Instructions for Authors — International Journal of Systematic and Evolutionary Microbiology

IJSEM Information for Authors – Page 1

Last updated 3rd September 2014

Information that has changed substantially since the previous version is highlighted

1. Scope and Editorial Policy

2. Preparing and Submitting a Paper

3. Style, Nomenclature and Units

4. Peer Review and Publication

1. Scope and Editorial Policy – Contents

1.1 Scope
1. 1.1.1 General
2. 1.1.2 Types of paper
1.2 Editorial policy
1.3 Submission and publication requirements

Queries or comments about online submission should be sent via the email links from the General enquiries should be sent to the Editorial Office:

IJSEM Editorial Office, SGM, Charles Darwin House, 12 Roger Street, London. WC1N 2JU.
Tel: +44 (0) 207 685 2671.
Email: ijsem{at}sgm.ac.uk.

1.1 Scope

1.1.1 General

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. 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; authors should consider a more general journal such as Microbiology. 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 Editorial Manager 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 , 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. Guidelines on the preparation of taxonomic subcommittee minutes are available here.

1.1.2 Types of paper

In order to save space in the journal, the Note will be considered to be the usual format for papers; however, to encourage conversion, Note papers are not identified as such in the journal. The Editors will insist that papers be shortened to the Note format where appropriate; it will be less troublesome for authors to submit their papers in this form in the first instance.

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 are reviewed to the same standard as full papers and are not considered to be preliminary communications. See 2. Preparing and Submitting a Paper for further details.

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 an Opinion. 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 an Opinion 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. Note that straightforward differences in taxonomic opinion are not generally considered as Requests for an Opinion.

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 two culture collections in different countries 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.

1.2 Editorial policy

1.2.1 Description of a new taxon

For a description of a new taxon, include the following:

A list of the strains included in the taxon.
A statement or tabulation of the characteristics of each strain (see Presentation of strain data).
A list of characteristics considered essential for membership in the taxon.
A list of characteristics which qualify the taxon for membership in the next higher taxon.
A list of diagnostic characteristics, i.e. characters which distinguish the taxon from closely related taxa.
Designation of the type for that taxon.
The reactions of the type strain of a new species.
For all characteristics that vary among strains within the species; e.g. if 80% of the strains ferment trehalose, the specific reaction of the type strain must be defined.

Please consult a recent 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.

1.2.2 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: ), now renamed as the International Code of Nomenclature of Prokaryotes.Alterations to the Code published since 1990 can be found online at . In summary, the requirements for the valid publication of new names and combinations are as follows:

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.
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 adjectives used as 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, -replaciineae; for family, -aceae; for subfamily, -oideae; for tribe, -eae; and for subtribe, -inae. Guidelines for the formation of correct names can be found in Appendix 9: Orthography to the International Code of Nomenclature of Prokaryotes (H.G. Trüper & J.P. Euzéby, Int. J. Syst. Evol. Microbiol.59, 2107-2113, 2009) (http://ijs.sgmjournals.org/content/59/8/2107.full.pdf+html?sid=8bbef75d-858e-4c66-af15-1c9069ae7cc9); How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature (H.G. Trüper, FEMS Microbiol. Rev.23, 231-249, 1999) and How to name new taxa of prokaryotes? (A. Oren, Taxonomy of Prokaryotes - Methods in Microbiology 38, 438-463. Edited by F. A. Rainey and A. Oren. Amsterdam: Elsevier/Academic Press). Assistance with names is often required of those with competence in Latin and Greek. Authors are encouraged to contact one of the journal's nomenclature reviewers: Bernhard Schink (bernhard.schink{at}uni-konstanz.de), Aharon Oren (aharon.oren{at}mail.huji.ac.il) or George Garrity (garrity{at}msu.edu) for guidance prior to the submission of their manuscripts.
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 validly published 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.
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 Nomenclature for Algae, Fungi and Plants and the International Code of Zoological Nomenclature. Excellent listings of names can be found online at 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: . 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.
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).
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. Culture Collections that are a members of the World Federation of Culture Collections generally qualify (for a list see . In cases of doubt the editors may be consulted.

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.

1.2.3 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. In the case of fungi, according to the rules of the International Code of Nomenclature for Algae, Fungi and Plants, a Latin diagnosis of the new taxon may be included, but is no longer compulsory, and the journal requires that an etymology/description in English in a style similar to that for bacteria be given. The Code also requires that all new names be registered in a public database.

1.3 Submission and publication requirements

1.3.1 Page and colour charges

There are no page charges for publishing in IJSEM.

Colour figures are published free of charge if the use of colour is judged to be necessary for scientific reasons, and no charges are levied on online-only supplementary material.

