| 1. |
- Yarza, P., et al.
(author)
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Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names
- 2013
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In: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 36:1, s. 69-73
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Journal article (peer-reviewed)abstract
- High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 “orphan” species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these “orphan” species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
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| 2. |
- Armengaud, J., et al.
(author)
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The Importance Of Naturally Attenuated Sars-Cov-2 In The Fight Against Covid-19
- 2020
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In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22:6, s. 1997-2000
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Journal article (peer-reviewed)abstract
- The current SARS-CoV-2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID-19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS-CoV-2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS-CoV-2 would offer significant relief, although vaccine developers have warned that design, testing, and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (1), but the earliest vaccines were based on live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS-CoV-2 will mutate and may naturally attenuate over time (2). What makes the current pandemic unique is that, thanks to state-of-the-art nucleic acid sequencing technologies, we can follow in detail how SARS-CoV-2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS-CoV-2 variants across the globe should be of key interest in our fight against the pandemic. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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| 3. |
- Munoz, R, et al.
(author)
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Evaluation of Matrix-Assisted Laser Desorption Ionization-Time Of Flight whole cell profiles for assessing the cultivable diversity of aerobic and moderately halophilic prokaryotes thriving in solar saltern sediments
- 2011
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In: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 34:1, s. 69-75
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Journal article (peer-reviewed)abstract
- The moderately halophilic, cultivable fraction of prokaryotes thriving in hyper-saline sediments of a solar saltern in Mallorca, Spain, has been studied by means of different cultivation media. A set of 374 isolates retrieved with six different culture conditions was screened, using whole-cell MALDI-TOF MS analysis to classify them into 25 phenotypic clusters at 52% similarity. The phylogenetic inference, made from comparative sequence analyses of the 16S rRNA genes of selected strains, indicated that each phenotypic cluster was comprised of a genealogically homogeneous set of strains. DNA–DNA hybridization (DDH) results among selected strains confirmed that each MALDI-TOF cluster encompassed members of the same species. On the other hand, the intra-cluster diversity, measured by several RAPD (Random Amplified Polymorphic DNA) amplifications, indicated that the clusters corresponded to several populations of the same phylogenetic unit coexisting in the same environment. The results encourage the use of MALDI-TOF MS for further exhaustive studies of the cultivable diversity of hyper-saline environments.
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| 4. |
- Murray, Alison E., et al.
(author)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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In: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
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Journal article (peer-reviewed)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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| 5. |
- Oren, A., et al.
(author)
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International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision)
- 2023
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In: International Journal of Systematic and Evolutionary Microbiology. - 1466-5026. ; 73:5A
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Journal article (peer-reviewed)abstract
- Fourteen years have passed since the International Committee on Systematics of Prokaryotes (ICSP) at its plenary meeting in Istanbul in 2008 approved the previous version of the International Code of Nomenclature of Prokaryotes (ICNP, the Prokaryotic Code, the Code), and we thank the Editors for overseeing its publication in 2019 [1]. Updating the Prokaryotic Code was long overdue in view of the large number of subsequent proposals to emend the General Considerations, Principles, Rules and Recom-mendations, and Appendices of the Code. In the period 2008-2020, 45 such proposals were published in the International Journal of Systematic and Evolutionary Microbiology [2]. Most of those were only recently discussed and voted on by the members of the ICSP, following the adoption of revised statutes in 2019 [3], which transferred responsibility for dealing with proposed emendations from the Judicial Commission to the Editorial Board of the ICNP. The current Editorial Board of the ICNP, appointed in 2020, has therefore prepared proposals for emendation of the Code, which were submitted for balloting among the full and co -opted members of the ICSP, in accordance with its statutes [3]. The ballot took place in April-June 2022 and we present here the 2022 revision of the Code, incorporating the changes approved by the voting members of the ICSP. To comply with Article 4(d) of the statutes of the ICSP that state that the business of the ICSP should be conducted publicly, the voting was preceded by a 6 -month period (July-December 2021), during which anyone interested could post comments via an online platform [4]. The editorial board of the ICSP is pleased with the lively discussions that developed on many issues relating to the Code. Numerous suggestions and ideas to improve the text of the Code were brought forward during this public discussion and many are incorporated in the current revision. Two previously approved major changes are also included in the new revision: (1) The rank of phylum was added to the ranks covered by the rules of the Code. This important change was approved by the ICSP in a separate ballot held in 2021 after a public discussion was held on this topic [5]. (2) The formal inclusion of the Cyanobacteria in the rules of the Code [6], a change that required modification of numerous rules to harmonize the treatment of the nomenclature of the Cyanobacteria with the relevant rules of the International Code of Nomenclature for algae, fungi, and plants [7]. This change was also approved by the ICSP in a separate ballot held in 2021, following a public discussion. Numerous minor modifications of the Code have been made that clarify its meaning, affecting topics such as notes, nomenclatural types, and effective publications, as well as valid publication, legitimacy, priority and orthography of names. The Judicial Commission of the ICSP issued numerous opinions in the past few years, and Appendix 5 - Opinions Relating to the Nomenclature of Prokaryotes - has been updated to include the latest opinions issued. Based on those opinions, Appendix 4 - Conserved and Rejected Names of Prokaryotic Taxa - has been updated, as well. Numerous additions have been made in Appendix 9 - Orthography. The new version of this Appendix should be useful for assisting authors in proposing correctly formed names that comply with the rules of the Code. We aimed to shorten and simplify the ICNP where possible. Therefore, we have not reprinted the prefaces to the earlier versions of the Code and have not included the extended information about the older versions of the different codes of nomenclature (Appendix 1), the recipients of the van Niel International Prize prior to 2014 (Appendix 12) and activities of the congresses prior to 2019 (Appendix 13). These changes were endorsed by the ICSP. The earlier information is available in the 2008 revision of the ICNP [1].
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| 6. |
- Oren, A., et al.
(author)
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Proposals to emend Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes
- 2022
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In: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 72:12
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Journal article (peer-reviewed)abstract
- To complete the ongoing revision of the International Code of Nomenclature of Prokaryotes, we here propose emendation of Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a and Appendix 7. These proposed emendations deal with: the nomenclatural type of taxa above genus; the suitability of names published in supplementary material or in papers published on e -print servers for effec-tive publication; the number of culture collection designations to be included in an effective publication of a name of a species or subspecies to qualify for validation of the name; the kinds of restrictions that may be attached to deposits of type strains; and the question whether elevation of a subspecies to the rank of species or lowering of a species to the rank of subspecies establish new combinations. Some of these emendations change the meaning of the Code while others are mere textual clarifications.
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| 7. |
- Kyrpides, Nikos C, et al.
(author)
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Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
- 2014
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In: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 12:8
-
Journal article (peer-reviewed)abstract
- Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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| 8. |
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| 9. |
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| 10. |
- Oren, Aharon, et al.
(author)
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Preparing a revision of the International Code of Nomenclature of Prokaryotes.
- 2021
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 71:1
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Journal article (peer-reviewed)abstract
- The Editorial Board of the International Code of Nomenclature of Prokaryotes here explains the proposed procedure towards the production of the next revision of the Prokaryotic Code, to include public discussion of a draft version, to be prepared by the editors, followed by balloting of the members of the International Committee on Systematics of Prokaryotes.
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