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      Peptostreptococcus faecalis sp. nov., new bacterial species isolated from healthy indigenous congolese volunteer

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          Abstract

          The Microbial Culturomics Project aiming to discover several bacterial species made it possible to isolate the strain Marseille-P4308 T from a stool sample of a healthy indigenous Congolese volunteer. Strain Marseille-P4308 T is a Gram-positive coccus shaped bacterium that optimally grows at 37 °C. The 16S rRNA gene sequence of the strain has a 96.2% sequence similarity to Peptostreptococcus anaerobius strain NCTC 11460 T (GenBank accession number: NR_042847.1). In addition, the average nucleotide identity of strain Marseille-P4308 T with its closest related species was 71.1%, which was far below the recommended threshold (>95–96%). The genome of the strain Marseille-P4308 T has a length of 2.14 Mbp with G + C content of 30.4 mol%. Based on phenotypic, biochemical, genomic and phylogenetic analysis, strain Marseille-P4308 T (= CSUR P4308 = CECT 9960) clearly appears to be a new species for which the name Peptostreptococcus faecalis sp. nov., is proposed.

          Abstract

          Peptostreptococcus faecalis; Gut microbiote; Indigenous congolese; Culturomics; Taxonogenomics

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            Prokka: rapid prokaryotic genome annotation.

            T Seemann (2014)
            The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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              Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

              Ivica Letunic, Peer Bork (2021)
              The Interactive Tree Of Life ( https://itol.embl.de ) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Graphical Abstract iTOL: an online tool for the tree display and annotation.
              Article 0 comments Cited 2684 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Cheikh Ibrahima Lo
                Journal
                Journal ID (nlm-ta): Heliyon
                Journal ID (iso-abbrev): Heliyon
                Title: Heliyon
                Publisher: Elsevier
                ISSN (Electronic): 2405-8440
                Publication date PMC-release: 14 March 2022
                Publication date Collection: March 2022
                Publication date (Electronic): 14 March 2022
                Volume: 8
                Issue: 3
                Electronic Location Identifier: e09102
                Affiliations
                [a ]Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
                [b ]IHU-Méditerranée Infection, Marseille, France
                [c ]University of Balamand, Faculty of Medicine and Medical Sciences, Amioun, Lebanon
                [d ]Laboratoire National de Santé Publique, Brazzaville, Congo
                [e ]Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
                Author notes
                [∗ ]Corresponding author. cibrahimalo@ 123456gmail.com
                [1]

                Geor Mongo Ndombe passed away.

                Article
                Publisher Item ID: S2405-8440(22)00390-5 Publisher ID: e09102
                DOI: 10.1016/j.heliyon.2022.e09102
                PMC ID: 8933677
                PubMed ID: 35313487
                SO-VID: 07bee02a-9719-44cc-8969-4b2f2d00c6af
                Copyright © © 2022 Published by Elsevier Ltd.
                License:

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                Date received : 17 August 2021
                Date revision received : 10 December 2021
                Date accepted : 9 March 2022
                Categories
                Subject: Research Article

                Keywords: peptostreptococcus faecalis,gut microbiote,indigenous congolese,culturomics,taxonogenomics
                Data availability:
                Keywords: peptostreptococcus faecalis, gut microbiote, indigenous congolese, culturomics, taxonogenomics

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