38) and ulcerative colitis (UC; n=20) patients cultured ex vivo, but not in non-IBD patients (n=21). IL-1β secretion was greater in patients with more severe disease. Pre-fermentation of oligofructose by whole-microbe intestinal washes from non-IBD patients or remission patients reduced secretion of IL-1β, while whole microbe intestinal washes from severe IBD patients were unable to ferment oligofructose or reduce cytokine secretion. Fiber effects on IL-1β secretion in biopsies positively correlated with effects on barrier integrity in T84 cells. Fiber-associated immune responses in patient biopsies cultured ex vivo (ELISA) correlated with fiber avoidance (FFQ) and gut microbiome (sequencing) in matching patient samples. Conclusions Our findings demonstrate that intolerance and avoidance of prebiotic fibers in select IBD patients is associated with the inability to ferment these fibers, leading to pro-inflammatory immune responses and intestinal barrier disruption. This highlights select disease state scenarios, in which administration of fermentable fibers should be avoided and tailored dietary interventions should be considered in IBD patients. Funding Agencies CIHRWeston Foundation

Abstract Background The etiology of inflammatory bowel diseases (IBD) remains unknown, although gut microorganisms and diet have been implicated. Dietary fibers pass through the bowel undigested and are fermented within the intestine by microbes, promoting gut health. However, many IBD patients describe experiencing sensitivity to fibres. Interestingly, fiber receptors on immune cells are able to interact with fibers typically found on the surface of fungal cells (which share properties with dietary fibers), for example, resulting in a paradoxical pro-inflammatory response. Aims As an altered microbial composition is a hallmark of IBD, we hypothesized that the loss of fiber fermenting-microbes populating the IBD gut could lead to dietary fibers not being efficiently broken down into their beneficial biproducts, resulting in binding of intact fibers to pro-inflammatory host cell receptors. This can ultimately drive pro-inflammatory responses and a microenvironment that promotes continued dysbiosis and increased pathogenicity of select microbes, as observed in IBD. Methods Fiber receptor expression gut was examined using immunohistochemistry and flow cytometry and demonstrated elevated receptor expression due to increased presence of immune cells in IBD patient biopsies. Cytokine secretion, in response to fiber (5mg/mL) or pre-fermented fibers, cultured with microbes of interest, was measured by ELISAs in cell lines in vitro and biopsy tissues cultured ex vivo. Results Whole-fibers induced pro-inflammatory cytokine production in macrophage, monocytes, and neutrophils. Specific microbes were capable of fermenting fiber, measured by gas chromatography. Pre-fermentation of fibers by these microbes reduced inflammatory cytokine production. The fiber oligofructose increased IL-1β in pediatric CD (n=44) and UC (n=29) biopsies cultured ex vivo but not in non-IBD (n=25). The increase was greater in patients with more severe disease. Pre-fermentation of oligofructose by bacteria reduced this secretion of IL-1β. Whole-microbe intestinal washes from severe IBD patients were unable to ferment oligofructose or reduce fiber-associated inflammation in macrophage cells compared to remission or non-IBD children. Statistical analysis of food frequency questionnaire (FFQ) data on fiber consumption demonstrated that fiber-associated inflammation in patient biopsies cultured ex vivo (ELISA and qPCR) correlated with fiber avoidance (FFQ). Conclusions Comparing in vitro findings to our patient FFQs, intestinal washes (microbe abundance), and detailed patient history will better define the relationship between microbes, dietary fibers, and gut inflammation in IBD. This will allow for tailored dietary intervention through dietary recommendations, prebiotic, and/or probiotic therapies. Funding Agencies CCCWeston Foundation, WCHRI

