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Authors must use the Bench>Press online submission and peer-review system The benefits of online submission include reduced time taken to give you a decision and savings in courier and postal charges. Papers should be prepared as described in these Instructions, but to aid in online reviewing it is particularly important that double line spacing is used and that continuous line numbering is provided in the PDF or Word file. Click here for more details.
Submissions via e-mail will be returned to the author for submission via Bench>Press.
Papers that were submitted via ESPERE before 1 January 2008 must now be revised through the Bench>Press system. The revised version should be treated as a new submission; the check-box 'This paper is a resubmission' should be selected and the ESPERE manuscript number must be given. A response to the comments of the editor and reviewers must also be supplied.
IJSEM Editorial Office
Society for General Microbiology
Marlborough House
Basingstoke Road
Spencers Wood
Reading RG7 1AG
UK
Any queries should be directed to Dr Melanie Scourfield (Senior Staff Editor) at the Editorial Office.
e-mail: ijsem{at}sgm.ac.ukScope. The International Journal of Systematic and Evolutionary Microbiology (IJSEM) publishes papers dealing with all phases of the systematics of all micro-organisms, including taxonomy, nomenclature, identification, characterization and culture preservation. Papers dealing only with characteristics that are differential below the subspecies level, primarily of epidemiological interest, will not be considered. Descriptions of cyanobacterial species already described under the Botanical Code will not be re-described under the Bacteriological Code. The journal does not encourage the submission of results of intraspecific characterization, e.g. typing methods such as rrn operon sequence microheterogeneities, nor the development of identification systems based upon these results to be used for diagnostic purposes. Infrasubspecific taxa are not covered by Rules of the Bacteriological Code and papers on such taxa are outside the scope of the journal. IJSEM will publish molecular environmental papers that have a strong taxonomic or evolutionary content.
It is a requirement of IJSEM and the ICSP that authors of new names and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). Papers will not be accepted until such documentation has been received by the Editor.
The IJSEM Submission Declaration now forms part of the Bench>Press submission process. The Declaration asks submitting authors to confirm that all of the authors of the paper have agreed to the submission. It also asks submitting authors, if their paper includes the proposal of new species or subspecies names (or new combinations) under the Bacteriological Code, to indicate whether they already have obtained confirmation of deposit and availability from two (or more) culture collections or whether the strains have been deposited and confirmation of deposit and availability will be provided as soon as it is available.
As required by the Bacteriological Code, the IJSEM publishes Validation Lists containing new names that were effectively published in other journals. For validation of new names published elsewhere, authors should submit a covering letter and two reprints or photocopies or a PDF file of the published article(s) to the Editorial Office. The requirements for validation are identical to those for publication in IJSEM; i.e. authors must provide evidence that types are deposited in two recognized culture collections in two different countries.
Send items relating to the International Committee on Systematics of Prokaryotes (ICSP), formerly International Committee on Systematic Bacteriology (ICSB), including its Judicial Commission and Subcommittees (such as Requests for Opinions), in the same way as normal online submissions.
Originality, authorship and copyright. Aside from ICSP matters, any papers submitted to the journal must represent reports of original research, and the original data must be available for review by the Editors if necessary. Papers are considered for publication on the understanding that (a) they report unpublished work that is not under consideration for publication elsewhere; (b) all named authors have agreed to the submission; and (c) if the paper is accepted for publication in IJSEM, all the authors (or other copyright holder) will assign to the International Union of Microbiological Societies (IUMS) the copyright (including electronic reproduction rights) of the paper. Neither a whole paper nor a substantial part of a paper may subsequently be published elsewhere in the same form, in any language or any medium, without the consent of the Society for General Microbiology, which has been authorized by the IUMS to act on its behalf in this matter.
Click here to download a Copyright Transfer Agreement form/Licence to Publish.
Self-archiving. Authors may mount a PDF file of their accepted manuscript on their own or their institution's website or on a centrally organized repository (such as PubMed Central), provided that the PDF is not publicly available until 12 months after online publication in the journal. The PDF file must correspond exactly to the accepted version of the manuscript. Authors may not mount a PDF of the final published version (with the exception indicated below), although they should include a link to the published version. Author manuscripts must not be mounted less than 12 months after publication in the online version of IJSEM (again with the exception indicated below); nor must they be mounted on a server for the purpose of commercial sale or systematic external distribution by a third party (e.g. via an e-print server).
Details of the policy of the SGM towards depositing accepted manuscripts in PubMed Central and other repositories can be found here.
