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Background Inflammatory Bowel Disease (IBD) and Irritable Bowel Syndrome (IBS) are two intestinal disorders with unknown aetiology. IBD presents two main forms which are Crohn’s disease (CD) and ulcerative colitis (UC). It has been reported recently that bacterial communities present in the colon of patients with either IBD or IBS are structurally different compared to those found in healthy individuals. This dysbiosis mainly consists of a decrease of butyrate producing bacteria and, therefore, the recovery of this metabolic group should be at the baseline of any successful treatment. The main goal of this proof-of-concept study was to test the capacity of a new prebiotic of selected dietary fibre obtained from grape to balance the dysbiosis found in patients with different intestinal disorders. Methods In this study, fresh faecal samples from 6 healthy subjects, 3 CD, 3 UC, and 3 IBS were collected at the Hospital Universitari Dr. Josep Trueta. Fresh samples were diluted 1:5 with fermentation buffer and incubated with 200 mg of prebiotic at 37 ºC under agitation for 72 h. Results were compared with those obtained with various commercial prebiotics after simulating in vitro digestion: inulin, grape pectin, and grape seed extract (GSPE). Total DNA was extracted and the abundance of butyrate-producing bacterial markers: F. prausnitzii (Fpra), its two phylogroups (PHGI and PHGII), Roseburia spp. (Ros) and S. variabile (Sva) was analysed by qPCR. Bacterial activity was determined by measuring short chain fatty acids (SCFA) concentration (butyrate, acetate, and propionate) by gas chromatography. Results The abundance of all butyrate-producing bacteria analysed increased after incubation with the new prebiotic. Among them, Ros presented significantly higher abundance values with respect to negative control in healthy, CU, and IBS patients. It also showed a significant increase in all individuals analysed compared to inulin, grape pectin, and GSPE. Fermentation of the tested new prebiotic, produced significantly higher concentrations of SCFA (p < 0.001) when compared to negative control and all other commercial fibres. Acetate concentration was a 241% higher than negative control, followed by butyrate (187%), and propionate (169%). Conclusion The studied prebiotic produces in vitro an increase of the abundance and enhancement of the metabolism of butyrate-producing bacteria, when compared to commercial prebiotics. These results suggest that this new fibre is a promising prebiotic to be used in promotion of intestinal microbiota restoration at mucosa.

Background Crohn’s disease (CD) and ulcerative colitis (UC) evolve with alternate outbreaks and remissions of variable duration. Tumour necrosis factor α antagonists (anti-TNFα) have enhanced the treatment of patients with inflammatory bowel disease (IBD), improving the patient’s quality of life by reducing the number of surgeries and hospitalizations. Despite these advances, about 10–30% of patients do not respond to the treatment after the induction period. Recent studies have pointed, on one hand, gut microbiota can play a role in the anti-TNFα treatment response as gram-positive bacteria can modulate the response of NOD proteins and, on the other hand, gram-negative bacteria can stimulate TLR4 receptors causing activation of NFkß. This study aimed to define a microbial signature that could be used to predict the response of patients with CD and UC to anti-TNFα treatment. Methods This observational study consisted of obtaining a stool sample from 38 IBD patients before starting an anti-TNFα treatment. Patients were recruited at Hospital Universitari Dr. Josep Trueta (Girona) and Hospital Universitari de Bellvitge (l’Hospitalet de Llobregat). During the one-year follow-up period, disease activity levels, faecal calprotectin evolution, and anti-TNFα antibody levels were analysed to assess response to treatment, differentiating 2 groups: responders and non-responders. From each sample, DNA was purified and used in a qPCR for the quantification of the following markers: F. prausnitzii (Fpra) and its phylogroups (PHG-I and PHG-II), E. coli (Eco), A. muciniphila (Akk), Ruminococcus sp. (Rum), Bacteroidetes (Bac), M. smithii (Msm), and the total bacterial load (Eub). Results In this proof of concept, the predictive ability to identify anti-TNFα treatment responders was analysed. Individually, none of biomarkers demonstrated the ability to differentiate between groups with high sensitivity and specificity. However, an algorithm consisting of the combination of 5 microbial markers (Msm, Fpra, PHGII, Rum, and Eub) showed a high capacity to discriminate between responders and non-responders. The algorithm proved high sensitivity and specificity reporting values ​​of 93.33% and 100%, respectively, with a positive predictive value of 100% and a negative predictive value of 75% for predicting response to biologic treatment. Conclusion A specific microbial signature could beneficiate patients with IBD by predicting the therapeutic effectiveness of an anti-TNFα treatment, which could lead to a personalized therapy, improving the patients’ quality of life, saving costs, and gaining time in patient recovery.A larger prospective study will be needed to validate these results.

