Information for Authors
- 1. General information
- 2. Editorial processes
- 3. Ethics and research integrity
- 4. How to prepare your article
- 5. Pre-submission checklists
- 6. How to submit a standard research article
- 7. References
- 8. Tables
- 9. Figures
- 10. Supplementary material
- 11. How to submit a revised article
- 12. Author forms
- 13. Post-acceptance
All articles must be submitted online using the Editorial Manager manuscript submission system. Please visit the Microbiology Society's publications list to choose the journal you wish to directly submit to, and follow the 'Submit now' link to access Editorial Manager. Submissions are not accepted in hard copy or by email. When using the Editorial Manager submission system, once the author has provided a title for their submission, they can exit the system and continue submitting it at another time, without needing to 'save' it. The author will find their unfinished submission in the 'Incomplete Submissions' folder on their Main Menu.
All pre-submission or general editorial queries should be directed to each journal's Editorial Office contact at:
2.1 Editorial quality check
Upon submission, articles are checked by a member of the Editorial Office to ensure language quality, and that they are compliant with the pre-submission checklists as well as the requirements of the Society's Information for Authors. If any formatting problems are noticed by editorial staff, articles will be returned to the submitting author to amend before it can be assigned to an Editor.
2.2 Peer Review
Once an article has been assigned to an appropriate Editor, the Editor is then responsible for making the decision on the article's suitability for the journal, based on the journal scope. Editors are entitled to pre-screen reject submissions at this stage based on the nature of the study, quantity and quality of data, general conclusions, standard of presentation, language quality and if the article falls outside of the journal's scope.
Articles that pass the pre-screening stage will be sent to typically two independent reviewers. Reviewers will review the paper for originality and significance of the work described, and judge its acceptability for publication. The reviewers may also make critical comments and, where necessary, suggest improvements or additional experiments that could be done in support of the findings.
If the Editor is facing difficulty in obtaining reviewers, then he/she may also act as a reviewer or seek comments from another Editor. Authors may suggest at least three reviewers upon submitting their paper, ensuring that an institutional email address is provided. The use of reviewers suggested by the authors is at the discretion of the Editor after checks have been made to validate the suggested reviewers' details and authenticity.
Note that Microbial Genomics has a double-blind peer review policy, ensuring that the name(s), institution(s) and submitting country of author(s) are hidden from peer reviewers and vice versa. Authors are required to remove all author names and institutions from their article. This information will be requested through our submission system instead. Please double check that all author names are removed from all material submitted, including the author comments section.
After reviewer recommendations have been obtained, it is the Editor who makes the final decision as to the acceptability of the article, based on the reviews and their own assessment of the article.
There are three possible decision types: accept, revise (major or minor) and reject. Revise decisions imply that the article requires modifications that could be carried out within a specified time frame.
Articles are reviewed as quickly as possible, and authors should usually expect to receive a first decision within 4-6 weeks.
The Microbiology Society is a member of the Committee on Publication Ethics (COPE) and its editors operate within the COPE Code of Conduct for Journal Editors. The Society promotes the COPE International Standards for responsible research publication for authors and Editors. Common reasons for investigation include suspected instances of: Redundant (duplicate) publication; Plagiarism; Breach of copyright; Fabricated data; Problems with authorship; Undisclosed conflict of interest; Appropriation of ideas or data by a reviewer.
The Microbiology Society supports the Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals by the International Committee of Medical Journal Editors (ICMJE).
3.1 Originality and authorship
Research papers submitted to the Microbiology Society's journals must report work that has not been published previously and is not under consideration for publication elsewhere. For papers that have been published preliminarily online, please refer to the Society’s Preprint policy.
All authors must have agreed to the submission and to the order of their names on the title page, and will be asked to confirm this at submission. They must also have agreed that the corresponding author may act on their behalf throughout the editorial review and publication process. Requests for changes in authorship after submission, e.g. to order of the authors or deletion or addition of authors, must be approved by all authors in a signed agreement. Individuals who have contributed to the work but do not meet authorship criteria should be noted in the Acknowledgments section of the manuscript.
If a table or figure has been published before, the authors must obtain written permission to reproduce the material in both print and electronic formats from the copyright owner. The original source should be cited in the figure caption or table footnote.