Authors who pay for immediate open access through our Open Option scheme may deposit the published PDF file of their paper in PubMed Central (or other repositories) at the time of publication with no delay to public access, in addition to their paper being freely available to all without a subscription immediately on online publication.
Page charges and offprints. There are no page charges. Authors receive 25 offprints free; further copies may be purchased in multiples of 25.
Proof corrections. Papers should be written to the highest standard before submission: the proof stage must not be regarded as an opportunity to correct careless errors. Excessive correction of factual or careless mistakes on proofs may be charged to the authors.
Editorial handling of papers. Submitted papers are sent by the Editorial Office to an Editor, and are normally evaluated by at least two experts in the field as well as by the Editor. In determining suitability for publication, the following considerations, among others, are taken into account. (i) Is the paper within the scope of the IJSEM? (ii) Are the title and the summary brief and to the point? (iii) Is the scientific content sufficiently high? (iv) Is the text written in a concise and lucid manner, and is it arranged according to these guidelines? (v) Is the textual matter placed in the proper sections? (vi) Is the Methods section complete and accurate? (vii) Are the tables necessary, and if so, are they easily understood? (viii) Are the figures necessary, and if so, are they of high quality? (ix) Are the conclusions valid?
Papers on taxonomy are evaluated on the basis of their scientific content and the accordance of nomenclatural proposals with the relevant Code, and not on the taxonomic opinions of the author. It is understood, therefore, that acceptance of taxonomic papers does not necessarily imply acceptance by the Editor and the reviewers of the opinions expressed in the paper. Descriptions of new taxa should comply with the relevant Minimal Standards.
Papers returned for revision that have not been resubmitted within 40 days of the author receiving the request for revision are treated as new submissions and given a new date of receipt unless a later date is agreed between the author and editor.
Ethics of human and animal experimentation. Papers describing any experimental work with humans should include a statement that the Ethical Committee of the institution in which the work was done has approved it, and that the subjects gave informed consent to the work.
Experiments with animals should be done in accordance with the legal requirements of the relevant local or national authority. Procedures should be such that experimental animals do not suffer unnecessarily. Papers should include details of the procedures and of anaesthetics used. The online submission process includes a question regarding compliance with ethical standards.
The Editors will not accept papers where the ethical aspects are, in their opinion, open to doubt.
Supplementary data. Authors have the facility to attach supplementary data files (e.g. extensive tables of taxonomic data, figures such as large phylogenetic trees, sequence alignments, colour pictures, movies, etc.) to their paper in IJSEM Online. Click here to browse the supplementary data in IJSEM Online. This facility should be used to shorten papers wherever possible, and also to enhance papers. This material may be submitted at the same time as the main paper; it should significantly enhance the paper. Supplementary material should be clearly identified. The Editors may insist that figures or tables that the author has included within a paper should be converted into supplementary data.
Supplementary data are, and will continue to be, freely available to all readers regardless of whether they have a subscription to IJSEM Online. It is the SGM's policy to maintain the online journals and the supplementary data therein in perpetuity.
The text of the paper should normally contain a reference to the supplementary material, along the lines of 'The online version of this paper contains a supplementary figure showing the sequence alignment' or 'A fuller phylogenetic tree is available as supplementary data with the online version of this paper. If supplementary items are numbered, they should be numbered as Supplementary Fig. (or Table) S1, S2 etc.; for example, 'A extended tree containing a larger number of reference sequences is available as Supplementary Fig. S1 in IJSEM Online'.
A short text description should be supplied for each supplementary data item. This can be just a heading, or a more detailed explanation, as appropriate.
File types and formatting for supplementary data. Almost any file type can be used for supplementary data. The file type(s) should be indicated by the author on submission. Authors should try to avoid files that require unusual software, because these will be of limited use to readers. Very large files (more than about 2 Mb) should also be avoided where possible because they can be slow to download.
Sequence data should preferably be submitted as output from the alignment program, i.e. plain text.
Line figures should preferably be supplied as GIFs (.gif), and photographs as JPEGs (.jpg), because these are easy to download.
Cover illustrations. The Editors welcome the submission of striking pictures, preferably in colour, for possible use on the front cover, and will pay £75 towards expenses for each one used. Pictures need not be linked to a paper in the journal.
Submission of papers in electronic form. Accepted manuscripts (including tables) of all types are copy-edited as word-processor files; authors must provide their paper in this form if it is revised or at acceptance if no revision cycle has taken place. The word-processor file must exactly match the final, accepted version of the paper.
Any computer files and disks sent to the Editorial Office must be scanned with up-to-date antivirus software.
A paper by Kämpfer et al. (2003) outlining a standardized format for the description of a novel species of an established genus is freely available in IJSEM Online; authors are encouraged to follow this model where possible.