BackgroundInflammatory bowel diseases (IBD) are a group of complex and multifactorial disorders with unknown etiology. Chronic intestinal inflammation develops against resident intestinal bacteria in genetically susceptible hosts. We hypothesized that host intestinal immunoglobulin (Ig) G can be used to identify bacteria involved in IBD pathogenesis.ResultsIgG-bound and -unbound microorganisms were collected from 32 pediatric terminal ileum aspirate washes during colonoscopy [non-IBD (n=10), Crohn disease (n=15), and ulcerative colitis (n=7)], and composition was assessed using the Illumina MiSeq platform. In vitro analysis of invasive capacity was evaluated by fluorescence in situ hybridization and gentamicin invasion assay; immune activation was measured by qPCR. Despite considerable inter-individual variations, IgG binding favored specific and unique mucosa-associated species in pediatric IBD patients. Burkholderia cepacia, Flavonifractor plautii, and Rumminococcus sp. demonstrated increased IgG binding, while Pseudomonas ST29 demonstrated reduced IgG binding, in IBD. In vitro validation confirmed that B. cepacia, F. plautii, and Rumminococcus display invasive potential while Pseudomonas protogens did not.ConclusionUsing IgG as a marker of pathobionts in larger patient cohorts to identify microbes and elucidate their role in IBD pathogenesis will potentially underpin new strategies to facilitate development of novel, targeted diagnostic, and therapeutic approaches. Interestingly, this method can be used beyond the scope of this manuscript to evaluate altered gut pathobionts in a number of diseases associated with altered microbiota including arthritis, obesity, diabetes mellitus, alcoholic liver disease, cirrhosis, metabolic syndrome, and carcinomas.

The association between diet and inflammatory bowel disease remains largely unknown. To date, few studies have been conducted to investigate the association between the inflammatory potential of a diet and disease activity in patients with inflammatory bowel disease. We conducted this study to evaluate the relationship between dietary inflammatory index (DII) and fecal calprotectin (FCP) levels in a cohort of ulcerative colitis (UC) patients. This was a cross-sectional study on adult UC patients who were in clinical remission (partial Mayo<3). Dietary intake in the past year was assessed using a validated self-administered food frequency questionnaire (Diet History Questionnaire II). Intake of 29 macro- and micronutrients as well as caffeine was used to calculate total DII score (minimum score: -3.6 maximum score:3.5). A greater DII was indicative of a more pro-inflammatory diet. FCP was measured using ELISA. FCP >250 µg/g which is associated with higher disease activity and increased probability of UC relapse was considered as high. Fifty-nine UC patients were recruited. Their mean age was 40.3 ± 14.2 years and 61% of them were females. Their mean DII score was -0.3 ± 1.9. Patients with high FCP had higher DII scores than patients with low FCP (0.8 ± 1.7 vs. -0.8 ± 1.8, P=0.004). UC patients with a more pro-inflammatory diet (DII score > -0.5 (median value)) were more likely to have high fecal calprotectin in comparison to patients with a less pro-inflammatory diet (44.8 vs. 16.7%, P=0.02, Odds ratio: 4.1, 95% confidence interval: 1.2–13.6). In addition, Spearman analysis suggested a significant correlation between FCP and DII scores (r=0.35, P=0.007). Among different components of DII, FCP was correlated significantly with dietary intake of alcohol (r= -0.29), β-Carotene (r= -0.44), fiber (r= -0.23), polyunsaturated fatty acids (r= -0.22), and vitamin E (r= -0.42). We found that a pro-inflammatory diet was related to increased FCP in UC patients. These findings suggest that an association between diet and increased disease activity or relapse might be mediated through inflammatory properties of the diet. Alberta Innovates - Bio Solutions