4.1 Preparing files for submission
Articles can be submitted initially either as a single PDF file or as a separate Word file with accompanying figure files, which will be compiled into a single PDF by the submission system. However, authors are advised, where possible, to upload files individually to ensure that Editors and Reviewers can access the high-resolution figure files.
Supplementary material should be submitted as a combined PDF separate file, and this will be incorporated into the system-generated PDF.
For information on submitting a revised article, please click here.
4.1.1 Submission as a single PDF
The submitted PDF should preferably not be much larger than 1 MB.
4.1.2 Submission as a separate Word and/or figure files
Most standard word-processor files (including .docx files produced in Word 2007 or 2010) will convert successfully to PDF. Times, Times New Roman, Courier, Helvetica and Arial, and the Symbol font for special characters, are the recommended fonts. Other fonts are not guaranteed to convert successfully to PDF. Tables for the main paper must be prepared as part of the word-processor file; they must not be supplied as images or Excel files. Excel files are, however, acceptable for supplementary material. Word-processor files including inserted image files will normally be converted successfully to PDF by the system, but please note that files using OLE (Object Linking and Embedding) technology to display information or embedded files are not supported. If the conversion is not satisfactory, either convert the file to PDF yourself, and submit that, or submit the image files separately.
The file types that are supported for submission as separate figure files for conversion to PDF are PDF, GIF, TIFF, EPS, JPEG and PPT. A resolution of 300 d.p.i. at a reasonable size of reproduction is recommended; in other words, an image intended to fit in a single column of the journal should be around 1000 pixels wide and an image intended to fit across two columns should be around 2000 pixels wide. The following file types are not supported at the initial submission stage as they cannot be converted to PDF by the system: bitmap (.bmp), PICT (.pict), Excel (.xls), Photoshop (.psd), Canvas (.cnv), CorelDRAW (.cdr) and locked or encrypted PDFs. Image files will be converted to PDF and added to the end of the paper PDF produced by the system. If any of the image files are very large, it is advisable to reduce their size before submission if possible.
4.1.3 Cover letter
Journal of Medical Microbiology and International Journal of Systematic and Evolutionary Microbiology (IJSEM) both require cover letters. For all other journals it is preferable but not mandatory. Please use the following as an indication as to what you should include:
- What is the current knowledge of the subject?
- What are the new findings being reported here?
- What impact will your findings have on scientific/clinical practice or policy in the foreseeable future
- Any citations of personal communications or unpublished results should be confirmed in the cover letter
For further information for the IJSEM cover letter requirements, please see the IJSEM pre-submission checklist.
4.1.4 Nomenclature, style and units
For uniformity of our published research it is important for submissions to adhere to our agreed nomenclature guidelines. Details on nomenclature, style and units to use in your submitted article are available here.
Articles that do not meet these set requirements may encounter problems during peer review and will need to be amended before publication.
4.2 Data depositories
For articles containing new sequence data, the sequence(s) will need to be available through a database upon publication. Authors must include on the title page, the footnote 'The GenBank/ EMBL/ DDBJ/ PIR] accession number for the XXXXXX sequence of XXXXX is XX00000. If the sequence(s) is not yet available, the database flat file (GenBank *.gbk; or, EMBL *.embl) or the NCBI Sequin file (*.sqn) should be made available for review. These files will not be published, but they are essential for reviewing the paper.
All journals welcome the deposition of supporting data.
Microbial Genomics has a mandatory open data policy. Authors are required to provide access to all supporting data, which have either led to the conclusions drawn in their paper, or to allow the procedure described in the paper to be repeated.
When submitting to Microbial Genomics authors are also required to provide a Data Bibliography. Please ensure that on submission this Data Bibliography does not include any author names. If authors are associated with the data, please remove all author names and replace with ‘XXXX’ to ensure that the journal’s double-blind peer review policy is respected. Authors will be able to add in the author names at first proofs stage.
Microbial Genomics has partnered with Microreact, a free data visualisation and sharing platform that allows scientists and health professionals worldwide to better collaborate to understand disease outbreaks. The journal is encouraging authors to upload their data files to Microreact, which can then provide interactive querying of the data via trees, maps, timelines and tables, and published in Microbial Genomics via a permanent web link.