Notes. Notes are reviewed to the same standard as full papers and are not considered to be preliminary communications. The Note format is particularly suitable for the description of new taxa that are not based on a large number of strains. Each Note must have a brief summary. Do not use standard section headings (except for Acknowledgements and References) in the body of a Note; report introduction, methods, results and discussion in a single section, but see the instructions below for guidance as to content. Paragraph lead-ins are permissible. The text should be kept to a minimum and if possible should not exceed 2000 words; the number of figures and tables should also be kept to a minimum. Present acknowledgements as in Full papers. The References section is identical in format to that of Full papers.
Note and Full papers. Papers must be written in clear and concise English, normally in the past tense, and should normally comprise: (a) Title page (b) Summary; (c) Introduction; (d) Methods; (e) Results and Discussion; (f) Acknowledgements, if any; (g) References. Figures and tables must only be used to illustrate essential data that cannot easily be described in the text.
Style and layout. Authors should consult a recent (2003–on) issue of IJSEM for guidance on the layout of headings, tables, etc. More detailed guidance on the presentation of individual sections is given below. This includes some hints on how to improve the impact of a paper by appropriate presentation.
Title page. This should carry the following information.
Exercise care in using scientific names of bacteria. Scientific names used by themselves or unless otherwise qualified refer to all the constituent elements of the taxa to which the names refer. When only selected elements of a taxon were studied, the title should reflect this. The use of strain designations when applicable and feasible not only results in an accurate title but also permits more useful indexing.
Never use the name of a bacterial taxon in a general sense in a title if the nomenclatural type (see Valid publication of names of bacterial taxa) of the taxon was not included in the study. For example, a statement about the genus Pseudomonas which does not include a consideration of Pseudomonas aeruginosa, the type species, would not be valid.
Note: Keywords are no longer published in the journal.
Summary. This section is likely to be read by more people than the full paper, and many abstracting services use authors' summaries without modification. It is therefore important that this section is clear and comprehensible in its own right.
All new names and combinations proposed in the text and all type and neotype strains designated therein must be cited in the summary. Full details of the description of new taxa should not be given. References should not be cited, and any non-standard abbreviations used must be defined.
Introduction. This section should be very brief (approx. 350 words) and must not contain a detailed summary of the results.
Methods. This section should describe only important novel details, not standard methods; these can often be replaced by a statement such as 'standard methods were used' or by the appropriate reference. The suppliers of chemicals and equipment should be indicated only if this may affect the results. Suppliers' addresses should not be given unless this is considered essential for a particular reason.
Results and Discussion. There should be sufficient subheadings to make clear how the work was organized. If new names or combinations are proposed, the formal description should appear at the end of this section. In order to save space in the journal, the amount of repetition of data between the Results and Discussion sections, the Description where appropriate, and the Tables must be kept to an absolute minimum.
Reproducibility. It should be stated how many times an experiment was repeated and whether means or representative results are shown. Variability should be indicated statistically wherever possible; when error terms are given, the measure of dispersion and the number of observations should be stated. Statistical techniques used must be specified, and where necessary they should be described fully or a reference given. If results are expressed as percentages, the absolute value corresponding to 100% should be stated.
DNA base composition. The DNA base composition should be should be reported as G+C content in mol% only to the nearest significant digit.
Presentation of strain data. Present the characteristics of each strain in the text if practical or in a strain table if the list is complex. Only differential data should appear in Tables. Obviously, with very large numbers of strains, it may not be practical to provide individual strain data (see Supplementary data); instead, cite the percentage of strains that gave a positive or negative result for each character determined.
References. All papers submitted must use the name–year system.
References in the text should be cited as follows: two authors, Smith & Jones (2002) or (Smith & Jones, 2002); three or more authors, Smith et al. (2002) or (Smith et al., 2002). References to papers by the same author(s) in the same year should be distinguished in the text and the reference list by the letters a, b, etc. (e.g. 2002a or 2002a, b).
References at the end of the paper must be given in alphabetical order, except for papers with three or more authors, which should be listed in chronological order after any other papers by the first author. References must include the title of the paper as well as both initial and final page numbers. Titles of journals should be abbreviated according to the system followed by BIOSIS Serial Sources. No stops should be used after abbreviated words.
References to books should include year of publication, title (in full), edition, editor(s) (if any), town of publication and publisher, in that order. When the reference is to a particular part of a book, the inclusive page numbers and, if appropriate, chapter title, must be given. Examples of journal and book references are given in the At-a-glance style guide. Please pay particular attention to the style of book citations, especially the order of the editors' surnames and initials.
