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Abstract Background Recurrent Clostridioides difficile infection (CDI) in patients with inflammatory bowel disease (IBD) is a clinical challenge. Fecal microbiota transplantation (FMT) has emerged as a recurrent CDI therapy. Anecdotal concerns exist regarding worsening of IBD activity; however, prospective data among IBD patients are limited. Methods Secondary analysis from an open-label, prospective, multicenter cohort study among IBD patients with 2 or more CDI episodes was performed. Participants underwent a single FMT by colonoscopy (250 mL, healthy universal donor). Secondary IBD-related outcomes included rate of de novo IBD flares, worsening IBD, and IBD improvement—all based on Mayo or Harvey-Bradshaw index (HBI) scores. Stool samples were collected for microbiome and targeted metabolomic profiling. Results Fifty patients enrolled in the study, among which 15 had Crohn’s disease (mean HBI, 5.8 ± 3.4) and 35 had ulcerative colitis (mean partial Mayo score, 4.2 ± 2.1). Overall, 49 patients received treatment. Among the Crohn’s disease cohort, 73.3% (11 of 15) had IBD improvement, and 4 (26.6%) had no disease activity change. Among the ulcerative colitis cohort, 62% (22 of 34) had IBD improvement, 29.4% (11 of 34) had no change, and 4% (1 of 34) experienced a de novo flare. Alpha diversity significantly increased post-FMT, and ulcerative colitis patients became more similar to the donor than Crohn’s disease patients (P = 0.04). Conclusion This prospective trial assessing FMT in IBD-CDI patients suggests IBD outcomes are better than reported in retrospective studies.

Faecal or biopsy samples are frequently used to analyse the gut microbiota, but issues remain with the provision and collection of such samples. Rectal swabs are widely-utilised in clinical practice and previous data demonstrate their potential role in microbiota analyses; however, studies to date have been heterogenous, and there are a particular lack of data concerning the utility of swabs for the analysis of the microbiota’s functionality and metabolome. We compared paired stool and rectal swab samples from healthy individuals to investigate whether rectal swabs are a reliable proxy for faecal sampling. There were no significant differences in key alpha and beta diversity measures between swab and faecal samples, and inter-subject variability was preserved. Additionally, no significant differences were demonstrated in abundance of major annotated phyla. Inferred gut functionality using Tax4Fun2 showed excellent correlation between the two sampling techniques (Pearson’s coefficient r = 0.9217, P  < 0.0001). Proton nuclear magnetic resonance ( 1 H NMR) spectroscopy enabled the detection of 20 metabolites, with overall excellent correlation identified between rectal swab and faecal samples for levels all metabolites collectively, although more variable degrees of association between swab and stool for levels of individual metabolites. These data support the utility of rectal swabs in both compositional and functional analyses of the gut microbiota.

Antibiotic treatment significantly disrupts the gut microbiome and promotes vancomycin-resistant enterococci (VRE) intestinal colonisation. These disruptions cause the intestine to act as a reservoir for VRE that seed difficult-to-treat infections. Here we show that antibiotics that promote VRE intestinal colonisation increase the concentration of a wide range of nutrients and decrease the concentration of a wide range of microbial metabolites. We show significant but incomplete suppression of VRE growth by individual short chain fatty acids that were decreased in antibiotic-treated faecal microbiomes. However, mixtures of short chain fatty acids provide complete or near complete suppression of VRE growth. We show that VRE use most nutrients increased in antibiotic-treated faecal microbiomes as carbon or nitrogen sources to support their growth, where Enterococcus faecium and Enterococcus faecalis have some common and some distinct preferences for the use of these specific nutrients. Finally, we show that E. faecium and E. faecalis occupy overlapping but distinct nutrient-defined intestinal niches that promote high growth when cultured with each other and when cultured with carbapenem-resistant Enterobacteriaceae . Our results demonstrate that VRE occupy distinct intestinal niches in the antibiotic-treated intestine, defined by their abilities to utilise specific enriched nutrients and their abilities to grow with reduced concentrations of inhibitory microbial metabolites. Here, the authors show that vancomycin-resistant enterococci grow in the antibiotic-treated gut microbiome by utilising enriched nutrients in the presence of reduced concentrations of inhibitory microbial metabolites.

