International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2114–2121 DOI 10.1099/ijs.0.013649-0 Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria N. A. Logan,1 O. Berge,2 A. H. Bishop,3 H.-J. Busse,4 P. De Vos,5 D. Fritze,6 M. Heyndrickx,7 P. Ka¨mpfer,8 L. Rabinovitch,9 M. S. Salkinoja-Salonen,10 L. Seldin11 and A. Ventosa12 Correspondence 1Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens N. A. Logan Road, Glasgow G4 0BA, UK [email protected] 2CEA Cadarache, DSV/IBEB/SBVME, LEMIRE, Baˆt. 161, F-13108 St Paul-lez-Durance Cedex, France 3Molecular Biology, Biosciences Group, dstl Porton Down, Building 384, Room 21, Salisbury SP4 0JQ, UK 4Institut fu¨r Bakteriologie, Mykologie & Hygiene, Veterina¨rmedizinische Universita¨t, Veterina¨rplatz 1, A-1210 Vienna, Austria 5Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium 6DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany 7Instituut voor Landbouw en Visserijonderzoek (ILVO), Technology and Food Sciences, Brusselsesteenweg 370, B-9090 Melle, Belgium 8Institut fu¨r Angewandte Mikrobiologie Fachbereich Agrarwissenschaften, O¨ kotrophologie und Umweltmanagement, Justus-Liebig-Universita¨t Giessen, Heinrich-Buff-Ring 26–32, D-35392 Giessen, Germany 9Laborato´rio de Fisiologia Bacteriana, Instituto Oswaldo Cruz, Fiocruz. Av. Brasil, 4365, Rio de Janeiro, RJ 21405-900, Brazil 10Department of Applied Chemistry and Microbiology, University of Helsinki, PO Box 56, Biocenter 1A Viikinkaari 9, FIN-00014, Finland 11Instituto de Microbiologia Prof. Paulo de Go´es, CCS - Centro de Cieˆncias da Sau´de - Bloco I, Avenida Carlos Chagas Filho, 373, Cidade Universita´ria, Ilha do Funda˜o, CEP 21941-902, Rio de Janeiro, Brazil 12Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, E-41012 Seville, Spain Minimal standards for describing new taxa within the aerobic endospore-forming bacteria are proposed, following Recommendation 30b of the Bacteriological Code (1990 Revision). These minimal standards are recommended as guidelines to assist authors in the preparation of descriptions for novel taxa. They encourage broad polyphasic characterization and the construction of descriptions that are practically useful in routine diagnostic laboratories. The proposals have been endorsed by the Subcommittee on the Taxonomy of the Genus Bacillus and Related Organisms of the International Committee on Systematics of Prokaryotes. Introduction A detailed listing of the aerobic, endospore-forming bacteria, together This paper proposes minimal standards for describing new with a brief historical account of the taxonomy of these organisms, and a list of relevant curated 16S rRNA gene sequences of aerobic genera and species of aerobic, endospore-forming bacteria, endospore-formers and relatives are available as supplementary material in order to address Recommendation 30b of the with the online version of this paper. Bacteriological Code (Lapage et al., 1992) and also the Downloaded from www.microbiologyresearch.org by 2114 013649 G 2009 IUMS Printed in Great Britain IP: 54.70.40.11 On: Tue, 18 Dec 2018 20:14:18 Minimal standards for aerobic endospore-formers remit of the Subcommittee on the Taxonomy of the Genus ten or more; observations on a minimum of three strains Bacillus and Related Organisms of the International are necessary to have some indication of natural variability. Committee on Systematics of Prokaryotes (ICSP). It is Preferably, strains should have been isolated from more important first to clarify the scope of these minimal than one location and, ideally, from several locations. If standards. They cover all of the aerobic, endospore-forming strains are from a single source, their non-clonality should bacteria among the low-G+C Gram-positive bacteria be checked using a nucleic acid fingerprint technique. (Firmicutes); that is to say all species of Bacillus (including Proposals based upon single isolates should be avoided those that are described as strictly anaerobic, and those for wherever possible. Each habitat, or source of isolates, must which sporulation has not been demonstrated, but that are be described in sufficient detail, and geographical locations seen to be placed phylogenetically in the vicinity of aerobic must be specified, in order to allow the isolation work to be endospore-forming bacteria), all those genera accommod- repeated. Isolation procedures must be fully specified and ating species originally allocated to Bacillus and all the other include details of medium formulation, pH and inocu- genera that have been proposed to accommodate new lation methods, of the gaseous composition of the species of aerobic endospore-formers that were