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      Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients

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          Abstract

          Higher probability of the development of Crohn’s disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/ Shigella spp.

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          Most cited references 41

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          Meta-analyses of human gut microbes associated with obesity and IBD.

          Recent studies have linked human gut microbes to obesity and inflammatory bowel disease, but consistent signals have been difficult to identify. Here we test for indicator taxa and general features of the microbiota that are generally consistent across studies of obesity and of IBD, focusing on studies involving high-throughput sequencing of the 16S rRNA gene (which we could process using a common computational pipeline). We find that IBD has a consistent signature across studies and allows high classification accuracy of IBD from non-IBD subjects, but that although subjects can be classified as lean or obese within each individual study with statistically significant accuracy, consistent with the ability of the microbiota to experimentally transfer this phenotype, signatures of obesity are not consistent between studies even when the data are analyzed with consistent methods. The results suggest that correlations between microbes and clinical conditions with different effect sizes (e.g. the large effect size of IBD versus the small effect size of obesity) may require different cohort selection and analysis strategies.
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            A review of activity indices and efficacy end points for clinical trials of medical therapy in adults with ulcerative colitis.

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              High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

              Background The gut microbiota is thought to play a key role in the development of the inflammatory bowel diseases Crohn's disease (CD) and ulcerative colitis (UC). Shifts in the composition of resident bacteria have been postulated to drive the chronic inflammation seen in both diseases (the "dysbiosis" hypothesis). We therefore specifically sought to compare the mucosa-associated microbiota from both inflamed and non-inflamed sites of the colon in CD and UC patients to that from non-IBD controls and to detect disease-specific profiles. Results Paired mucosal biopsies of inflamed and non-inflamed intestinal tissue from 6 CD (n = 12) and 6 UC (n = 12) patients were compared to biopsies from 5 healthy controls (n = 5) by in-depth sequencing of over 10,000 near full-length bacterial 16S rRNA genes. The results indicate that mucosal microbial diversity is reduced in IBD, particularly in CD, and that the species composition is disturbed. Firmicutes were reduced in IBD samples and there were concurrent increases in Bacteroidetes, and in CD only, Enterobacteriaceae. There were also significant differences in microbial community structure between inflamed and non-inflamed mucosal sites. However, these differences varied greatly between individuals, meaning there was no obvious bacterial signature that was positively associated with the inflamed gut. Conclusions These results may support the hypothesis that the overall dysbiosis observed in inflammatory bowel disease patients relative to non-IBD controls might to some extent be a result of the disturbed gut environment rather than the direct cause of disease. Nonetheless, the observed shifts in microbiota composition may be important factors in disease maintenance and severity.
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                Author and article information

                Contributors
                katarina.soltys@gmail.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                7 April 2020
                7 April 2020
                2020
                : 10
                Affiliations
                [1 ]ISNI 0000000109409708, GRID grid.7634.6, Department of Microbiology and Virology, , Faculty of Natural Sciences, Comenius University in Bratislava, ; Ilkovicova 6, 84215 Bratislava, Slovakia
                [2 ]ISNI 0000000109409708, GRID grid.7634.6, Comenius University Science Park, , Comenius University in Bratislava, ; Ilkovicova 8, 84104 Bratislava, Slovakia
                [3 ]ISNI 0000000109409708, GRID grid.7634.6, Department of Molecular Biology, , Faculty of Natural Sciences, Comenius University in Bratislava, ; Ilkovicova 6, 84215 Bratislava, Slovakia
                [4 ]National Transplant Organization, Limbova 14, 83303 Bratislava, Slovakia
                [5 ]ISNI 0000000406190087, GRID grid.412685.c, Department of Internal Medicine, , Faculty of Medicine, Division of Gastroenterology, Comenius University in Bratislava and University hospital Bratislava, ; Ruzinovska 6, 826 06 Bratislava, Slovakia
                [6 ]ISNI 0000000109409708, GRID grid.7634.6, Department of Computer Science, , Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynska dolina F1, ; 842 48 Bratislava, Slovakia
                [7 ]Department of Gastroenterology, St Michael Hospital, Bratislava, Slovakia
                Article
                62811
                10.1038/s41598-020-62811-4
                7138827
                32265456
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: FundRef https://doi.org/10.13039/501100008530, EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj);
                Award ID: 26240220086
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100005357, Agentúra na Podporu Výskumu a Vývoja (Slovak Research and Development Agency);
                Award ID: APVV–0672-11
                Award ID: APVV-17-0099
                Award ID: APVV–0672-11
                Award ID: APVV–0672-11
                Award ID: APVV–0672-11
                Award ID: APVV–0672-11
                Award Recipient :
                Categories
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                © The Author(s) 2020

                Uncategorized

                metagenomics, molecular medicine, microbiome

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