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      Gut Microbiome Alterations and Functional Prediction in Chronic Spontaneous Urticaria Patients

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          Abstract

          The effects of the gut microbiome on both allergy and autoimmunity in dermatological diseases have been indicated in several recent studies. Chronic spontaneous urticaria (CSU) is a disease involving allergy and autoimmunity, and there is no report detailing the role of microbiota alterations in its development. This study was performed to identify the fecal microbial composition of CSU patients and investigate the different compositions and potential genetic functions on the fecal microbiota between CSU patients and normal controls. The gut microbiota of CSU patients and healthy individuals were obtained by 16s rRNA massive sequencing. Gut microbiota diversity and composition were compared, and bioinformatics analysis of the differences was performed. The gut microbiota composition results showed that Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia were dominant microbiota in CSU patients. The differential analysis showed that relative abundance of the Proteobacteria ( p = 0.03), Bacilli ( p = 0.04), Enterobacterales ( p = 0.03), Enterobacteriaceae ( p = 0.03) was significantly increased in CSU patients. In contrast, the relative abundance of Megamonas, Megasphaera, and Dialister (all p < 0.05) in these patients significantly decreased compared with healthy controls. The different microbiological compositions impacted normal gastrointestinal functions based on function prediction, resulting in abnormal pathways, including transport and metabolism. We found CSU patients exhibited gut microbiota dysbiosis compared with healthy controls. Our results indicated CSU is associated with gut microbiota dysbiosis and pointed out that the bacterial taxa increased in CSU patients, which might be involved in the pathogenesis of CSU. These results provided clues for future microbial-based therapies on CSU.

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          Most cited references41

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          Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

          mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
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            Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

            Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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              A human gut microbial gene catalogue established by metagenomic sequencing.

              To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
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                Author and article information

                Journal
                J Microbiol Biotechnol
                J Microbiol Biotechnol
                Journal of Microbiology and Biotechnology
                The Korean Society for Microbiology and Biotechnology
                1017-7825
                1738-8872
                28 May 2021
                19 March 2021
                19 March 2021
                : 31
                : 5
                : 747-755
                Affiliations
                [1 ]Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an 710004, P.R. China
                [2 ]College of Science, Northwest University, Xi’an 710069, P.R. China
                Author notes
                [* ] Corresponding author Phone: +86-185-0920-1702 E-mail: guokun11@ 123456126.com
                Article
                jmb-31-5-747
                10.4014/jmb.2012.12022
                9723274
                33746191
                b470ee0f-9eab-461a-b564-608089d54668
                Copyright © 2021 by The Korean Society for Microbiology and Biotechnology

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.

                History
                : 9 December 2020
                : 2 March 2021
                : 16 March 2021
                Categories
                Research article
                Biotechnology and Bioengineering (BB)
                Host-Microbe Interactions and Pathogenesis

                gut microbiome,urticaria,dysbiosis,bacterial diversity
                gut microbiome, urticaria, dysbiosis, bacterial diversity

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