1.3.2 Originality, authorship and copyright

Aside from ICSP matters, papers submitted must report work that has not been published previously and is not under consideration for publication elsewhere. Papers submitted to IJSEM that have been published preliminarily online (e.g. in Nature Precedings, Faculty of 1000 posters or PLoS Currents) will only be considered if there is a significant amount of additional novel data and analysis to warrant publication. IJSEM considers preliminary online publication as prior publication, and reviewers and Editors must be able to clearly identify how the paper differs from the preliminary report and that substantially more work is incorporated into the manuscript.

All the authors must have agreed to the submission, and to the order of their names on the title page. They must also have agreed that the corresponding author may act on their behalf throughout the editorial review and publication process. The corresponding author is responsible for obtaining such agreement. Requests for changes in authorship after submission must be accompanied by signed agreements from all the parties involved.

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.

1.3.3 Ethics of 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 Editors will not accept papers where the ethical aspects are, in their opinion, open to doubt. Authors may wish to consult the ARRIVE guidelines for reporting in vivo experiments [Kilkenny et al. (2010). PLoS Biol 8(6), e1000412 ].

1.3.4 Research integrity

SGM is a member of the (COPE) and its editors operate within the COPE Code of Conduct for Journal Editors. Complaints of unethical behaviour will be investigated by SGM in line with for such investigation. Common reasons for such investigation include:

Redundant (duplicate) publication. Publication of an already published article, or a substantial portion of a published article, including unauthorized publication in translation.
Plagiarism. Plagiarism is the unauthorized and/or uncredited reuse of content or ideas generated by another person. Plagiarism can occur without a breach of copyright, as it covers more than simple copying-and-pasting.
Breach of copyright. The unauthorized reuse of copyright material, that is the copying of significant amounts of text or tables or figures. This can include unauthorized reuse by an author of their own material that is now copyright of another publisher. SGM makes use of the service to detect text duplication.
Fabricated data. This can include figures that have been digitally manipulated, for example to mask gel bands or alter contrast to make certain features more or less visible or to give the impression that data from separate experiments were in fact obtained in the same experiment.
Problems with authorship. Authorship problems include complaints that individuals have been inappropriately excluded from authorship or included without their knowledge, as well as accusations of guest, ghost or gift authorship.
Undisclosed conflict of interest.
Appropriation of ideas or data by a reviewer.

SGM promotes the for responsible research publication for authors and Editors.

Further guidance on research integrity can be obtained from the .

Conflict of interest. A conflict of interest may exist when your interpretation of the results or presentation of information may be influenced by your personal or financial relationship with other people or organizations. Examples of potential financial conflicts of interest include receipt of funding or salary from an organization that might gain or lose financially from publication of your paper, if you hold stocks or shares in such an organization or if you hold or are applying for a patent relating to the content of this manuscript. Examples of non-financial conflicts of interest might include political, religious or intellectual conflicts.

Reagent sharing. Authors of papers published in IJSEM are expected to make biological materials, such as strains, plasmids and antibodies, that are described for the first time in the paper available to bona fide researchers in reasonable quantities and at reasonable cost, for non-commercial purposes. Supply of such materials must conform to current local and national laws and regulations.

Materials and results obtained from outside the authors' laboratory. If a paper includes results that were not obtained by the authors' own experiments (e.g. production of antibodies, properties of strains) this must be explicitly stated, and appropriate acknowledgement be included where appropriate.

1.3.5 Policy on security and censorship

The policy of SGM Council on scientific publication, security and censorship can be found .

1.3.6 Open Access options

SGM allows authors to publish their work under the ‘Gold’ Open Access model. The SGM Open fee is £1750+VAT. Click to access the Open Access Article Processing Charge form. Gold open access has the following benefits:

The final version of the article is available free, without a subscription, immediately upon online publication.
The article is published under a Creative Commons, Attribution () licence.
The published article will be deposited, by SGM, in PubMed Central (and mirror sites such as UKPMC), with this version of the paper being freely accessible on publication of the definitive version in the online journal, to comply with the requirements of the Wellcome Trust and other funding bodies. Authors who have paid the Open Option fee may also deposit the PDF version of the published paper in an institutional repository at this point.

Papers published in Microbiology, Journal of General Virology and Journal of Medical Microbiology are freely available online 12 months after publication, and papers published in International Journal of Systematic and Evolutionary Microbiology are freely available 24 months after publication.

In addition, SGM is a signatory of the National Institutes of Health (NIH) Portfolio Agreement; as a result, papers that acknowledge funding from NIH will be deposited by SGM in PubMed Central and will be freely available from PubMed Central 12 months after publication. Because SGM has signed the Portfolio Agreement, authors are no longer able to deposit their own manuscripts in PubMed Central.

Authors may mount a PDF file of their accepted manuscript on their own or their institution's website or on a centrally organized repository, 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, 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, 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).

For full details, please see SGM's Open Access policy.

1.3.7 Archiving your paper

SGM's policies on Preprints and Author Accepted Manuscripts provide full information. Please note that the Author Accepted Manuscript policy does not apply to articles that are published with Gold open access.