A lot of time in the Editorial Office is spent checking references – whether cited references are listed (and vice versa), spelling of authors names, year of publication, journal title, etc. It is the authors' responsibility to ensure the accuracy of this information, which is becoming increasingly important with the advent of interjournal linking via the Internet.
Only papers accepted for publication but not yet published may be cited as ‘in press’ in the reference list and must be accompanied by the title of the paper and the name of the journal. Relevant papers should be submitted in PDF format to the ESPERE system as additional files. Alternatively, two copies of relevant papers cited as ‘in press’ should be forwarded to the Editorial Office.
References to papers not yet accepted should be cited in the text as unpublished results, giving the surname(s) and initials of all of the author(s). Such papers should not appear in the list of references and must not include data essential to nomenclatural proposals.
References to personal communications, web sites, sequence databases, suppliers' catalogues, etc., should not appear in the list.
Tables. These should be broadly comprehensible without reference to the text, but repetition of methods descriptions should be avoided.
Footnote symbols should not be used in table headings. If a footnote symbol is attached to a heading, the footnote should probably be converted to a legend (see below)
It is not obligatory to have a legend, but general information that applies to the whole table (experimental conditions, methods of data analysis, etc.) should be given in this form. Symbols that apply to the whole table (such as +/–, v, d) should normally be defined in the legend.
The symbols * † ‡ § ¦ ¶ # should be used for footnotes, rather than superscript letters or numbers.
When results are expressed as percentages, the absolute value(s) corresponding to 100% must be stated. Statements of reproducibility should be included (see Reproducibility of results).
Figures. These must be selected to illustrate specific points. They should not be used to present results that can be described by a brief statement in the text. The legend(s) should be on a separate sheet to the figure(s). The points outlined above for tables regarding comprehensibility, relative values and reproducibility also apply to figures and their legends.
Lettering and size of figures. Lettering should be in a sans-serif font such as Arial or Helvetica, except in the case of sequence data where a non-proportional font such as Courier may be used. Figures should be designed so that there is a minimal amount of blank space in the journal following reduction of the whole figure to 84, 105 or 176 mm wide: figures will be reduced in size as much as possible, and normally to 84 mm. The size of the lettering should be such that it can withstand this reduction. The maximum printed size for a figure, including the legend, is 176 mm wide x 235 mm high.
Figures are classified here under the headings line drawings, bar diagrams, sequence data, photographs, digitally generated images and colour photographs.
Line drawings. These should be of a quality suitable for direct reproduction and approximately twice the size that they will appear. Line thicknesses and symbol sizes should be sufficient to allow for reduction (normally about 0.4 mm and 2–3 mm, respectively). The preferred symbols for graphs are 
, 
,
, 
, 
, 
, 
, 
. Graph lines should not appear inside open symbols. Where possible, the same symbol should be used for the same quantity in different figures. The scale-marks on graphs should be inside the axes.
Tints (i.e. shading made up of fine dots) should not be used in line drawings, because they do not reproduce clearly when printed in the journal. Solid black/white or broad hatching is better.
A top set of figures must be prepared for use by the printers, and these should be forwarded to the Editorial Office after notification of acceptance for publication.
Bar diagrams. Simple bar diagrams reporting only a few values are normally unnecessary; the data should instead be given in a table or in the text. It is editorial policy not to publish bar diagrams with ‘three-dimensional’ bars unless there is a specific justification for their use. Tints should not be used as shading for bars (see above).
Sequence data.The journal will not normally publish such data. The results of nucleic acid and protein sequence analyses should be presented concisely with little or no redundancy. For partial sequences, the number of bases determined and regions sequenced should be specified. For phylogenetic analyses, the number of positions, portion of the sequence analysed, and taxa should be specified. Figures showing full gene sequences are not published (see section below for guidelines).
If included, figures representing nucleotide or amino acid sequences should be in high-quality camera-ready form, with numbering of nucleotides or amino acid residues at appropriate intervals. Tints should not be used to highlight parts of sequences. For adequate legibility, the height of the characters should be not less than 1.5–2 mm (or 6–8 point). For printing at full page width with this size of type, a layout with 80–100 nucleotides per line is appropriate (or 60–70 if there are spaces between the codons). For a single-column layout, 50–60 nucleotides per line is about right. The spacing between the lines of sequence should be as close as is consistent with clarity. Note that sequence data must be submitted to on of the sequence databases (see section below).
