The Phylum Spirochaetaceae
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Comparative Genomic Analysis of the Genus Leptospira
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. Derrick E Fouts, Michael A Matthias, Haritha Adhikarla, Ben Adler, Luciane Amorim-Santos, Douglas E Berg, Dieter Bulach, Alejandro Buschiazzo, Yung-Fu Chang, Renee L Galloway, et al. To cite this version: Derrick E Fouts, Michael A Matthias, Haritha Adhikarla, Ben Adler, Luciane Amorim-Santos, et al.. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Lep- tospira.. PLoS Neglected Tropical Diseases, Public Library of Science, 2016, 10 (2), pp.e0004403. 10.1371/journal.pntd.0004403. pasteur-01436457 HAL Id: pasteur-01436457 https://hal-pasteur.archives-ouvertes.fr/pasteur-01436457 Submitted on 16 Apr 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons CC0 - Public Domain Dedication| 4.0 International License RESEARCH ARTICLE What Makes a Bacterial Species Pathogenic?: Comparative Genomic Analysis of the Genus Leptospira Derrick E. Fouts1*, Michael A. Matthias2, Haritha Adhikarla3, Ben Adler4, Luciane Amorim- Santos3,5, Douglas E. Berg2, Dieter Bulach6, Alejandro Buschiazzo7,8, Yung-Fu Chang9, Renee L. Galloway10, David A. Haake11,12, Daniel H. Haft1¤, Rudy Hartskeerl13, Albert I. -
This Is an Open Access-Journal's PDF Published in Stackebrandt, E
Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. Item Type Article Authors Stackebrandt, Erko; Chertkov, Olga; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan- Fang; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Pan, Chongle; Rohde, Manfred; Gronow, Sabine; Göker, Markus; Detter, John C; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Woyke, Tanja; Kyrpides, Nikos C; Klenk, Hans-Peter Citation Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. 2013, 8 (2):228-38 Stand Genomic Sci DOI 10.4056/sigs.3617113 Journal Standards in genomic sciences Rights Archived with thanks to Standards in genomic sciences Download date 01/10/2021 19:56:40 Link to Item http://hdl.handle.net/10033/311146 This is an Open Access-journal’s PDF published in Stackebrandt, E., Chertkov, O., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J.-F., Tapia, R., Goodwin, L.A., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Mikhailova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K., Land, M., Pan, C., Rohde, M., Gronow, S., Göker, M., Detter, J.C., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Woyke, T., Kyrpides, N.C., Klenk, H.-P. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (HT), and emendation of the species Turneriella parva (2013) Standards in Genomic Sciences, 8 (2), pp. -
Spirochaetes Dominate the Microbial Community Associated with the Red
www.nature.com/scientificreports OPEN Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum Received: 10 February 2016 Accepted: 18 May 2016 on a broad geographic scale Published: 06 June 2016 Jeroen A. J. M. van de Water1,*, Rémy Melkonian1,*, Howard Junca2, Christian R. Voolstra3, Stéphanie Reynaud1, Denis Allemand1 & Christine Ferrier-Pagès1 Mass mortality events in populations of the iconic red coral Corallium rubrum have been related to seawater temperature anomalies that may have triggered microbial disease development. However, very little is known about the bacterial community associated with the red coral. We therefore aimed to provide insight into this species’ bacterial assemblages using Illumina MiSeq sequencing of 16S rRNA gene amplicons generated from samples collected at five locations distributed across the western Mediterranean Sea. Twelve bacterial species were found to be consistently associated with the red coral, forming a core microbiome that accounted for 94.6% of the overall bacterial community. This core microbiome was particularly dominated by bacteria of the orders Spirochaetales and Oceanospirillales, in particular the ME2 family. Bacteria belonging to these orders have been implicated in nutrient cycling, including nitrogen, carbon and sulfur. While Oceanospirillales are common symbionts of marine invertebrates, our results identify members of the Spirochaetales as other important dominant symbiotic bacterial associates within Anthozoans. The economically valuable red coral Corallium rubrum is an important habitat-forming species that provides structural complexity to benthic communities in the Mediterranean Sea. While commercial over-exploitation for use in jewellery is one of the main threats, ocean acidification1 and elevated seawater temperatures2 may also pose a risk to C. -
A Phylogenomic and Molecular Signature Based
ORIGINAL RESEARCH ARTICLE published: 30 July 2013 doi: 10.3389/fmicb.2013.00217 A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum Radhey S. Gupta*, Sharmeen Mahmood and Mobolaji Adeolu Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada Edited by: The Spirochaetes species cause many important diseases including syphilis and Lyme Hiromi Nishida, Toyama Prefectural disease. Except for their containing a distinctive endoflagella, no other molecular or University, Japan biochemical characteristics are presently known that are specific for either all Spirochaetes Reviewed by: or its different families. We report detailed comparative and phylogenomic analyses Viktoria Shcherbakova, Institute of Biochemistry and Physiology of of protein sequences from Spirochaetes genomes to understand their evolutionary Microorganisms, Russian Academy relationships and to identify molecular signatures for this group. These studies have of Sciences, Russia identified 38 