Background Dysbiosis is a widely used but unspecific term. It has been defined as any change in the composition of resident microbial communities relative to the ones found in healthy individuals. But it is still unclear which are the appropriate communities to define it and the reference values to measure it. Different studies have described dysbiosis in various diseases such as Inflammatory Bowel Disease (IBD), diabetes, rheumatoid arthritis, and autism, among others. Besides, the microbiota can be altered by transient factors such as antibiotics, diet, stress, or infections. Therefore, different degrees of severity can be associated with the term dysbiosis from which pathological and transient dysbiosis can be differentiated. This work aimed at defining more specifically the term intestinal dysbiosis and to differentiate both transient and pathological dysbiosis. Methods Fifteen key microbial markers belonging to the principal families, classes and orders found in the human intestinal microbiota were accurately selected based on its functionality: F. prausnitzii (Fpra), E. coli (Eco), Firmicutes (Fir), Bacteroidetes (Bac), A. muciniphila (Akk), Ruminococcus sp. (Rum), Roseburia sp. (Ros), Gammaproteobacteria (Gam), Clostridia cluster I (Clo), Clostridia cluster XIV (XIV), Enterococcus sp., Lactobacillus sp. (Lac), C. albicans (Can), M. smithii (Msm), and the total bacterial load (Eub). The dysbiosis was defined using stool samples in a cohort of healthy subjects (n=24) and then validated with 9 patients diagnosed with intestinal diseases 4 IBD and 2 Irritable Bowel Syndrome (IBS)). Total DNA was extracted and the abundance of microbial markers was analysed by qPCR. Together with the establishment of the most common range in which each microbial marker was found, an index to define the pathological dysbiosis was calculated. Results Almost all healthy subjects analysed presented one or two slightly altered markers. The affected microbial markers in this “transient dysbiosis” were Fpra, Akk, and Ros, which are indicative of the mucous layer state, Firm as indicative of the lifestyle and fiber intake, Gam as characteristic of the pro-inflammatory state of the gut, and Msm as an altered intestinal habit and gas production. All patients analyzed (IBD and IBS) presented alterations mainly of the bacteria inhabiting the mucosa and an alteration of the opportunistic species related to the disrupted mucous layer and defining “pathological dysbiosis”. Conclusion This study establishes an appropriate abundance range of key microbial markers in the gut, leading to a specific definition of dysbiosis which allows to differentiate the pathological from the transient dysbiosis. These results need further validation in a larger patient cohort.

Background Inflammatory Bowel Disease (IBD) is a clinical condition of the gastrointestinal tract of unknown aetiology. The two main forms of IBD are Crohn’s disease (CD) and Ulcerative colitis (UC). Recently, it has been reported that the bacterial communities present in the colon of patients with IBD are structurally different compared with those in healthy individuals. This particular dysbiosis consists of a decrease of butyrate producing bacteria and an increase of the pro-inflammatory species. The goal of this work was to test a new prebiotic of selected dietary fibre made from grape for its capacity to balance the dysbiosis typically found in patients with intestinal disorders. Methods Faecal samples from 16 healthy subjects and 11 IBD patients (5 CD and 6 UC) were collected by the Hospital Universitari Dr. Josep Trueta. Fresh stool samples were incubated with 200 mg, 600 mg of prebiotic, and 200 mg of apple pectin. A negative control without substrate addition was also performed. The tubes were incubated under continuous stirring for 72 hours at 37 ºC in semi-anaerobic atmosphere. Total DNA was extracted and the abundances of butyrate-producing bacterial markers (Faecalibacterium prausnitzii, and its phylogroups I and II, Roseburia hominis and Subdolinogranulum variabile) were analysed by qPCR. Concentrations of both butyrate and acetate were determined by gas chromatography as an indication of the bacterial metabolic activity. Results A significant increase of butyrate producing species, such as S. variabile, R. hominis and F. prausnitzii was observed in CD and UC samples when incubated with 200 mg of prebiotic compared with the negative control. F. prausnitzii phylogroup II, which is underrepresented in UC patients, also increased. No differences were found when samples were incubated with 600 mg. Regarding apple pectin, the increase on the abundance of butyrate producing bacteria was higher than the prebiotic in UC samples. In samples from healthy subjects, an increase in the butyrate producing species abundances was observed in both concentrations of prebiotic when compared with the negative control. In those samples no differences were observed when comparing apple pectin with the prebiotic. Concerning butyrate and acetate production, these substances increased in all prebiotic-supplemented samples when compared with the negative control. Conclusion The studied prebiotic causes an increase of the abundance and activity of butyrate-producing bacteria in both IBD patients and healthy subjects. These results points to this new dietary fibre as a promising prebiotic to maintain eubiosis and to promote the microbiota restoration of the intestinal mucosa.