[...]there is a clear case for further delineation of the underlying pathogenic processes of psoriasis, with a key aim being to exploit these for novel targeted therapeutics. Jingwen and colleagues’ initial analysis explored the transcriptome of the psoriatic plaques, to gain insight into possible gene expression differences among the three diseases. [...]the study found increased expression of neutrophil-associated genes, abnormal neutrophil counts and neutrophil migration in lesion skin, reinforcing the above-mentioned role of innate immunity in psoriasis.

We investigated intestinal permeability and fecal, plasma, and urine metabolomic profiles in methotrexate-treated active psoriatic arthritis (PsA) and how this related to clinical response following one sham or fecal microbiota transplantation (FMT). This exploratory study is based on the FLORA trial cohort, in which 31 patients with moderate-to-high peripheral PsA disease activity, despite at least 3 months of methotrexate-treatment, were included in a 26-week, double-blind, 1:1 randomized, sham-controlled trial. Participants were randomly allocated to receive either one healthy donor FMT (n = 15) or sham (n = 16) via gastroscopy. The primary trial end point was the proportion of treatment failures through 26 weeks. We performed a lactulose-to-mannitol ratio (LMR) test at baseline (n = 31) and at week 26 (n = 26) to assess small intestinal permeability. Metabolomic profiles in fecal, plasma, and urine samples collected at baseline, weeks 4, 12, and 26 were measured using H Nuclear Magnetic Resonance. Trial failures (n = 7) had significantly higher LMR compared with responders (n = 19) at week 26 (0.027 [0.017-0.33]) vs. 0.012 [0-0.064], P = 0.013), indicating increased intestinal permeability. Multivariate analysis revealed a significant model for responders (n = 19) versus failures (n = 12) at all time points based on their fecal (P < 0.0001) and plasma (P = 0.005) metabolomic profiles, whereas urine metabolomic profiles did not differ between groups (P = 1). Fecal N-acetyl glycoprotein GlycA correlated with Health Assessment Questionnaire Disability Index (coefficient = 0.50; P = 0.03) and fecal propionate correlated with American College of Rheumatology 20 response at week 26 (coefficient = 27, P = 0.02). Intestinal permeability and fecal and plasma metabolomic profiles of patients with PsA were associated with the primary clinical trial end point, failure versus responder.

Background Psoriasis is a chronic inflammatory disease of the skin affecting 2–3% of UK population. 30% of people affected by psoriasis will develop a distinct form of arthritis within 10 years of the skin condition onset. Although the pathogenesis of psoriatic arthritis is still unknown, there is a genetic predisposition triggered by environmental factors. Limited but convincing evidence link the gut microbiome to psoriatic arthritis. The Microbiome in Psoriatic ARThritis (Mi-PART) study propose is to characterise the microbiome-metabolic interface in patients affected by psoriatic arthritis to deepen our understanding of the pathogenesis of the disease. Methods This is a multicentre, prospective, observational study. Psoriatic arthritis ( n  = 65) and ankylosing spondylitis ( n  = 30) patients will be recruited in addition to a control group of healthy volunteers ( n  = 30). Patients eligibility will be evaluated against the Criteria for Psoriatic Arthritis (CASPAR), the Bath Ankylosing Spondylitis Activity Index (BASDAI) and the healthy volunteers who fulfil study inclusion and exclusion criteria. Information regarding their medical and medication history, demographics, diet and lifestyle will be collected. All the participants in the study will be asked to complete a 7-day food diary, to provide stool samples and to complete quality of life questionnaires. Routine clinical laboratory tests will be performed on blood and urine samples. Patients and healthy volunteers with gastrointestinal symptoms, previous history of cancer, gastrointestinal surgery in the previous 6 months or alcohol abuse will be excluded from the study. Discussion The aim of this trial is to characterise the microbiome of psoriatic arthritis patients and to compare it with microbiome of healthy volunteers and of patient with ankylosing spondylitis in order to define if different rheumatologic conditions are associated with characteristic microbiome profiles. Investigating the role of the microbiome in the development of psoriatic arthritis could deepen our understanding of the pathogenesis of the disease and potentially open the way to new therapies.

