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      Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis

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          Abstract

          The abundance and diversity of host-associated Prevotella species have a profound impact on human health. To investigate the composition, diversity, and functional roles of Prevotella in the human gut, a population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease samples from western populations. A higher abundance and diversity of Prevotella copri species enriched in complex plant polysaccharides metabolizing enzymes, particularly pullulanase containing polysaccharide-utilization-loci (PUL), were found in Indian and non-western populations. A higher diversity of oral inflammations-associated Prevotella species and an enrichment of virulence factors and antibiotic resistance genes in the gut microbiome of western populations speculates an existence of a mouth-gut axis. The study revealed the landscape of Prevotella composition in the human gut microbiome and its impact on health in western and non-western populations.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              Cytoscape: a software environment for integrated models of biomolecular interaction networks.

              Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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                Author and article information

                Contributors
                vineetks@iiserb.ac.in
                Journal
                NPJ Biofilms Microbiomes
                NPJ Biofilms Microbiomes
                NPJ Biofilms and Microbiomes
                Nature Publishing Group UK (London )
                2055-5008
                7 October 2021
                7 October 2021
                2021
                : 7
                : 77
                Affiliations
                [1 ]GRID grid.462376.2, ISNI 0000 0004 1763 8131, MetaBioSys Group, Department of Biological Sciences, , Indian Institute of Science Education and Research Bhopal, ; Bhopal, Madhya Pradesh 462066 India
                [2 ]GRID grid.17635.36, ISNI 0000000419368657, Department of Animal Science, Department of Food Science and Nutrition, , University of Minnesota, ; Saint Paul, MN 55455 USA
                [3 ]GRID grid.421010.6, ISNI 0000 0004 0453 9636, Behaviour and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, ; Lisbon, 1400-038 Lisboa Portugal
                [4 ]GRID grid.263791.8, ISNI 0000 0001 2167 853X, Animal Disease Research & Diagnostic Laboratory, South Dakota State University, ; Brookings, SD 57007 USA
                Author information
                http://orcid.org/0000-0002-5299-8074
                http://orcid.org/0000-0002-2958-6215
                Article
                248
                10.1038/s41522-021-00248-x
                8497558
                34620880
                77bca218-cfc4-4e29-8489-0beb4b9ce734
                © The Author(s) 2021

                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/.

                History
                : 17 April 2021
                : 9 September 2021
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                © The Author(s) 2021

                metagenomics,microbiome
                metagenomics, microbiome

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