Matrices and trees. Similarity or distance matrices should not be presented unless specific features of the entire table are discussed. However, representative similarity values should be presented in the text. In taxonomic papers, trees should only be included for showing the importance of a phylogenetic analysis to a taxonomic description; the size of trees should be reduced - only nearest neighbours should be included, but the authors should, in the legend or Methods, list the other taxa (including strain and sequence accession numbers) used to generate the tree. Full matrices and trees may be attached as supplementary data to the published paper in IJSEM Online.
Trees must include the names of organisms, their strain number (with type strains indicated where appropriate by a superscript capital T) and sequence accession number (space permitting). The size and style of font and width of lines should be such that the figure can be reduced as much as possible, in order make economical use of space in the journal. It is important to ensure the accuracy of names (check them in the List of Bacterial Names with Standing in Nomenclature when making the final revision of the paper) and accession numbers in trees, as correction is expensive and may lead to the introduction of further errors.
Photographs. These should be well-contrasted prints and preferably scanned as TIF files at a resolution of 300 d.p.i. at approximately final size. For micrographs, magnification should be shown by a bar marker. Photographs may be grouped to form a composite picture; to avoid loss of definition, the component parts should be submitted as separate files (prints; mounted on card or thick paper), rather than being rephotographed in the composite arrangement.
If it is not possible to scan photographic images, photographic prints can be mailed to the Editorial Office after receipt of notification of acceptance.
Digitally generated images. Authors' printed output from digitally generated halftone images often reproduce poorly in the journal. The ‘screening’ process used by the journal's printers to produce halftone illustrations converts the image into a pattern of dots. When this process is applied to an image that already consists of dots, as for scans, the two dot patterns often interfere and produce unacceptable results.
To avoid these problems, authors should submit their digital halftones in electronic form. For this purpose, the figures must be saved as ‘raw’ TIFF files of the images as output by the scanner or digital camera. Labels, pointers, etc., must not be added to these files: they should instead be indicated on a printout (this is to avoid problems of incompatibility between authors' and printers' software). Graphics files should be supplied as a separate file(s) from the text of the paper, with the file(s) clearly identified. Two versions should be supplied; one unlabelled and the other with the positions of any labels clearly marked.
Colour photographs. These are accepted, at the discretion of the Editors, only if they are essential for an understanding of the work described. The printers can produce black-and-white images from colour originals if necessary, but this is not recommended. Colour versions of black-and-white images may be attached as supplementary data to the published paper in IJSEM Online.
All types of paper should be submitted electronically via the Bench>Press system.
Reviews. Reviews should be brief summaries (limit of 6 printed pages excluding references) of developments in fast-moving areas. They must be based on published articles; they may address any subject within the scope of the IJSEM. Reviews may be either solicited or proffered by authors responding to a recognized need. Irrespective of origin, reviews are subject to editorial review.
Letters to the Editor. Critiques of taxonomic papers, when done in good taste, will be considered for publication. Letters to the Editor must include data to support the writer's argument and are intended only for comments on articles published previously in the journal. They should be no more than 500 words long. The letter will be processed and sent to the Editor who handled the article in question. If the Editor believes that publication is warranted, a reply will be solicited from the corresponding author of the article and make a recommendation to the Editor-in-Chief. Final approval for publication rests with the Editor-in-Chief.
Taxonomic Notes. This section permits the presentation of material or proposals in advance of formal discussion at a meeting of the ICSP so that there may be international awareness of the item. Notes may also transmit, in concise form, items of importance to systematics arising from publications other than the IJSEM, from the ICSP, or from individual scientists. Final approval for publication rests with the Editor-in Chief.
Requests for Opinions. When strict adherence to the Rules of bacteriological nomenclature would only produce chaos or would not result in nomenclatural stability, exceptions to the Rules may be requested of the Judicial Commission of the ICSP. Requests for Opinions must be accompanied by a fully documented statement of the relevant facts: when a request is not supported by adequate evidence, it will be returned to the author for revision. When challenging a Request for an Opinion, authors must state the basis of the challenge and support it by a documented statement of the relevant facts. If an Opinion is requested in the text, ‘Request for an Opinion’ should appear in the title.
Designation of neotype strains. A neotype strain is a strain that replaces, by international agreement, a type strain which is no longer in existence. The neotype should possess the characteristics given in the original description; any deviations should be explained. A proposal of a neotype strain must be published in the IJSEM together with a reference (or references) to the first description and name for the micro-organism, a description (or reference to a description) of the proposed neotype strain, and a record of the author's designation for the neotype strain and of at least one culture collection from which cultures of the strain are available. The neotype strain becomes established 2 years after the date of its publication in the IJSEM, provided that there are no objections, which must be referred within the first year of the publication of the neotype to the Judicial Commission for consideration. A neotype strain should be proposed only after a careful search has shown that none of the strains on which the original description was based is extant. If an original strain is subsequently discovered, the matter should be referred immediately to the Judicial Commission.