Background Inflammatory bowel disease (IBD) is defined as a group of autoimmune diseases that affects the digestive tract by causing chronic inflammatory processes. Crohn’s disease (CD) is one of the major types of IBD. Although there are several efficient drugs for its treatment, almost 80% of patients will require an intestinal resection throughout their lives. Some bacterial species found in faecal samples can be used as indicators to diagnose and monitor activity in CD patients. However, this methodology has not yet been tested in patients that underwent an intestinal resection. The aim of this study was to investigate the changes in the abundance of these species associated with total or partial intestinal resection. Methods In this study, we used 30 faecal samples from patients diagnosed with CD in remission withdrawn from the Biobank of the Hospital Universitari Dr. Josep Trueta of Girona. Fifteen samples corresponded to patients who underwent an intestinal resection. The following markers were quantified by qPCR: Faecalibacterium prausnitzii (Fpra), F. prausnitzii phylogroup I (PHG-I), F. prausnitzii phylogrup II (PHG-II), Escherichia coli (Eco), Akkermansia muciniphila (Akk), Ruminococcus sp. (Rum), Bacteroidetes (Bac) and Methanobrevibacter smithii (Msm). Results The abundances of Fpra, PHG-I, PHG-II, Rum, and Msm were significantly lower (p < 0.05) in resected CD patients, whereas Eco was significantly more abundant in those patients. No significant differences were observed in the abundances of Akk and Bac. Conclusion In resected CD patients, beneficial butyrate-producing bacteria are underrepresented, whereas pro-inflammatory species are overpopulated. Any quantitative relationship of these indicators with the relapse probability would help to stratify these patients for a better orientation of therapeutic strategies.

Background Crohn disease (CD) and Ulcerative colitis (UC) are characterised by episodes of exacerbations and remissions. Monitoring disease activity based on intestinal lesion is mandatory prior to any change in the therapeutic strategy. Colonoscopy is the gold standard technique to monitor the disease activity in IBD patients, but it is usually discarded because of costs and risk issues. The concentration of Faecal Calprotectin (FC) is widely used as a non-invasive marker of inflammation of the intestinal mucosa, allowing the assessment of the disease activity. Recently, different studies have demonstrated that certain microbial species, part of intestinal microbiota which can be detected in stool samples, are capable of correlating with disease activity in CD and UC patients. The purpose of this study was to analyse the correlation between these microbial indicators and the FC to monitor the disease activity in CD and UC patients. Methods FC levels were used to define inflammatory disease activity, the predetermined cut-off of 250 μg/g of faeces was used, higher values indicated an active inflammation and lower values indicated disease in remission. Two cohorts consisting of 61 patients of CD (25 with active inflammation and 36 with remission) and 90 of UC (42 with active inflammation and 48 with remission) were recruited by the Gastroenterology department of 4 Catalan hospitals. A sample of faeces was collected from each patient. FC and the following markers were quantified by qPCR: Faecalibacterium prausnitzii (Fpra), Escherichia coli (Eco), Akkermansia muciniphila (Akk), Ruminococcus sp. (Rum), Bacteroidetes (Bac) and Methanobrevibacter smithii (Msm) for each sample. Results The bacterial markers presented different behaviour depending on the disease analysed. The abundances of Eco and Bac were higher in CD with active inflammation compared with CD with remission. In contrast, no significant differences were found for Fpra, Akk, Rum, and Msm. Besides, a significant positive correlation between Eco abundance and FC levels (0.280, p = 0.029) and a significant negative correlation between Msm and FC levels (−0.299, p = 0.021) were observed. According UC patients, while the abundance of Eco was higher in patients with active inflammation, the abundance of Rum was significantly less abundant. No significant differences were found for Fpra, Akk, Bac, and Msm. Moreover, we also observed a significant negative correlation between Rum and FC levels (−0.308, p = 0.003, respectively). Conclusion The abundance of Eco and Msm in CD patients and the abundance of Rum in UC patients correlate to FC in order to determine inflammatory disease activity. So, these markers can also be an accurate discriminator of active disease in CD and UC patients.