Microreact has been developed in the David Aanensen Research Group at Imperial College London and The Centre for Genomic Pathogen Surveillance. It is a React.js application taking full advantage of the Phylocanvas API (trees), the Google Maps API (maps) and vis.js library (timeline).
4.3 Pre-submission language editing
Prior to submitting your article, authors may wish to have it edited for correct use of English, particularly if English is not your first language. This step is not compulsory but it may assist the editorial staff, Editors and reviewers to fully understand the content of your article. However, language editing does not guarantee that your article will be sent out for peer review or accepted for publication. For the Journal of Medical Microbiology, articles with poor use of English will be rejected and authors invited to resubmit only once the language has been improved. Authors are advised to ensure the correct use of English in their articles before submitting to the journal.
A large number of language-editing services are available. While you may use any professional scientific editing service of your choice, the Microbiology Society has partnered with Editage to provide publication-focused editing services to Society authors at a 15% discount. If the editorial team finds any language issues in text that Editage has edited, then Editage will re-edit the text for free. To take advantage of this offer click here. If you’re an existing Editage customer, you may get the discount by using the code MICSOC10 while making a submission.
This information is intended to aid authors prior to submitting their article to the Editorial Manager submission system, in order to avoid delays upon submission and ensure that the article can be assigned to an Editor as quickly as possible.
Please find below journal pre-submission checklists:
- Journal of General Virology
- International Journal of Systematic and Evolutionary Microbiology
- Microbial Genomics requires authors to adhere to article templates. Click here for Microbial Genomics article templates.
- JMM Case Reports requires authors to adhere to article templates. Click here for JMM Case Reports article templates.
For all journals, authors must also include in their paper:
- Permission for reuse of published content not published by the authors must be uploaded during initial submission. We accept emails, letters and RightsLink confirmation that must be from the copyright holder. Any citations of personal communications or unpublished results must be confirmed in a cover letter
- A title page
- Ensure that citations of references in the text and references list conform to journal style, e.g. standard Vancouver reference style
- Use continuous line numbering throughout the paper in order to facilitate online reviewing
Via the Editorial Manager submission system, authors must:
- Agree to the submission and agree that the corresponding author may act on their behalf throughout the review and publication process. Authors are asked to confirm their co-authorship once the paper has been submitted to the relevant Editorial Manager site
- Recommend one Editor from the Editorial Board who would be suitable to act as Handling Editor
- Suggest at least three potential reviewers (with institutional email addresses only) to peer review their article
- Indicate the word count of the main text (including in-text citations and any appendices, but not including the title page, figure and table legends, acknowledgements, table bodies and footnotes, or reference list)
- Upload any supplementary material associated with the article as a supplementary file(s) and refer to the supplementary material within their article. Please note for Microbial Genomics, it is preferred that supplementary material are deposited to external repositories, unless they are text-only files. Please review the journal's open data policy for further information.
- Upload any figures associated with the article as figure files and refer to the figures within their article. Figure legends should be included the end of the article and not in the figure
- Upload any cited articles that have been accepted for publication but are not yet published as a supplementary file(s)
- Upload a cover letter (if requested by the journal)
- Specify, if any, the funding received for the paper
For standard research articles, please follow the section order given below. Note that for Journal of General Virology only, Methods should follow Discussion.
For guidance on style and layout of articles submitted to Microbial Genomics, please refer to the relevant submission templates on the journal's submission requirements page.
For guidance on style and layout of articles submitted to JMM Case Reports, please refer to the relevant submission templates.
6.1 Title page (All articles)
- The title of the article; this should provide a concise statement of the contents of the article. A good title is very important as it will attract readers and facilitate retrieval by online searches, thereby helping to maximise citations. The title should include topical keywords and allude to the interesting conclusions of the article. A title that emphasises the main conclusions, or poses a question, has more impact than one that just describes the nature of the study.
6.1.2 Authors and affiliations
- Author names should be given in upper- and lower-case, not in all capitals, to avoid ambiguities such as 'van' and 'Van'. The author for correspondence must be clearly indicated. It is permissible to include the names of more than one author as corresponding author, but a single author must act as the point of communication during the peer review process.
- The name and address of the laboratory or laboratories where the work was done, and present addresses of authors who have since moved.
