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      Gut Microbiome Changes in Patients with Active Left-Sided Ulcerative Colitis after Fecal Microbiome Transplantation and Topical 5-aminosalicylic Acid Therapy

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          Abstract

          Ulcerative colitis (UC) is an inflammatory bowel disease, and intestinal bacteria are implicated in the pathogenesis of this disorder. The administration of aminosalicylates (5-ASA) is a conventional treatment that targets the mucosa, while fecal microbial transplantation (FMT) is a novel treatment that directly targets the gut microbiota. The aim of this study was to identify changes in fecal bacterial composition after both types of treatments and evaluate clinical responses. Sixteen patients with active left-sided UC underwent enema treatment using 5-ASA ( n = 8) or FMT ( n = 8) with a stool from a single donor. Fecal microbiota were analyzed by 16S rDNA high-throughput sequencing, and clinical indices were used to assess the efficacy of treatments. 5-ASA therapy resulted in clinical remission in 50% (4/8) of patients, but no correlation with changes in fecal bacteria was observed. In FMT, remission was achieved in 37.5% (3/8) of patients and was associated with a significantly increased relative abundance of the families Lachnospiraceae, Ruminococcaceae, and Clostridiaceae of the phylum Firmicutes, and Bifidobacteriaceae and Coriobacteriaceae of the phylum Actinobacteria. At the genus level, Faecalibacterium, Blautia, Coriobacteria, Collinsela, Slackia, and Bifidobacterium were significantly more frequent in patients who reached clinical remission. However, the increased abundance of beneficial taxa was not a sufficient factor to achieve clinical improvement in all UC patients. Nevertheless, our preliminary results indicate that FMT as non-drug-using method is thought to be a promising treatment for UC patients.

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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              Metagenomic biomarker discovery and explanation

              This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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                Author and article information

                Journal
                Cells
                Cells
                cells
                Cells
                MDPI
                2073-4409
                13 October 2020
                October 2020
                : 9
                : 10
                : 2283
                Affiliations
                [1 ]Institute of Animal Physiology and Genetics of the Czech Academy of Science, v.v.i., 142 20 Prague, Czech Republic; fliegerova@ 123456iapg.cas.cz (K.O.F.); kvasnova@ 123456iapg.cas.cz (S.K.)
                [2 ]Hepatogastroenterology Department, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic; brej@ 123456ikem.cz (J.B.); lukasbajer1@ 123456gmail.com (L.B.); padr@ 123456ikem.cz (P.D.)
                Author notes
                [* ]Correspondence: schierova@ 123456iapg.cas.cz (D.S.); mrazek@ 123456iapg.cas.cz (J.M.); Tel.: +420-2-6709-0509 (D.S.); +420-2-6709-0506 (J.M.)
                Author information
                https://orcid.org/0000-0001-9906-9072
                https://orcid.org/0000-0003-1907-3333
                https://orcid.org/0000-0001-9439-8168
                https://orcid.org/0000-0002-2296-7795
                https://orcid.org/0000-0002-3815-3120
                Article
                cells-09-02283
                10.3390/cells9102283
                7602113
                33066233
                10e2998d-0b63-4711-aa81-94ab9043ef56
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 25 August 2020
                : 09 October 2020
                Categories
                Article

                ulcerative colitis,microbiome,fecal microbiome transplantation,5-asa

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