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How to prepare an article for submission

Submission checklist

Articles should be submitted as a single file, preferably readable by Microsoft Word, using a standard typeface such as Times New Roman or Arial. For standard Research Articles, please follow the outline below. Please check our Article types page for information on the various options at each journal, including recommendations over word count and structure.

The Microbiology Society operates a format-free submission policy. This means that authors need only ensure the materials as described in the Submission checklists below are present for a manuscript to be submitted and to begin the peer review process. For reference, guidance on the full article structure is also described below, and Society-specific formatting requests will be made at the revision stage of peer review.

New submission checklist

To avoid delays at submission and ensure that your article can be assigned to an Editor as quickly as possible, we ask that you run through the submission checklist below. The International Journal of Systematic and Evolutionary Microbiology also has a pre-submission checklist relating specifically to research articles reporting novel taxa.

  • Title page: the first page of the article contains the title, author list with affiliations, the corresponding author’s email address, an abstract, and keywords.
  • Line numbers: the article has continuous line numbering throughout, for ease of reviewing.
  • Conflicts of interest: if there are no potential conflicts, a sentence stating this. 
  • Ethical approval: a statement of approval by an Ethical Committee for human or animal research and consent to participate, if required.
  • Sequencing data: all new sequence data generated should be deposited in a public database and accession numbers included. For Microbial Genomics, Access Microbiology and International Journal of Systematic and Evolutionary Microbiology, this data must also be publicly available. For all journals, where any data has been used that was not generated by the authors, those who generated the data should be cited and a link provided to the database in which the information can be accessed. 
  • Strains: where a microbial strain has been used, the culture collection accession number or source of the strain is included.
  • References: as long as citations are consistent, these can be in any style. The list should include author name(s), journal or book title, article or chapter title (if necessary), year of publication, volume and issue (if appropriate), page numbers and DOIs, where possible.
  • Re-using published work: if you are re-using previously published work, you have the permission from the Copyright holder. If you are using unpublished data, you have the explicit consent from the appropriate person and have stated this.
  • Access Microbiology only: 
    • Data Summary: a description of all supporting data, software or code, including the DOI(s), and/or accession number(s), and the associated URL.
    • Funding information: the name of the funding body and the grant number. If no funding was received, a sentence stating this is present.
    • Author contributions: full author contributions using the CRediT taxonomy format.
    • Consent for publication for Case Reports: a statement in the manuscript that this has been obtained and a signed Consent for Publication form is uploaded. If there are no potential identifiers, a sentence stating this.
    • Figures and tables: inclusion of these in the manuscript file, with legends.
    • Supplementary Material: if you are providing supplementary information, it is presented as a single PDF or as a combined Excel file, and presented as you wish it to be posted publicly.

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Revised submission checklist

You should submit your revised article by the date indicated in the revision email, but if you need more time then you should contact the Editorial Office to request a new deadline. To avoid delays at revision, we ask that you run through the New submission checklist described above, respond to requests by the Editorial Office, and provide the following items:

  • A clean version of the article: uploaded as a Microsoft Word file with line numbers.
  • A version of the article with tracked changes: used to help the Editor and reviewers.
  • Response to reviewers: a detailed rebuttal letter, detailing your response to each point raised by the reviewers and Editor, using line numbers to do so.
  • Funding information: the name of the funding body and the grant number in the manuscript. If no funding was received, a sentence stating this is present.
  • Licence form: a Licence to Publish form for subscription articles, or Creative Commons CC-BY form for Open Access articles, as described in the Copyright and licenses section on our Submission and peer review page (exception: for Access Microbiology, you will be asked for the Creative Commons form at acceptance instead).
  • Figures: uploaded as separate, editable, high-resolution files.
    • Access Microbiology only: include figures within the main manuscript file, as well as uploading these separately.
  • Supplementary Material: if you are providing supplementary information, it is a single PDF file or as a combined Excel file, presented as you wish it to appear at publication.
  • Change of authorship: if the order or number of authors has changed from initial submission, we will need the consent of all co-authors. You can provide this either by email, or uploading a Change of Authorship form.

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Article templates

If you would prefer to follow a pre-written template to help you structure your article, these can be found below. They are not mandatory. If you use one of our templates, please remember to delete instructional text in italics before you submit. For Research Articles describing new taxa in International Journal of Systematic and Evolutionary Microbiology please refer to these guidelines rather than the templates below.

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Article structure

Title page  

Title: a concise statement of the contents of your article that emphasises the main conclusions.