- Author names and institutions should not be included in articles submitted to Microbial Genomics, as it has a double-blind peer review policy. This information will be requested through our submission system instead.
- Acknowledgements should not be included during initial submission to Microbial Genomics as the journal operates double-blind peer review. Acknowledgements can be added to the Proof of the article upon acceptance.
6.1.3 Corresponding author details
- An email address and telephone number for the corresponding author.
- Corresponding author information should not be included in articles submitted to Microbial Genomics, as it has a double-blind peer review policy.
- Select keywords that will make your article easily searchable.
6.1.5 Subject category
- Each submitted article should be assigned a subject category through the Editorial Manager submission system, in addition to an article type. This enhances discoverability and allows filtering of published content on the website.
- Subject categories are limited for scope, are journal- specific, and are particularly important for submissions to IJSEM. For a list of available categories per journal please visit the ‘About’ page for the relevant publication here:
6.1.6 Word count
- The word count of the article is made up of the abstract and main text, excluding table and figure legends and references
6.1.7 Depositories (where applicable).
- When reporting new sequence data, the accession number must be given, e.g. 'The GenBank[/EMBL/DDBJ] accession number for the [16S rRNA gene/gyrA, etc.] sequence of XXXXX is XX00000'.
6.1.8 Abbreviations (where applicable)
- A footnote defining any non-standard abbreviations. Guidance on abbreviations not requiring definition can be found here.
This section is likely to be read by more people than the full article, and many abstracting services use authors' summaries without modification. It is therefore important that this section is clear and comprehensible in its own right. The abstract should, if possible, introduce the subject in the first sentence and present the main conclusion in the last sentence. References should not be cited, and any non-standard abbreviations used must be defined. Abstracts are unstructured for all journals, except JMM Case Reports and Journal of Medical Microbiology.
This should state the objectives of the work, but should not contain a detailed summary of the results. Authors should not assume that all readers will know why an area is worth studying; they should briefly make this clear. Previous relevant work should be sufficiently cited but this should not constitute a full review.
Sufficient detail should be provided to allow the work to be repeated. The suppliers of chemicals and equipment should be indicated if this may affect the results. If the name of suppliers or equipment changes between your work and submission, please ensure this is clearly indicated. Suppliers' addresses should not be given unless this is considered essential for a particular reason.
There should be sufficient subheadings to make clear how the work was organised, what the key questions being addressed were, how one experiment led to another, and perhaps what conclusions were reached. A reader should gain a clear picture of the work from the subheadings.
Reproducibility of results should be indicated. 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.
This should not recapitulate the results, and should not be too long. Excessive discussion of few facts often gives an impression of poor science. Subheadings should be used where appropriate, to highlight the points under discussion. It may be helpful to list the main conclusions at the end. A combined Results and Discussion section is encouraged where appropriate.
6.7 Author statements
The following author declaration statements must be included at the end of the article in the order of Funding information, Acknowledgments, Conflicts of interest and Ethical statement. The sections below provide information of regarding what is required for each author statement.
6.7.1 Funding information
Authors should describe the sources of funding that supported this work and ensure that this information is detailed and accurate. Authors must state the names of funding bodies and grant numbers. Authors associated with specific funding sources should be named. Authors must also state whether any persons employed by the funders (other than the authors) played any role in the study or in the preparation of the article or decision to publish. These persons need to be named and their role must be described. If no funding was received, please state that this work received no specific grant from any funding agency.
An Acknowledgements section is not compulsory but may be included. Authors may also wish to acknowledge individuals who have contributed materials, expertise or time to the study who are not named as authors. Personal acknowledgements should precede those of institutions or agencies. Please do not refer to the Editor who handled your submission in this section.
If materials and results were obtained from outside the authors' laboratories (e.g. production of antibodies, properties of strains), this must be explicitly stated, and an acknowledgement must be included where appropriate.
When initially submitting to Microbial Genomics, Acknowledgements should not be included as the journal operates double-blind peer review. Acknowledgements can be added to the Proof of the article upon acceptance.
6.7.3 Conflicts of interest
Authors must declare any potential conflicts of interest in the manuscript. 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 organisations. If no conflict exists, authors need to declare that that there is no conflict of interest.
