Nomenclature Of Bacteria Research Articles

Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists

Taxonomy is the science of the classification of various living organisms consisting of three independent, but interrelated disciplines, namely classification, nomenclature and identification. With the advent of molecular biological methods and sequencing, a revolution is currently occurring with regards to the reporting of novel taxa and changes in the taxonomy of already described bacterial species. The applications of taxonomic changes can be broad ranging: they may impact the clinical care of patients, through variations in choosing the appropriate antimicrobial susceptibility testing standards or data interpretation, or even their clinical relevance and epidemiology. The aim of this paper was to aid healthcare professionals and pharmaceutical scientists to navigate through the ‘maze’ of bacterial taxonomy, and to aid in finding authentic information regarding the description of taxonomic changes and to present some examples of changes in bacterial taxonomy which have proven to be clinically significant.

Limiting the retroactive effects of the note to Rule 61 of the International Code of Nomenclature of Bacteria.

At the plenary session of the Judicial Commission at the 1999 IUMS-BAM International Congress in Sydney changes were made to Rule 61 of the International Code of Nomenclature of Bacteria to prevent extensive grammatical or orthographic corrections to names and epithets that had been included on the Approved Lists, the Validation Lists and the Notification Lists. These changes were implemented by the addition of a note to Rule 61. However, that note appears to be retroactive and has an undesirable effect, appearing to prohibit some of the changes already published. Changes need to be made to Rule 61 to limit the retroactive effects of the note.

On the valid publication of names and combinations

The valid publication of names and combinations in a single journal was one of the innovations in the 1975 revision of the International Code of Nomenclature of Bacteria. A number of assumptions are often made with regards the way names or combinations are evaluated as being validly published. A re-examination of the process of valid publication is appropriate.

Updating Rule 15 of the International Code of Nomenclature of Bacteria.

The wording of Rule 15 as originally published in the 1975 and 1990 revisions of the International Code of Nomenclature of Bacteria with regard to the definition ofnomenclatural typeswas not clearly expressed and was modified by the Judicial Commission in 2008. However, there is a difference between the wording as proposed and that accepted. On reflection there is justification for re-examining both the proposed and the accepted wording.

The experience introduction on the novel Francisella guangzhouensis for identifying and validating a novel bacterial species

Francisella guangzhouensis was used as an example to illustrate how to utilize the bioinformatics resources to identify the novel species, how to name the novel species with Latinized letters, and how to validate a novel species in the clinical microbiology laboratories.Some related rules of International Code of Nomenclature of Bacteria was also introduced.（Chin J Lab Med,2014,37:796-798） Key words: Francisella; Classification

Demystifying the nomenclature of bacterial plant pathogens

A unified approach to naming bacteria ensures accurate communication among scientists, regulators and the public. Rules for nomenclature, set out in the International Code of Nomenclature of Bacteria (ICNB), ensure that proposals for new names and combinations follow a logical and standardized progression that maintains the integrity of the established nomenclature while facilitating changes based on scientific inquiry into relationships among organisms. However, these Rules only apply to ranks at the level of subspecies and above and not to lower taxonomic ranks. The pathovar is one infraspecific rank that is widely used in the classification and nomenclature of plant pathogenic bacteria and is often included in legislation to provide statutory control of bacterial plant pathogens. Thus, phytobacteriologists must rely on two discontinuous but, complimentary systems: the Rules set forth in ICNB for naming down to subspecies level, and the Standards in the International Standards for Naming Pathovars of Plant Pathogenic Bacteria to name pathovars. A framework for determining the priority of names is provided by the Approved Lists of Bacterial Names, which gives genus, species and subspecies names and their corresponding type strains, and subsequent lists of validly published names appearing in the International Journal of Systematic and Evolutionary Microbiology. For pathovar names priority is based on the date of valid publication of legitimate names. A list of pathovar names and pathotype strains is maintained by the Committee on the Taxonomy of Plant Pathogenic Bacteria of the International Society of Plant Pathology. To help researchers avoid common pitfalls encountered when developing nomenclature for novel classification systems, this manuscript clarifies several key Rules and Standards. It aims to promote best practice, in that names developed to conform to the ICNB should also consider precedents set by previous nomenclatural designations as per the International Standards for Naming Pathovars of Plant Pathogenic Bacteria, thus ensuring continuity across the nomenclature of all phytopathogenic bacteria.

