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      Alteration of the fecal microbiota in Chinese patients with Schistosoma japonicum infection Translated title: Altération du microbiote fécal chez les patients chinois atteints d’une infection à Schistosoma japonicum

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          Abstract

          Schistosoma japonicum infection causes pathological injury to the host. Multiple studies have shown that intestinal helminth infection causes dysbiosis for the gut microbial community and impacts host immunology. However, the effect of acute S. japonicum infection on the gut microbiome structure (abundance and diversity) is still unclear. We collected fecal samples from healthy and infected patients from a single hospital in Hunan Province, China. The bacterial community was analyzed using 16S ribosomal RNA gene sequencing of the V4 hypervariable region using the HiSeq platform. Compared with healthy subjects, infected patients exhibited an increase in relative abundance of the TM7 phylum. At the genus level, there were seven differentially abundant genera between groups. The most significant finding was a Bacteroides enterotype in patients with acute schistosomiasis. These results suggest that S. japonicum infection has a significant effect on microbiome composition characterized by a higher abundance of the TM7 phylum and development of a Bacteroides enterotype.

          Translated abstract

          L’infection à Schistosoma japonicum provoque des lésions pathologiques chez l’hôte. Plusieurs études ont montré qu'une infection intestinale par les helminthes provoque une dysbiose de la communauté microbienne intestinale et a un impact sur l’immunologie de l’hôte. Cependant, l’effet de l’infection aiguë à S. japonicum sur la structure du microbiome intestinal (abondance et diversité) n’est toujours pas clair. Nous avons collecté des échantillons fécaux de patients sains et infectés dans un hôpital de la province du Hunan, en Chine. La communauté bactérienne a été analysée par séquençage du gène de l’ARN ribosomal 16S de la région hypervariable V4 en utilisant la plateforme HiSeq. Par rapport aux sujets sains, les patients infectés ont présenté une augmentation de l’abondance relative du phylum TM7. Au niveau du genre, il y avait sept genres différentiellement abondants entre les groupes. La découverte la plus significative était un entérotype Bacteroides chez les patients atteints de schistosomiase aiguë. Ces résultats suggèrent que l’infection à S. japonicum a un effet significatif sur la composition du microbiome caractérisé par une plus grande abondance du phylum TM7 et le développement d’un entérotype Bacteroides.

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          Most cited references 64

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            FLASH: fast length adjustment of short reads to improve genome assemblies.

            Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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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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                Author and article information

                Journal
                Parasite
                Parasite
                parasite
                Parasite
                EDP Sciences
                1252-607X
                1776-1042
                2021
                08 January 2021
                : 28
                : ( publisher-idID: parasite/2021/01 )
                Affiliations
                [1 ] National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention 200025 Shanghai PR China
                [2 ] Chinese Center for Tropical Diseases Research 200025 Shanghai PR China
                [3 ] World Health Organization Collaborating Centre for Tropical Diseases 200025 Shanghai PR China
                [4 ] Key Laboratory of Parasite and Vector Biology, National Health Commission of the People’s Republic of China 200025 Shanghai PR China
                [5 ] McDonnell Genome Institute, Washington University in St Louis St Louis 63001 MO USA
                [6 ] Department of Medicine, UConn Health Farmington 06023 CT USA
                [7 ] Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine St Louis 63001 MO USA
                Author notes
                Article
                parasite200114 10.1051/parasite/2020074
                10.1051/parasite/2020074
                7792497
                33416489
                © Y. Jiang et al., published by EDP Sciences, 2021

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 3, Tables: 2, Equations: 0, References: 58, Pages: 10
                Categories
                Research Article

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