Examples of potential financial conflicts of interest include:
- Receipt of funding or salary from an organisation that might gain or lose financially from publication of your paper. E.g. Dr Jones' work has been funded by XXXX; Dr Smith has consulted for XXXX Company and received a salary for this employment.
- If you hold stocks or shares in such an organisation. E.g. Dr Brown has received compensation as a member of the scientific advisory board of XXXX and owns shares in the company.
- 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.
6.7.4 Ethical statement
Articles 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. The Editors of the Society's journals will accept papers describing experiments conducted using animals. However, such experiments must be carried out in accordance with the legal requirements of the relevant local or national authority and authors must provide a statement affirming the approval of these experiments by the relevant Ethical Committee. Details of the procedures followed must be provided, and must be such that experimental animals do not suffer unnecessarily. The Editors will not accept papers in which, in their opinion, the ethical aspects are open to doubt. Authors are encouraged to consult the ARRIVE guidelines for reporting experiments involving animals.
Please include any non-standard abbreviations referred to within your paper. A list of standard abbreviations can be found here.
References in the text should be cited using the Vancouver referencing system (citation-sequence reference system).
References are listed at the end of the manuscript and numbered in the order that they appear in the text. All listed references must be cited in the text. In the text, cite the reference number in square brackets, e.g. Studies have shown that RegB/RegA controls many energy generating and energy utilising systems such as photosynthesis .
Author names must be in bold. Abbreviate journal names according to MEDLINE and journal titles should be properly abbreviated and italicized. Page numbers should not be truncated.
For references with five or fewer authors, give the names of all authors in the form 'Surname Initials' and separate each with a comma. For references with more than five authors, list the first five followed by et al.
7.2 In-text examples:
7.2.1 Sample journal:
Cerdà-Cuéllar M, Rosselló-Mora RA, Lalucat J, Jofre J, Blanch A.Vibrio scophthalmi sp. nov., a new species from turbot (Scophthalmus maximus). Int J Syst Bacteriol 1997;47:58–61.
Pasta F, Sicard MA. Exclusion of long heterologous insertions and deletions from the pairing synapsis in pneumococcal transformation. Microbiology 1996;142:695–705.
7.2.2 Sample journal reference for more than five authors:
Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 1996;388:539–547.
7.2.3 Sample reference to a whole book:
Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989.
7.2.4 Sample reference to a book chapter or section:
Romano AH, Saier MH Jr. Evolution of the bacterial phosphoenolpyruvate:sugar phosphotransferase system. I. Physiological and organismic considerations. In: Mortlock RP (editor). The Evolution of Metabolic Function. Boca Raton, FL: CRC Press; 1992. pp. 171–204.
7.2.5 References to websites
Essential items that must be provided are:
- an author(s) (which may be a company name or organisation).
- a year of 'publication' (which may be the year that the site was last updated).
- the URL (web address) of the page;
- a page title (which will hopefully allow the page to be found using a search engine if the URL subsequently changes).
For a website that is frequently updated, it may be useful to provide the date that the site was accessed, particularly if specific information is quoted that may have changed when the article is read.
7.3 Bibliography style points:
- Only articles accepted for publication but not yet published may be cited as 'in press' in the reference list and the reference must include the name of the journal. Relevant articles cited as 'in press' should be included as supplementary material with the online submission. References to articles not yet accepted should be cited in the text as unpublished results, giving the surname(s) and initials of all the author(s). Such articles should not appear in the list of references.
- Permission must be obtained for any personal communications or citations of other workers' unpublished results. Permission from the copyright holder must be included at initial submission.
These should be broadly comprehensible without reference to the text, but it is not necessary to repeat detailed descriptions of methods, etc. The symbols [markup] * † ‡ § || # 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 above). Tables should not be used to present results that can be described by a brief statement in the text.
If using figures or tables that have been previously published elsewhere, it is the responsibility of the authors to obtain permission from the original copyright holder prior to submission. Permission must be included at initial submission.
9.2 Colour figures
For Microbiology, Journal of General Virology, Journal of Medical Microbiology, and International Journal of Systematics and Evolutionary Microbiology, figures are published in colour free of charge in print if the use of colour is judged to be necessary for scientific reasons. There are no charges for supplementary material.