Inflammatory bowel diseases (IBD), including Crohn disease and ulcerative colitis, are chronic and severely debilitating gastrointestinal disorders, with rising prevalence, especially in children. While the etiology of IBD remains poorly understood, gut microorganisms and diet have been implicated in IBD pathogenesis. Interestingly, dietary fibers pass through the small bowel undigested and are fermented within the large intestine by specific gut microbes, promoting gut health by altering the gut microenvironment, modulation of the immune system, and altered energy metabolism. Our previous work indicates an altered balance between commensal and pathobiont microbes in IBD, suggesting one opportunity for the misregulation of fiber fermentation within the IBD gut. Interestingly, specific carbohydrate receptors on the surface of immune cells interact with fibers, such as those expressed by certain species of fungi, driving an inflammatory response. Here we hypothesize that the altered microbiota in IBD causes significant changes in fiber fermentation, ultimately driving intestinal inflammation. Bacterial growth rates in response to specific fibers were examined by OD600 growth curves. Bacterial fiber fermentation patterns were evaluated by mass spectrometry of SCFAs. The effects of specific fibers on bacterial pathogenicity when co-cultured with human HT29 epithelial cells was measured by gentamicin protection assays and visualized by microscopy. Immunohistochemistry of biopsy tissues collected from pediatric IBD (n=14) and control patients (n=7) was utilised to examine expression levels of fiber receptors expressed on human cells. We have demonstrated that commensal microorganism, isolated live from IBD patients, display a different pattern of fiber fermentation compared to pathobiont species. Specific fibers also increase the invasive potential of these pathobionts. Preliminary immunohistochemistry suggests that there is increased expression of specific carbohydrate receptors in IBD, suggesting an increased sensitivity to unfermented dietary fibers in these patients. These results suggest that some patients may display a sensitivity to specific dietary fibers due to a lack of appropriate fiber fermenting microbes in their gut. Profiling the patient specific microbiota of IBD patients may allow us to make more specific dietary recommendations to assist in reducing intestinal inflammation in IBD. Comparing in vitro findings to our readily available patient food frequency questionnaires (FFQs) and detailed patient history will allow us to define key disease features of IBD and also identify new and improved treatment options, such as microbe-altering treatments, and tailored nutritional recommendations. CCCCCFC

Gut microorganisms have been associated with the development of Crohn disease (CD) and ulcerative colitis (UC) in a number of studies to date; however, most studies focused on identifying microbial changes have examined only samples from stool or inflamed areas of the intestine, limiting the ability to differentiate between cause and effect. Therefore, we focused on bacteria from non-inflamed areas and sought to develop a method to specifically identify pathobionts. Our hypothesis was that immunoglobulin (Ig)G, an antibody naturally formed in response to invasive microbes, can be used as a novel marker of pathobionts in IBD patients. Building on our recent work that demonstrated altered composition and diversity of bacteria from the uninflamed terminal ileum (TI) in paediatric UC patients, we focused on microbes proximal to diseased areas as we believe they may drive inflammation distally. Intestinal washes were collected during endoscopy from the TI of paediatric IBD patients and non-IBD controls. Using fluorescence-activated cell sorting (FACS) we separated IgG-bound (IgG+) from unbound (IgG-) bacteria, extracted their DNA, and analysed composition by 16S and metagenomic sequencing using the Illumina MiSeq platform. We then confirmed virulence of specific IgG-bound bacteria in-vitro. FACS was efficient in separating IgG+ from IgG- bacteria; the method was validated by Image Cytometry. Greater numbers of IgG-bound microbes were observed in CD (2-fold) and UC (1.5-fold) patients, compared with non-IBD. Interestingly, while there was relatively little difference in species abundance between IBD and non-IBD patients, IgG binding favoured specific Bacteroidetes, Firmicutes, and Proteobacteria in CD, and specific Bacteroidetes and Proteobacteria in UC. Many of these changes were more prominent in moderate/severe disease than in cases that were mild/in remission. When examined in-vitro, selective IgG+ species displayed pro-inflammatory effects and invasive potential, supporting their pathobiont potential. Using FACS to isolate IgG-bound bacteria collected from luminal washes in children with IBD we selectively identified previously unrecognised mucosa-associated microbes with apparent pathobiont qualities, associated with IBD. Further characterizing the role of specific bacterial species bound by IgG may provide insight into IBD pathogenesis and could assist in directing therapies to those patients most likely to respond, including by use of microbe-altering treatments.