Please consult a recent (2003–on) issue of the journal for guidance as to style and format of descriptions.
Suitable photomicrographs and, if necessary, electron micrographs may be used as part of the description to show any morphological or anatomical characters that may be pertinent to its classification. See Photographs.
Valid publication of names of bacterial taxa. The Principles and Rules of nomenclature are published in the International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code (Washington, DC: American Society for Microbiology). In summary, the requirements for the valid publication of new names and combinations are as follows.
(i) The new name or combination must be published in the IJSEM. If published elsewhere, the new name or combination is not validly published until it is published in the IJSEM. The date of publication of the new name or combination is the date of publication in the IJSEM.
(ii)The name should be in the correct form. Generic and suprageneric names are single words, in Latin form, spelled with an initial capital letter. Names of species are binary combinations or words, in Latin form, consisting of a generic name and a single, specific epithet, the latter spelled with an initial lowercase letter. A subspecific name is a ternary combination consisting of the name of a species followed by the term ‘subspecies’ (abbreviation: subsp.), and this in turn is followed by a single subspecific epithet. The gender of specific or subspecific epithets must agree with each other and with the genus to which they belong. [‘Variety’ (abbreviation: var.) is sometimes used in place of ‘subspecies’, but the latter term must be used because the term ‘variety’ has no standing in nomenclature.] Names of taxa from the rank of order to tribe inclusive are formed by the addition of the appropriate suffix to the stem of the name of the type genus ( see below). The suffix for order is -ales; for suborder, -ineae; for family, -aceae; for subfamily, -oideae; for tribe, -eae; and for subtribe, -inae. Assistance with names is often required of those with competence in Latin and Greek. An authority with special interest in bacteria is Professor Dr Hans G. Trüper, Department of Microbiology, Universität Bonn, D-53115 Bonn, Germany (Fax: +49 228 737 576).
(iii) The name should be clearly proposed as a new name or combination and should be accepted by the author at the time of publication. New names are ordinarily proposed by an author appending the phrase ‘species nova’ (abbreviation: sp. nov.), ‘genus novum’ (abbreviation: gen. nov.), ‘nomen novum’ (abbreviation: nom. nov.), ‘combinatio nova’ (abbreviation: comb. nov.), or the like after the name or combination being proposed as new: alternatively, the author may make a statement to the effect that he/she is introducing a new name or combination. All names that were not validated in the Approved Lists or Index (see Nomenclature of bacteria) or by subsequent listing and validation in the IJSB/IJSEM are available, although discretion must be observed in their use to avoid confusion.
(iv) The nomenclature of prokaryotes is not independent of virological, botanical and zoological nomenclature. When naming new taxa in the rank of genus or higher, due consideration is to be given to avoiding names which are regulated by the International Code of Virus Classification and Nomenclature, the International Code of Botanical Nomenclature and the International Code of Zoological Nomenclature. Excellent listings of names can be found online at Species 2000 and in the online databases given below, and also in the following books. Algae: De Toni, J. B. (1889) Sylloge Algarum; Index Kewensis, 1895–present, London: Royal Botanic Gardens. Bacteria: see Nomenclature of bacteria. Fungi: Clements, F. E. & Shear, C. L. (1931), The Genera of Fungi, New York: H. W. Wilson; Saccardo, P. A. (1882–1921) Sylloge Fungorum, Pavia, 25 vol.; Index to Fungi (1940–present), Kew: Commonwealth Mycological Institute. Yeasts: see Nomenclature of unicellular eukaryotes. Protozoa: Index Zoologicus (1902–present), London: Zoological Society.
(v) The taxon must be accompanied by a description or by a reference to a previously published description of the taxon (see Description of a new taxon, for information to be included in descriptions).
(vi) The nomenclatural type of the taxon must be designated. For species and subspecies, the type strain should be described by itself and designated by the author's strain number as well as by the strain numbers under which it is held by at least TWO culture collections in TWO different countries from which the strain is available. For new combinations, the type strain must be cited.
A nomenclatural type is that constituent element of a taxon to which the name of the taxon is permanently attached. The type of a species or a subspecies is a strain, that of a genus is a species, and that of an order, suborder, family, subfamily, tribe or subtribe is the genus on whose name the name of the higher taxon is based [ see (ii) above]. According to the new Rule 18 of the Bacteriological Code, a description, preserved (non-viable) specimen, or illustration may not serve as the type. However, the Editors may allow only a vernacular name if the description is very limited in scope, e.g. little more than a DNA or RNA molecular sequence. In these cases, prior consultation is advised.