Nomenclature and taxonomy of halophilic archaea - comments on the proposal by DasSarma and DasSarma for nomenclatural changes within the order Halobacteriales

P. DasSarma & S. DasSarma [Saline Systems 4 (2008), 5] have proposed far-reaching changes in the nomenclature and taxonomy of the halophilic archaea of the order Halobacteriales, family Halobacteriaceae. While re-evaluation of the taxonomic classification of strains within the group is to be encouraged, the nomenclatural changes proposed are in violation of the General Considerations, Principles and Rules of the International Code of Nomenclature of Bacteria.

Are the concepts of legitimate and illegitimate names necessary under the current International Code of Nomenclature of Bacteria? A proposal to make changes to the Code

The International Code of Nomenclature of Bacteria (the Code) has retained the concept of legitimate and illegitimate names, despite the fact that the principle underlying valid publication of a name could easily dispense with this concept. Furthermore, changes in wording to the Code are proposed that would help to clarify the issue of names that contravene the Code.

Clarifying Rule 24a of the International Code of Nomenclature of Bacteria

Note 1 of Rule 24a of the International Code of Nomenclature of Bacteria can be interpreted in an ambiguous fashion, because the wording is not sufficiently clear. It is proposed that the wording of this note be modified to clarify this point.

Against conservation of specific epithets formed wrongly as nominative nouns in apposition

Together with 31 other incorrectly formed (i.e. as nominative nouns in apposition) specific epithets, the epithet of Streptomyces scabies was corrected to Streptomyces scabiei in Taxonomic Notes published in 1997 and 1998. A subsequent Request for an Opinion, published in 2001, to reinstate the incorrect epithets for ten of these species was denied by the Judicial Commission in 2002. In 2007, a further Request for an Opinion was submitted to the Judicial Commission which proposed the conservation of the incorrect epithet of Streptomyces 'scabies' over the corrected one, scabiei. After having stated once that the corrections made to the epithets were performed according to the correct application of the International Code of Nomenclature of Bacteria (now 'of Prokaryotes', ICNP), the Judicial Commission would lose authority and credibility if it were to follow a request to abandon even one of the now correct 32 epithets in favour of its incorrectly formed predecessor. Microbiologists who accept changes in names of genera should also accept the correction of grammatical or orthographical changes in specific epithets.

OnRickettsiaNomenclature

his issue of Emerging Infectious Diseases contains 2 independent reports of Rickettsia sibirica infections in Spain and Portugal. The authors identify the agent both as a subspecies (1) and as a strain (2). This inconsistency refl ects a lack of consensus regarding the use of subspecies designations for Rickettsia taxa, so appropriate designation of these pathogens as strains or subspecies remains problematic. Tick-borne typhus of northern Asia (or North Asian spotted fever) was fi rst discovered in the 1930s, and its etiologic agent, R. sibirica, was formally described in 1949. In 1993, an isolate designated “mongolitimonae” was fi rst discovered in the People’s Republic of China (3), considered a new species (4), and fi nally described as a new genotype of R. sibirica (5). A proposal to create 2 subspecies, R. sibirica sibirica and R. sibirica mongolitimonae, was recently published (6). A new prokaryote name must be both effectively and validly published. To become effectively published, a name must meet certain rules, as defi ned by the International Code of Nomenclature of Bacteria (7). To become validly published, the name must then appear on a Validation List published in the International Journal of Systematic and Evolutionary Microbiology (8). This provides an orderly system for bacterial names to be properly introduced and published in the scientifi c literature. Valid and nonvalid names are listed on regularly updated websites (9,10). Names introduced without being validated have no standing in bacterial nomenclature. That is currently the status of these proposed R. sibirica subspecies. Therefore, the use of strain designations is still appropriate. If, and when, the subspecies names are validated, they are likely to be adopted and routinely used in the literature. Rickettsial taxonomy continues to evolve, and future changes should be determined by critical scientifi c judgments and general consensus within the scientifi c community. Dr Massung is chief of the Rickettsial Zoonoses Branch, Division of Viral and Rickettsial Diseases, National Center for Zoonotic, Vector-borne and Enteric Diseases, Centers for Disease Control and Prevention. His research interests include laboratory and epidemiologic investigations targeting the detection, prevention, and control of rickettsial and Bartonella spp. diseases and Q fever.

(261–275) Assorted proposals to clarify the Code

TAXONVolume 53, Issue 4 p. 1090-1094 Proposals to Amend the CodesFree Access (261–275) Assorted proposals to clarify the Code R.K. Brummitt, R.K. Brummitt r.brummitt@rbgkew.org.uk The Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE U.KSearch for more papers by this author R.K. Brummitt, R.K. Brummitt r.brummitt@rbgkew.org.uk The Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE U.KSearch for more papers by this author First published: 01 November 2004 https://doi.org/10.2307/4135590AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Volume53, Issue4November 2004Pages 1090-1094 RelatedInformation

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