There are no colour charges for publishing in JMM Case Reports and Microbial Genomics as they are online-only journals.
Figures should not be used to present results that can be described by a brief statement in the text. The points outlined above for tables regarding comprehensibility, relative values and reproducibility also apply to figures and their legends. The inclusion of large amounts of tabular data in figures is discouraged and authors may be asked to move such data to the text or a separate table. Authors should be aware that after publication, tabulated data within figures are not accessible via online text searching. Where possible, please also supply line drawings, bar diagrams and sequence data in the original file format in which they were generated and/or as EPS (Encapsulated PostScript), PowerPoint or CorelDraw files. Do not supply as PostScript files as these cannot be used.
Figures must be referred to in the text as Fig. 1(a) not Fig. 1A or Figure 1(A) or as (Fig. 1a) not (Figure 1A). Multipart figures should be labelled (a), (b), etc., not (A), (B), etc.
All figure files should not include a figure legend. The figure legends should be included in the Word document of the main text file.
9.3.1 Line drawings.
These should be of a quality suitable for direct reproduction. The maximum printed size, including lettering and legends, is 176 x 235 mm. Line thicknesses and symbol sizes should be sufficient to allow for reduction. The preferred symbols for graphs are filled and open circles, squares, triangles or diamonds. Where possible, the same symbol should be used for the same quantity in different figures.
9.3.2 Bar diagrams.
Simple bar diagrams reporting only a few values are usually unnecessary; the data can normally be given in a few lines of text. It is editorial policy not to publish bar diagrams with 3-D bars unless there is a specific justification for their use.
9.3.3 Sequence data.
Figures showing full gene sequences are not published, but selected sequence data, with appropriate annotation, may be published where there is justification. The layout of sequence figures should be designed to fit either the full width of the page (176 mm) or a single column (84 mm). 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 GenBank, EMBL or DDBJ.
The Microbiology Society does 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. Limited sequence alignments of nucleic acids and proteins are acceptable provided they make a significant point. See above for guidance on presentation of sequence figures. Sequence data that are not suitable for print publication can, where appropriate, be published as online-only supplementary material.
9.3.4 Photographs (halftones).
The preferred format for halftones (i.e. photographic images) is TIFF, but PDF, EPS and JPG/JPEG are also accepted. If image files are pasted into Word, PowerPoint, Photoshop etc., in order to add lettering or other annotation or to combine line and halftone images, the original unlabelled halftone images should also be supplied. A final print resolution of 300 d.p.i. or more is recommended. Colour images should use CMYK colour (which can be reproduced in print) rather than RGB (which cannot be reproduced faithfully using four-colour printing) (this setting can be accessed in Adobe Photoshop via Image:Mode:CMYK Color, for example). For some colour images, such as fluorescence micrographs, it may be useful to submit an RGB version of the image to be mounted online as supplementary material. For photomicrographs, the scale should be shown by a scale bar.
9.3.5 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. Strain names should be those provided by the original depositor of the sequence.
Trees must include the names of organisms, their strain name or number (as stated by the depositor of the sequence, 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 Prokaryotic Names with Standing in Nomenclature when making the final revision of the paper) and accession numbers in trees, as correction is time-consuming and expensive and may lead to the introduction of further errors.
Microreact has been developed in the David Aanensen Research Group at Imperial College London and The Centre for Genomic Pathogen Surveillance. It is a React.js application taking full advantage of the Phylocanvas API (trees), the Google Maps API (maps) and vis.js library (timeline). Microbial Genomics has partnered with Microreact, a free data visualisation and sharing platform that allows scientists and health professionals worldwide to better collaborate to understand disease outbreaks. The journal is encouraging authors to upload their data files to Microreact, which can then provide interactive querying of the data via trees, maps, timelines and tables, and published in Microbial Genomics via a permanent web link.
Supplementary material is associated material that does not directly pertain to the main research findings. It is material that is relevant to the article and is not only data but could be Methods etc. This should be included at initial submission for review purposes and will be published alongside the article’s version of record.
Supporting data refers to Microbial Genomics only. It refers to data that needs to be deposited in Figshare or the author’s chosen data repository; this is a submission requirement and authors should obtain a data doi and cite this in the published article.