Inflammatory bowel diseases (IBD) are chronic inflammatory conditions of the intestines that are believed to be induced by abnormal activation of the immune cells in response to resident intestinal bacteria in genetically susceptible hosts. Probiotics, prebiotics and dietary fibres alter the gut microbiota and improve its function, thus potentially counteracting the development of inflammation. Unlike the current standard medications for IBD, these supplements are relatively safe. As such they are suggested as promising novel adjuvant modalities in the treatment of IBD. Although the role of these compounds in the prevention and treatment of IBD is understudied, there seems to be a widespread, undocumented use of these supplements by patients. Identification of usage of probiotics and prebiotics in IBD patients, will allow for optimization of therapy, and improved clinical outcomes. To assess the intake of probiotics, prebiotics and dietary fibre supplements in patients with IBD in Edmonton, Alberta. A cross-sectional, observational study using a 20-item survey questionnaire was used in patients with a diagnosis of IBD in the IBD Clinic at the University of Alberta. Data regarding demographics, disease characteristics, use and knowledge of probiotics, prebiotics and dietary fibre supplements was collected and analyzed using Fisher’s exact test. In this pilot study, 23 participants with a known diagnosis of IBD (57% ulcerative colitis, 39% Crohn’s disease, 4% indeterminate colitis) completed survey questionnaires. Statistical analysis demonstrated that a large number of participants were knowledgeable about probiotics and dietary fibres, but less about prebiotics (87% probiotics, 74% fibres, 43% prebiotics, P < 0.38). Sixty five per cent of surveyed patients have used these products in the past. However, regular usage (in the last year), was much lower (48% probiotics, 28% fibres, 4% prebiotics). Of those who used these alternative treatments in the past, 31% of patients experienced an increase in quality of life (QoL). Those without a university degree were more likely to use these products (67%, P < 0.37). The effect of gender on usage was negligible (53% males, 47% females, P < 1.0). Preliminary results did not reach statistical significance. This pilot study shows that a large proportion of IBD patients have used probiotics, prebiotics and dietary fibre supplements in the past despite the lack of well-proven efficacy. Since these microbiota targeting strategies have a great potential to improve disease outcomes, it is important that clinicians and researchers document their use. CIHR

A relationship between ulcerative colitis and diet has been shown in epidemiological and experimental studies. To investigate the effectiveness of an anti-inflammatory diet for maintenance of remission in UC patients. In this 6-month randomized control trial, adult UC patients in clinical remission (partial Mayo score<3) who had a disease relapse within the previous 18 months were randomized to either an “Anti-inflammatory Diet (AID)” or “Canada’s Food Guide (CFG)” as the control group.A dietitian provided dietary recommendations to all patients in four face-to-face (baseline, month 1, 3, and 6) and three telephone (month 2,4,5) sessions. Menu plans provided to patients in the AID group were designed to increase dietary intake of fiber, prebiotics, probiotics, anti-oxidants, omega-3 fatty acids and to decrease dietary intake of red or processed meat, added sugar and alcohol. To assess clinical relapse, partial Mayo scoring was done monthly. Monthly 24h dietary recalls were used to assess adherence to the diets. At baseline and month 6 or relapse, fecal calprotectin (FCP), serum CRP, and quality of life were assessed. Metabolomic analysis was performed on urine (GC-MS, DI- LC MS/MS), serum (NMR, DI-LC MS/MS) and stool (NMR) samples collected at baseline and month 6 or relapse. Fifty-three patients were randomized to the two diet groups. The mean age of participants was 41.4 ± 14.7 y and 34 (64.2%) subjects were female. Five(19.2%) patients in the AID and 8(29.6%) patients in the control group relapsed during the trial (P=0.38). Patients following CFG had a statistically significant increase in FCP from baseline to month6/relapse, while patients following the AID showed no significant increase in their FCP over the 6 months (Figure1A). At baseline, the metabolomic profiles of patients randomized to the two groups were similar. However, at 6 months/relapse, the two groups had separated (Figure1B). In comparison to CFG group, patients in the AID group had higher glutamic acid(stool), creatinine (stool), and carnosine (urine) but lower 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (urine), hydroxymandelic acid (urine), phosphatidylcholines (serum), acetone (stool), and Sumiki’s acid (urine). In comparison to the CFG group, patients in the AID group had a significant increase in dietary intake of some nutrients including zinc, selenium and phosphorus from baseline to month 6 or relapse. Modification of diet towards an inclusion of anti-inflammatory and reduction of inflammatory foods alters host and microbial metabolic pathways and can help prevent increases in colonic inflammation in UC patients in remission. Figure 1.A) Comparison of changes in fecal calprotectin levels from baseline to month 6/relapse between the two diet groups;B) Partial least squares discriminant analysis plot showing a significant difference in the metabolome of patients randomized to the two diet groups at month 6/relapse as identified by metabolites in urine,serum and fecal samples. Alberta Innovates Health Solutions