The type strain is one of the strains on which the author who first described a named organism based his/her description and which he/she or a subsequent author definitely designated as the type; if the description was based on a single strain, this strain is the type by monotypy.
According to the new Rule 27(2)b, the derivation (etymology) of a new name (and if necessary of a new combination) MUST be given - see a recent issue of IJSEM.
Publication of names of unicellular eukaryotes. Much of what is written above for bacteria is relevant to the description of new taxa of unicellular eukaryotes. According to the Rules of the Botanical Code, a Latin Diagnosis of the new taxon must be provided, and the journal requires that an etymology/description in English in a style similar to that for bacteria be given.
Only those names of bacteria that were included in the Approved Lists of Bacterial Names (amended edition) (edited by V. B. D. Skerman, V. McGowan & P. H. A. Sneath) and the Index of the Bacterial and Yeast Nomenclatural Changes Published in the International Journal of Systematic Bacteriology since the 1980 Approved Lists of Bacterial Names (1 January 1980–1 January 1989) (edited by W. E. C. Moore & L. V. H. Moore), both published by the American Society for Microbiology in 1989, and those that have been validly published in the IJSB/IJSEM since 1 January 1989 have standing in nomenclature. Non-valid names must be enclosed in quotation marks and an appropriate statement concerning the nomenclatural status of the name should be made in the text (for an example, see Int J Syst Bacteriol30, 547–556, 1980).
A List of Bacterial Names with Standing in Nomenclature; see Int J Syst Bacteriol47, 590–592. The list is updated by J. Euzéby shortly after the publication of each issue of the IJSEM.
An online version of the Approved Lists, including nomenclatural changes validly published since January 1980, is published by the DSMZ, Braunschweig, Germany, as Bacterial Nomenclature Up-to-Date.
Please check all names, even common ones, before submission and during revision.
The following may also be useful:
Bergey's Manual of Systematic Bacteriology. Baltimore: Williams & Wilkins. Vol. 1 (1984), edited by N. R. Krieg & J. G. Holt; vol. 2 (1986), edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt; vol. 3 (1989), edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt; vol. 4 (1989), edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Volumes 1 (2001) and 2 (2005) of the second edition, covering the Archaea and the deeply branching and phototrophic Bacteria (Vol. 1; edited by D. R. Boone, R. W. Castenholz & G. M. Garrity) and the Proteobacteria (Vol. 2; edited by G. M. Garrity, N. R. Krieg & D. J. Brenner), have now been published by Springer.
Type strains. All type strains must be indicated at each occurrence in the text, tables and figures by a superscript capital T (e.g. ATCC 13546T = IJSM 0819T). The Code requires the designation of a type strain for a new species and recommends the deposition of a culture, the type strain. Type strains of cultivable species must be deposited in at least two or more public culture collections from two or more countries and accession numbers must be provided. An extensive listing of culture collections is available on-line.
Patent strains. Authors must inform the Editors, and must indicate in the paper, whenever strains under study are involved in a patent process. Strains other than the type strain should carry the superscript ‘PP’ if a patent is pending and ‘P’ if a patent has been issued for a type or any other strain. The description of a new species cannot be published while a patent is pending upon the intended type strain because that strain would not be available for study. In this circumstance, authors are to wait until the patent is issued.
Although names of genera and higher categories may stand alone to refer to the taxa with which they are associated, specific and subspecific epithets may not. A generic name followed by a specific epithet should be spelled out the first time it is used in the text; subsequently, it may be abbreviated to its capitalized initial letter if the context makes the meaning clear. If there are several generic names in the text with the same initial letter, the names should be spelled out at each occurrence. However, it should be noted that the Subcommittee on the taxonomy of Phototrophic Bacteria and the Subcommittee on the taxonomy of the family Halobacteriaceae recommend the use of three-letter abbreviations for some genera (see http://www.bacterio.cict.fr/abbreviations.html).
Vernacular names. Generic names are singular Latin nouns and do not take a plural verb. Authors should avoid the use of a generic name alone when the reference is to the members of the genus. Thus, ‘The strains (species or cultures) of Salmonella are…’ not ‘the Salmonella are…’. The latter implies more than one generic name Salmonella.
Many micro-organisms are known by their vernacular (common) names as well as by their scientific names. The vernacular name for an organism may vary from language to language or from place to place, even within the same country. There are no rules governing the use of vernacular names.