conserved signature indels (CSIs) that are specific for either all members David L. Bernick, University of of the phylum Spirochaetes or its different main clades. Of these CSIs, a 3 aa insert in California, Santa Cruz, USA the FlgC protein is uniquely shared by all sequenced Spirochaetes providing a molecular *Correspondence: Radhey S. Gupta, Department of marker for this phylum. Seven, six, and five CSIs in different proteins are specific Biochemistry and Biomedical for members of the families Spirochaetaceae, Brachyspiraceae, and Leptospiraceae, Sciences, McMaster University, respectively. Of the 19 other identified CSIs, 3 are uniquely shared by members of the 1280 Main Street West, Hamilton, genera Sphaerochaeta, Spirochaeta,andTreponema, whereas 16 others are specific for ON L8N 3Z5, Canada e-mail: [email protected] the genus Borrelia. -
Leptonema Illini Type Strain (3055(T))
Lawrence Berkeley National Laboratory Recent Work Title Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Permalink https://escholarship.org/uc/item/9mv4c6tj Journal Standards in genomic sciences, 8(2) ISSN 1944-3277 Authors Huntemann, Marcel Stackebrandt, Erko Held, Brittany et al. Publication Date 2013 DOI 10.4056/sigs.3637201 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2013) 8:177-187 DOI:10.4056/sigs.3637201 Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T) Marcel Huntemann1, Erko Stackebrandt2, Brittany Held1,3, Matt Nolan1, Susan Lucas1, Nancy Hammon1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,3, Lynne A. Goodwin1,3, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Manfred Rohde6, Sabine Gronow2, Markus Göker2, John C. Detter3, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Tanja Woyke1, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk2*, and Alla Lapidus1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, -
1917 and Leptonema Gen. Nov. KARI HOVIND-HOUGEN Departments of Biophysics and Treponematoses, Statens Seruminstitut, DK-2300 Copenhagen S, Denmark
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1979, p. 245-251 Vol. 29, No. 3 0020-77 13/79/03-0245/07$OZ.O/0 Leptospzraceae, a New Family to Include Leptospira Noguchi 1917 and Leptonema gen. nov. KARI HOVIND-HOUGEN Departments of Biophysics and Treponematoses, Statens Seruminstitut, DK-2300 Copenhagen S, Denmark The morphology of the cells of an organism formerly referred to as a member of Leptospira sp. serovar illini has been studied by electron microscopy. Cells of these strains differ morphologically from the cells of leptospires in the following: (i) cells of the former have cytoplasmic tubules which leptospires do not possess, and (ii) the structure of the basal complex on the flagella of the former is similar to that of gram-positive bacteria, whereas the corresponding structure on the flagella of leptospires is similar to that of gram-negative bacteria. Pillot (J. Pillot, thesis, University of Paris, Paris, France, 1965) proposed in 1965 that leptospires should constitute a family, Leptospiraceae. However, Pillot proposed this name in a thesis, which is not considered to be effective publication. Hence, Leptospi- raceae is here proposed as the name of a new family. In consequence of the new morphological evidence presented here together with the data from other publi- cations on the deoxyribonucleic acid base composition and serological and cultural properties of cells of strains of Leptospira sp. serovar illini, it is proposed that this family should consist of two genera: Leptospira Noguchi 1917 and Leptonema gen. nov. The type species of Leptonema is Leptonema illini, and the type strain of this species is strain 3055 (= NCTC 11301). -
Spirochaetes Dominate the Microbial Community Associated with the Red
www.nature.com/scientificreports OPEN Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum Received: 10 February 2016 Accepted: 18 May 2016 on a broad geographic scale Published: 06 June 2016 Jeroen A. J. M. van de Water1,*, Rémy Melkonian1,*, Howard Junca2, Christian R. Voolstra3, Stéphanie Reynaud1, Denis Allemand1 & Christine Ferrier-Pagès1 Mass mortality events in populations of the iconic red coral Corallium rubrum have been related to seawater temperature anomalies that may have triggered microbial disease development. However, very little is known about the bacterial community associated with the red coral. We therefore aimed to provide insight into this species’ bacterial assemblages using Illumina MiSeq sequencing of 16S rRNA gene amplicons generated from samples collected at five locations distributed across the western Mediterranean Sea. Twelve bacterial species were found to be consistently associated with the red coral, forming a core microbiome that accounted for 94.6% of the overall bacterial community. This core microbiome was particularly dominated by bacteria of the orders Spirochaetales and Oceanospirillales, in particular the ME2 family. Bacteria belonging to these orders have been implicated in nutrient cycling, including nitrogen, carbon and sulfur. While Oceanospirillales are common symbionts of marine invertebrates, our results identify members of the Spirochaetales as other important dominant symbiotic bacterial associates within Anthozoans. The economically valuable red coral Corallium rubrum is an important habitat-forming species that provides structural complexity to benthic communities in the Mediterranean Sea. While commercial over-exploitation for use in jewellery is one of the main threats, ocean acidification1 and elevated seawater temperatures2 may also pose a risk to C.