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      Pangenomics reveals alternative environmental lifestyles among chlamydiae

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          Abstract

          Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

          Abstract

          Chlamydiae are strictly intracellular bacteria that exist in a wide variety of environments but the diversity of the phylum is not well described. Here, the authors analyze 82 metagenome-assembled genomes, identify seven new families, and describe genomic signals of metabolic diversity.

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          Most cited references142

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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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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              The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

              SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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                Author and article information

                Contributors
                matthias.horn@univie.ac.at
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                29 June 2021
                29 June 2021
                2021
                : 12
                : 4021
                Affiliations
                [1 ]GRID grid.10420.37, ISNI 0000 0001 2286 1424, Centre for Microbiology and Environmental Systems Science, , University of Vienna, ; Vienna, Austria
                [2 ]GRID grid.451309.a, ISNI 0000 0004 0449 479X, DOE Joint Genome Institute, ; Berkeley, CA USA
                [3 ]GRID grid.4818.5, ISNI 0000 0001 0791 5666, Present Address: Laboratory of Microbiology, Wageningen University and Research, ; Wageningen, The Netherlands
                Author information
                http://orcid.org/0000-0001-6710-7572
                http://orcid.org/0000-0002-4100-832X
                http://orcid.org/0000-0002-5678-1366
                http://orcid.org/0000-0002-4932-4677
                http://orcid.org/0000-0001-9265-8341
                http://orcid.org/0000-0002-8309-5855
                Article
                24294
                10.1038/s41467-021-24294-3
                8242063
                34188040
                8d42a182-a28a-4ecf-98f8-e0f95a352a8b
                © 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
                : 4 February 2021
                : 10 June 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100002428, Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung);
                Award ID: P32112
                Award ID: DOC 69-B
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100006132, DOE | Office of Science (SC);
                Award ID: DE-AC02–05CH11231
                Award ID: DE-AC02–05CH11231
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100011199, EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013));
                Award ID: 281633
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2021

                Uncategorized
                microbial ecology,metagenomics,symbiosis
                Uncategorized
                microbial ecology, metagenomics, symbiosis

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