Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.

No abstract

No abstract

The nomenclature of the genus Salmonella has reached an unsatisfactory state of affairs, with two systems of nomenclature in circulation. One system, proposed in the 1980s by Le Minor and Popoff, has received wide acceptance, although it does not conform to the rules of the Bacteriological Code. The other system, which conforms to the rules of the Bacteriological Code, is being used by an ever-decreasing minority. As a result of a number of recent Requests for an Opinion, the Judicial Commission of the International Committee on the Systematics of Prokaryotes has issued an Opinion (Opinion 80) with the intention that it should solve these discrepancies. However, like all Opinions, it is limited to matters of nomenclature and does not help to interpret the taxonomic consequences. The Judicial Commission has therefore asked experts in the field of nomenclature and taxonomy to write a commentary on the nomenclatural and taxonomic consequences of Opinion 80. The present article explains the nomenclatural consequences of Opinion 80, together with a clear presentation of the taxonomy that results when applying the currently widely accepted interpretation that the genus Salmonella currently includes only two species.

The names ‘Mycobacterium abscessus subsp. abscessus’ and ‘Mycobacterium abscessus subsp. massiliense’, proposed by Leao et al. (2009, J Clin Microbiol 47, 2691–2698), cannot be validly published. The purpose of this report is to provide a description in accordance with the Rules of the Bacteriological Code (1990 Revision). Moreover, the proposal of the name ‘Mycobacterium abscessus subsp. massiliense’ is contrary to Rule 38 and the correct name of this taxon, at the rank of subspecies, is Mycobacterium abscessus subsp. bolletii comb. nov. A description of Mycobacterium abscessus subsp. abscessus subsp. nov. and an emended description of Mycobacterium abscessus are also given.

No abstract

No abstract

It is now 30 years since the concept of valid publication was introduced into prokaryote systematics in such a way that a system of registration/indexing was integrated. Despite the success of this system and the introduction of the Approved Lists of Bacterial Names, accompanied by a new starting date in prokaryote nomenclature, there is a need to review both the historical aspects and current practices so that the current generation of prokaryote systematists have an up-to-date overview of some of the key elements.