10.1 All journals
All of our journals welcome the submission of supplementary material. Material associated with an article but not suitable for publication as part of the article (e.g. large datasets, sequence alignments, 3D structures or movie files) can be included as online-only supplementary material. Data that are essential for interpretation of the results of the main article should be included in the main article. All supplementary material files will be reviewed along with the main article; these will not be published unless they significantly enhance the article. The Editors may suggest that figures or tables included within a paper should be converted into supplementary material.
Supplementary material must not include methods for results that are included in the main article, nor should they introduce different results or new discussion points.
All supplementary material is made freely available upon publication of the final version of the article.
10.2 Microbial Genomics
Microbial Genomics has a mandatory open data policy that requires authors to submit supporting data, protocols, and/or bioinformatics programmes and software to relevant depositories.
Authors are encouraged to submit supporting data such as large datasets, sequence alignments, 3D structures or movie files, to relevant subject-specific or general depositories. Text-based supplementary material more suited to PDF publication, may be submitted with your article. This will be published alongside the main paper exactly as supplied by the author.
10.3 JMM Case Reports translated abstracts
JMM Case Reports authors can now publish a translated version of their article’s abstract in their native language. The native language abstract is free to publish and authors can choose to write the abstract in the language of their choice. However, only a single translated abstract may be published per article.
To submit a translated abstract, authors need to complete the Translated Abstract template and submit it as part of their revised submission. Please note that the translated abstract will not be peer reviewed or typeset and authors need to ensure their accuracy. The translated abstract will be published as supplementary material and will only appear with the final version of the published article.
- Supplementary material should be uploaded at the time of submission; please upload as file type Supplementary Material on the Editorial Manager submission system.
- Supply all supplementary material in the file formats given below.
- Very large files or those requiring specialist software are not suitable as they will be difficult for the reader to download or view.
- Supplementary figures and tables should be named Fig. S1, Table S1, etc., and must be cited accordingly in the main paper. Figure and table legends should also be present in the main paper.
- Provide a heading and, if appropriate, a short text description with each supplementary material item.
10.6 File types
- Material should be submitted in PDF format; Please note that .doc(x) or .ppt(x) files are not suitable.
- Multiple figures, tables or text items should be supplied as a single PDF.
- Large datasets can be supplied in Excel format if you wish readers to be able to manipulate the data. If not, please convert to PDF.
- Audio, video and animations can be supplied as .mov, .avi or .mpeg files.
10.7 Processing of supplementary material
- Supplementary material will be published alongside the main article exactly as supplied by the author. They do not undergo typesetting or copyediting. It is the authors' responsibility to ensure that all files are presented clearly.
Revised articles should be submitted by the date indicated in the decision letter. If more time is required, the author should contact the Editorial Office or Editor to discuss a new deadline. If the revision is delayed by the author without prior agreement, the revised manuscript may be treated as a resubmission.
11.1 Revision checklist
As well as following the standard pre-submission checklist, authors are also asked to include the below when submitting a revised manuscript:
11.1.1 Rebuttal letter
- If the paper was peer reviewed, authors must provide a detailed rebuttal letter, detailing their response to each point raised by the reviewers.
11.1.2 Main text file
- Please upload a Word document, containing references, table and figure legends, and tables. Please do not include any highlighted text. Microsoft Word files are preferred; .docx files produced in Word 2007 or 2010 can be used as source files. TeX and LaTeX formats can not be used.
- Authors may upload a highlighted marked-up version of their revised article as a supplementary file in order to aid the Editors and reviewers. This is mandatory in Journal of General Virology.
- Tables must not be supplied as image files (TIFF, PDF, PowerPoint); files containing tables prepared as images (whether provided separately or pasted into a Word file) will be returned to the author and this may delay publication. Tables should be prepared using your software's table functions, with individual entries in individual table cells.
- Tables must not be supplied as tab- or space-separated text or as multiple entries separated by line breaks in single table cells.
- Tables prepared in Microsoft Excel can be accepted but are not desirable.
- Tables must be in an editable format.