Immune checkpoint inhibitors (CPIs) are a relatively newly licenced cancer treatment, which make a once previously untreatable disease now amenable to a potential cure. Combination regimens of anti-CTLA4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. To probe the impact of immune checkpoints on intestinal homoeostasis, mice are challenged with anti-CTLA4 and anti-PD-1 immunotherapy and manipulation of the intestinal microbiota. The immune profile of the colon of these mice with CPI-colitis is analysed using bulk RNA sequencing, single-cell RNA sequencing and flow cytometry. CPI-colitis in mice is dependent on the composition of the intestinal microbiota and by the induction of lymphocytes expressing interferon-γ (IFNγ), cytotoxicity molecules and other pro-inflammatory cytokines/chemokines. This pre-clinical model of CPI-colitis could be attenuated following blockade of the IL23/IFNγ axis. Therapeutic targeting of IFNγ-producing lymphocytes or regulatory networks, may hold the key to reversing CPI-colitis. Immune checkpoint inhibitors (CPI) could effectively target cancers that are resistant to traditional therapy but may initiate immune related adverse effects, such as colitis. Here, authors characterise the gut immune microenvironment during CPI-colitis by bulk RNA sequencing, single-cell RNA sequencing and flow cytometry, and find that interleukin 23 plays an important role in promoting inflammation via cytotoxic polyfunctional IFNγ-producing lymphocytes.

Background and AimsImmune checkpoint inhibitors (CPI) have revolutionised cancer treatment, with previously untreatable disease now amenable to potential cure. Combination regimens of anti-CTLA4 and anti-PD-1 show enhanced efficacy but are prone to off target immune-mediated tissue injury, particularly at the barrier surfaces. CPI-induced colitis is a common a serious complication.MethodsTo probe the impact of immune checkpoints on intestinal homeostasis mice were challenged with combination anti-CTLA4 and anti-PD-1 immunotherapy, manipulation of the intestinal microbiota and antibody blockade/depletion studies. Colonic immune responses were profiled using RNA-sequencing, including high-resolution single cell analyses, and flow cytometry.ResultsCPI-colitis was dependent on the composition of the intestinal microbiota and was characterized by remodelling of mucosal lymphocytes with induction of polyfunctional lymphocyte responses characterized by increased expression of interferon-γ (IFNγ), other pro-inflammatory cytokines/chemokines (Il22, Il17a Ccl3, Ccl4 and Ccl9), cytotoxicity molecules (Gzmb, Gzma, Prf1, Nkg7) and the chemokine receptor Cxcr6. In comparison with mucosal lymphocytes in the steady state, polyfunctional lymphocytes from both CD4+ and CD8+ lineages upregulated costimulatory molecules and checkpoint molecules in CPI-colitis, indicating that these cells are tightly regulated. CPI-colitis was attenuated following depletion of effector lymphocytes or following blockade of the IL23/IFNγ axis.ConclusionsThis study provides new mechanistic insights into CPI-colitis, identifying polyfunctional, cytotoxic lymphocytes as key mediators of disease. Therapeutic targeting of their effector response or regulatory networks, including the IL23/IFNγ axis holds the key to preventing and reversing CPI-colitis.