It is often convenient to use vernacular names coined from the generic names. In these forms, the initial capital letters are dropped and italics are not used. For plural forms of vernacular names, Latin or other plural endings are used, depending primarily on euphony. Thus, the vernacular singular for a member of the genus Spirillum is spirillum, and the plural generally used in the English language is spirilla (Latin plural), not spirillums (English plural). Occasionally, more than one common name arises from a generic name, such as treponema (plural treponemata or treponemas) and treponeme (plural treponemes) from Treponema.
Use only correct names of taxa. Although an organism may have a number of correct names, depending on its taxonomic placement, use one particular name consistently; if there are objections to its use, cite this name as a synonym. Taxa above the rank of genus must be written in roman. In all taxonomic matters, such as those exemplified for the bacteria, the relevant Code of nomenclature should be followed. For yeasts, authors should use the nomenclature employed in The Yeasts: a Taxonomic Study, 4th edn (1998) (Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier), and in Yeasts: Characteristics and Identification, 3rd edn (2000) (Cambridge: Cambridge University Press). If an author disagrees with this nomenclature, the first use of a scientific name in the text and in the Summary should be followed by the name, in parentheses, as given in The Yeasts.
In the absence of a detailed discussion of specific structural features, the nucleotide sequence or proposed secondary structure should not be presented. Such papers should be accompanied by substantial additional experimentation to characterize the gene(s) and products(s) concerned, and by substantial computer analysis. IJSEM will not normally publish DNA sequences from double-stranded genomes unless the two strands have been sequenced independently.
IJSEM will not publish figures whose principal function is to present primary sequence data, since the data can be accessed through the databases. To merit publication, sequence figures must be justified by the additional annotation they present; they should normally be limited to regions of particular interest. Sequence alignments of nucleic acids and proteins may be presented using the supplementary data facility in IJSEM Online. To assist the reviewers, authors must send a disk version of the complete sequence covered by their paper at the time of submission if it is not available from a public database. If avaliable via a database the authors must clearly indicate which database and ensure that it is available at the time of review. It is the authors' responsibility to ensure the accuracy of this information, which is becoming increasingly important with the advent of inter-resource linking via the Internet.
New sequences must be available for review; if the sequence(s) is not yet available from one of the public databases (it is permissible to request that the sequence not be publicly available until the paper is published), it must be provided in electronic form for use of the Editor and reviewers at the time of submission. Papers reporting new sequence data will not be published unless the sequence has an accession number from one of the public databases (GenBank, EMBL, DDBJ or PIR).
Submitted manuscripts containing sequence data should include, on the title page, the footnote ‘The GenBank[/EMBL/DDBJ] accession number for the [16S rRNA gene/gyrA, etc.] sequence of XXXXX is XX00000’.
When making comparisons between nucleotide or amino acid sequences, it is important to use the correct terminology. 'Homology' has a precise biological meaning of 'having a common evolutionary origin'. When a percentage comparison is made, the terms 'identity' or 'similarity', as appropriate, must be used.
Chemical and biochemical. Authors should follow the recommendations of IUPAC for chemical nomenclature, and those of the Nomenclature Committee of IUBMB and the IUPAC–IUBMB Joint Commission on Biochemical Nomenclature for biochemical nomenclature . A summary of nomenclatural recommendations, with references, is given in the Biochem J Instructions to Authors. The recommendations are given in full in Compendium of Biochemical Nomenclature and Related Documents, 2nd edn (1992), London: Portland Press.
Genetic. The following proposals should be adhered to wherever possible. Bacteria: Demerec, M. et al. (1966) Genetics54, 61–76 [also J Gen Microbiol (1968), 50, 1–14]. Plasmids: Novick, R. P. et al. (1976) Bacteriol Rev40, 168–189. Yeasts: Sherman, F. (1981) In The Molecular Biology of the Yeast Saccharomyces. I. Life Cycle and Inheritance, pp. 639–640 (edited by J. N. Strathern et al. New York: Cold Spring Harbor Laboratory). Aspergillus nidulans: Clutterbuck, A. J. (1973) Genet Res21, 291–296. Neurospora crassa: Neurospora Newsl (1978), 25, 29.
Enzyme. The system published in Enzyme Nomenclature (1992), London & New York: Academic Press, and its supplements is used. Enzyme Commission numbers should be given where appropriate.
Quantities, units and symbols. The recommended SI units should be used. For guidance, see Quantities, Units and Symbols, published by the Royal Society, 6 Carlton House Terrace, London SW1Y 5AG, UK, and Units, Symbols and Abbreviations, published by the Royal Society of Medicine, 1 Wimpole Street, London W1G 0AE, UK.
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