11.1.4 Line figures
- Line figures should be produced as vector rather than bitmap (raster) images. Acceptable formats are PDF, EPS, CorelDRAW (.cdr; version 15 or earlier), Adobe Illustrator (.ai), Microsoft Excel (.xls), Microsoft Word and Microsoft PowerPoint. Fonts must be embedded for figures supplied as PDF or EPS. TIFF and other bitmap formats are not recommended for line figures; if their use cannot be avoided, the resolution should be at least 600 d.p.i.
- Charts prepared in Microsoft Excel should be supplied in Excel format where possible. If they are copied and pasted into another Microsoft application, use Paste Special and select 'Picture (Enhanced Metafile)'.
11.1.5 Halftone figures (photographs)
- Authors are advised to supply halftones intended for publication as TIFF or EPS files. The resolution should be at least 300 d.p.i. at final size (approximately 1000 pixels wide for a single-column figure and 2000 pixels wide for a double-column figure). For photomicrographs, the scale should be shown by a scale bar.
11.1.6 Scanning images
- If images must be scanned, a resolution of 300 d.p.i. is usually sufficient for same-size reproduction of halftone (photographic) images without text, whereas 600 or 1200 d.p.i. should be used for figures containing lines and/or text. The scanned image should be cropped to remove as much white space as possible and supplied in TIFF format.
- Equations that cannot be represented using the keyboard can be prepared using the Word equation editor (in versions up to Word 2003) or MathType. Word 2007/2010 users should not use the default equation editor to prepare equations as it is not compatible with any other current software; equations in Word 2007/2010 should be prepared using the MathType equation editor or the 'legacy' equation editor included as part of Word (i.e. a Microsoft Equation 3.0 object, accessible from 'Insert Object' on the 'Insert' ribbon).
11.1.8 Supplementary material
- A combined PDF of all supplementary material.
For Microbiology, Journal of General Virology, Journal of Medical Microbiology, and JMM Case Reports a licence to publish form must be completed by authors. This means the copyright does not transfer to the publisher but should instead be categorised under one of the three following options:
Copyright Type A: This is to be used when the article is already in the public domain. One or more of the authors are employees of the US Federal government and they are acting in the course of their employment. Copyright is not assigned to anybody and thus nothing is noted on the article.
Copyright Type B: this is to be used when copyright is to be retained by the employer. One or more of the authors are employees of the copyright holder and acting in the course of their employment. It is displayed with an editable statement provided by the author/their company. (E.g. for UK government employees a ‘© 2015 Crown Copyright’ statement is used)
Copyright Type C: This is the standard copyright to be used when copyright belongs to the author. It will be displayed in the articles as: ‘©The Authors’.
For International Journal of Systematic and Evolutionary Microbiology a separate copyright form must be completed in all cases and the copyright is transferred to the IUMS. The IJSEM copyright assignment form can be found here.
For Microbial Genomics we offer both the CC-BY 4.0 license to publish form and also the CC-BY-NC 4.0. The CC-BY OpenMicrobiology licence to publish form can be found here. The CC-BY-NC license to publish form can be found here.
Authors are unable to complete the submission of their revised article until the relevant forms have been uploaded. All forms can be found here.
12.1 Licence to Publish form/Copyright form
All revised papers must be accompanied by a signed Licence to Publish or Copyright form. Please visit the Editorial policies page for information on the specific form required for your paper.
12.2 Change of Authorship form
If the order of authors has changed since submission, or if any authors have been removed or added, all authors will need to sign a Change of Authorship form, which must be uploaded with the revised article.
13.1 Continuous publication
Articles are published online in their final form (i.e. the typeset, copyedited, proofed and corrected copy) in the ‘Latest Articles’ section of the website in an 'open' issue. Once a month these issues will be 'closed' and moved to the 'Current Issue' section of the website and contain the final Version of Record of each article with pagination.
For further information on post-acceptance articles, please see our Post-print policy.
13.2 Proof corrections
Proofs are checked using our online author proofing system. A link to the proof of your article is sent to the email address supplied for the corresponding author. It is the authors' responsibility to inform the Editorial Office of any changes to this email address.
Only typographical and absolutely essential factual changes may be made at this stage.
After publication authors can order reprints of their article at any time from our affiliated CPrint+ platform.
Commercial reprints must be ordered directly through the Society. Please email our Journal Sales team.For information on our reprints policy, please click here.