Investigating the gut microbiome and metabolome frequently requires faecal samples, which can be difficult to obtain. Previous studies have shown that rectal swabs are comparable to faecal samples for analysing gut microbiota composition and key metabolites. In this study, 3D printed rectal swabs were compared with conventional flocked swabs and faecal samples, due to the potential advantages 3D printing as a technique offers for swab production and development. 16S rRNA gene sequencing, qPCR and metabolite profiling (using 1 H-NMR spectroscopy) were performed on swab and faecal samples from healthy participants. Faecal calprotectin and total protein analysis were performed on samples from inflammatory bowel disease (IBD) patients. There were no significant differences between both swab types and faecal samples when assessing key measures of alpha and beta diversity, and differences in the abundance of major phyla. There was a strong correlation between both swab types and faecal samples for all combined metabolites detected by NMR. In IBD patients, there was no significant difference in faecal calprotectin and total protein levels between both swab types and faecal samples. These data lead us to conclude that 3D printed swabs are equivalent to flocked swabs for the analysis of the gut microbiome, metabolome and inflammation.

Studies since early 1980s have shown the presence of subclinical gut inflammation in up to 60% of the patients with axial spondyloarthritis, 6% of which proceed to become inflammatory bowel disease (IBD) in 10 years. Here we aim to further explore the presence of gut inflammation using acute inflammatory markers in stool and serum and correlate the results with disease characteristics.MethodA collaborative group comprising of gastroenterologists and rheumatologists was formed between 2 healthcare trusts. Clinic lists and electronic operating systems were interrogated with appropriate ethical approval to identify patients with axSpA with or without IBD (axSpA-IBD and axSpA not-IBD, respectively) and psoriatic arthritis as disease controls. Eligible patients were called prior to their clinic appointments and were sent stool containers. On the day of their clinic appointments, patients were consulted for 15–30 minutes where their disease was carefully phenotyped, drug history obtained and they were consented in to the study. Stool and blood samples were collected and analysed for faecal calprotectin (FC) and ESR and CRP respectively.Results116 patients with axial spondyloarthritis (79 axSpA-not IBD, 22 axSpA-IBD and 15 psoriatic axSpA [axSpA-PsA] )and 22 patients with psoriatic peripheral spondyloarthritis (pPsA) were recruited.Total of 81 stool samples were analysed. Faecal calprotectin (FC) was elevated to above 50ug/g in 36 stool samples; 21 out of 44 (48%) patients with axSpA-not IBD (range 51- 587), 9 out of 18 (50%) patients with axSpA-IBD (range 51->2000), 2 out of 7 (29%) patients with axSpA-PsA (range 51–87) and 6 out of 14 (43%) patients with pPsA (range 57- 122). Of the elevated FC samples, only one patient with known Crohn’s disease had significant GI symptoms.10 out of 36 (28%) patients with elevated FC were taking daily NSAIDs compared to 4 out of 48 (8%) patients with normal FC. Daily NSAID users did not have higher mean FC.9 out of 11 (82%) patients who had disease duration of more than 10 years had elevated FC.18 out of 45 (40%) patients who were younger than 30 years old when they developed axSpA had elevated FC (median 51ug/g) compared to 19 out of 35 (54%) of patients who were older or equal to 30 years of age (median 36ug/g). 13 out of 28 (46%) patients with BASDAI index (axSpA disease activity score) of > 4 had elevated FC and 13 out of 33 (39%) with BASDAI < 4. BASDAI of above 4 reflects active disease.Patients on biological therapy were equally distributed across all cohorts.DiscussionOur study shows that significant proportion of patients with axSpA-not IBD have evidence of gut inflammation relatively independent of their NSAID use. There is some correlation between gut inflammation and age of symptoms onset, disease duration and serum inflammatory markers. As we had expected, mean faecal calprotectin in patients with axSpA-IBD is higher than patients with axSpA-not IBD. Based on this study, a discussion needs to be had for lowering the threshold of performing colonoscopies in axSpA-not IBD cohort.