not atmosphere for incubation and of the temperature and previously accommodated within Bacillus. At one time, the duration of incubation. If several isolates are available for family Bacillaceae encompassed all of the taxa with which the study, they should all be studied; the selection for study of Subcommittee was concerned, but these taxa are now found, a single strain from such a collection and the disregarding sometimes along with non-spore-formers, in several families of the other strains is strongly discouraged. A proposal of the order Bacillales: Bacillaceae,‘Alicyclobacillaceae’, based upon a single isolate should state this explicitly in the ‘Paenibacillaceae’, Pasteuriaceae, Planococcaceae and description. The description must outline the source(s) of ‘Sporolactobacillaceae’. A detailed listing of the aerobic, the isolates. Maintenance procedures must be adequately endospore-forming bacteria, together with a brief historical specified. The type strain must be deposited in two publicly account of the taxonomy of these organisms, appears in a accessible culture collections in different countries, as document that is available as supplementary material to this required by the Judicial Commission of the ICSP (De Vos paper in IJSEM Online. & Tru¨per, 2000), and it is strongly recommended that another, reference, strain of the same taxon is deposited at Species should be identifiable by readily available methods, the same time in order to allow confirmation of but published descriptions too often lack both adequate authenticity. For the practice of valid publication of names representation of within-taxon diversity and sufficient and deposit of type material, authors should consult features to allow a taxon’s recognition and distinction. Tindall et al. (2006), Tindall (2008) and Tindall & Garrity Phenotype, along with genotype, ‘continues to play a salient (2008). role in the decision about cut-off points of genomic data for species delineation ... [and] ... description of species ... should be based on the use of well-documented criteria, laboratory Cultivation protocols and reagents which are reproducible’ (Stackebrandt Cultivation procedures must be fully specified and include et al., 2002). The written description of a species or genus details of medium formulation and pH. Attempts should must be seen as a practically essential, integral part of any be made to grow organisms on standard media, but care taxonomic proposal, and care needs to be taken to ensure that should be taken that specific characters are not thereby lost. it is as comprehensive and practically useful as possible; the Failure to grow on standard media should be indicated, diagnostic characters should not be seen merely as adjuncts to and alternative media that satisfy the needs of the the delineation of a taxon that has been recognized primarily organisms should be given. The formulation of these on the basis of genomic data. A widespread problem is that should be fully described, as should the inoculation comparisons are often made with descriptions given in the methods and incubation conditions. Select an incubation literature, rather than by laboratory study of reference temperature that matches the optimum growth temper- cultures, so compilations as well as original descriptions ature of the organism(s) as closely as is practical. Certain should never be relied upon entirely. media and methods may be adapted for acidophilic and alkaliphilic organisms by adjusting the pH. Similarly, a Against a background of ever-increasing numbers of taxa and medium with NaCl or a mixture of salts should be used for rapid advances in characterization methodologies, we pro- the cultivation of halophiles. The description must state pose this set of minimal standards for the written descriptions the preferred growth medium for strains of the proposed of novel genera and species of aerobic endospore-formers. taxon, and indicate the incubation conditions required. Minimal standards Standardization Whatever methods are used for the description, standard- Isolates ization of methodologies and inclusion of reference strains It is strongly recommended that the number of strains to is crucial. The methods used to generate the characters be studied for each taxon should be at least five, and ideally included in species descriptions have not usually been Downloaded from www.microbiologyresearch.org by http://ijs.sgmjournals.org 2115 IP: 54.70.40.11 On: Tue, 18 Dec 2018 20:14:18 N. A. Logan and others standardized between laboratories, and the test results cell dimensions. Electron microscopy may be of value to shown in differentiation tables often include