Author names: first name(s) and family name in full, with the author for correspondence and any authors of equal contribution clearly indicated. The Society does not impose a set form on authors' names, and will honour each individual's preference for how their name appears in their published article, i.e. initials instead of given names. Our journals support ORCiD and CRediT, as described in the ‘Author Statements’ section below.  

Affiliation: the name and address of the institution(s) where the work was done, and current addresses of authors who have since moved.

Corresponding author: the email address for the corresponding author. 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. Corresponding authors based at a Publish and Read institute must use their institutional email to be eligible for fee-free Open Access.

Keywords: between three and six keywords that will make your article easily searchable.

Repositories: if your article contains new sequence data, please include the accession number(s) on the title page. More information about sequences is in the Data section below.

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Abstract

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 abbreviations used must be defined.

For Research Articles, Journal of Medical Microbiology mandates a structured abstract that includes the headings: Introduction, Hypothesis or Gap Statement, Aim, Methodology, Results, and Conclusion.

Microbiology encourages graphical abstracts to be included in all article types. Please provide your graphical abstract as a high-resolution image, preferably in 3:1 aspect ratio and provide a short legend.

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Data Summary

Microbial Genomics and Access Microbiology have a mandatory Open Data policy and as such ask authors to always include a Data Summary section describing all supporting external data, code or software, including the DOI(s) and/or accession numbers(s), and the associated URL. Please refer to our Open Data page for minimum standards, requirements and recommended repositories

Authors in our other journals are strongly encouraged to provide supporting external data and a Data Summary.

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Impact statement

For most article types in Microbial Genomics, authors should include an Impact statement that explains the significance of your article and how this adds to the literature in the field. An Impact Statement is encouraged for all other journals and the open research platform.

For BioResource articles, authors should include a Significance as a BioResource to the Community section in place of the Impact statement. This lay summary should a) provide a perspective of how the article adds to the literature in the field; b) identify breadth of interest/utility; and c) state the significance of output (incremental or step), in terms of relevance.

For Outbreak Reports, authors should include an Outcome section in place of the Impact statement. This lay summary should a) provide a perspective of how the article adds to the literature in the field; b) identify breadth of interest/utility; and c) state the significance of output (incremental or step), in terms of relevance.

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Introduction

State the objectives and cite any relevant work to set the scene. The Introduction should be succinct and sufficiently detailed to allow readers to interpret the rest of the article.

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Methods

The Methods section should be comprehensive and provide sufficient detail to allow your work to be replicated. Please consistently cite any software used, including its version and parameters. Authors are encouraged to include Research Resource Identifiers (RRIDs) for all plasmids, cell lines, model organisms, antibodies and tools. RRIDs can be found via the RRID portal: scicrunch.org/resources

We recommend you deposit your protocols in protocols.io. You can deposit your protocols with them privately, then add the DOI and link to your article. This will allow the reviewers and Editors to see your protocol during the peer review process. When your article is published the protocol becomes public too, and it will be automatically updated to link to your published article. For Access Microbiology, the protocol should be made public at point of submission.

Indicate the suppliers of chemicals and equipment wherever possible; if these suppliers’ names have changed between your work and submission, please ensure this is clearly indicated. Suppliers’ addresses are not required.

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Case Presentation

For Case Reports and Case Series in Access Microbiology, in place of the Methods and Results sections. 

This should present all relevant details concerning the case. The case presentation should contain a description of the patient's relevant demographic information (without adding any details that could lead to the identification of the patient); any relevant medical history of the patient; the patient's symptoms and signs; any tests that were carried out and a description of any treatment or intervention. 

We recommend authors follow the CARE guidelines and recommended structure when preparing their Case Report or Case Series.

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Results

Please organise your Results section with sufficient subheadings to allow readers to gain a clear understanding of the work. This section should include the outcomes of the experiments, any interpretation of the results and indicate the key questions being addressed. You may include figures and tables in the text to assist Editors and reviewers in assessing the work more easily.

To assess the reproducibility of your work, please include the number of times your experiment was repeated, and the type of result shown (mean, median, representative, etc.) Indicate the variability of the results statistically wherever possible.

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Figures and tables

Figures and tables should be broadly comprehensible without reference to the text, and add information to the article.

  • Figures and tables should not be used to present results that can be described by a brief statement in the text.
  • It is not necessary to repeat detailed descriptions of methods in table or figure legends.
  • If you have used abbreviations or icons, please define them in the legend.
  • Indicate the reproducibility of results.

Figure files

Figures will be required as separate files for publication at revision stage. We support figures supplied in PDF, GIF, TIFF, EPS, JPEG, PNG, and PPT. It is important to ensure that all figures are suitably high resolution for publication, usually no lower than 300 dpi. This means that line thicknesses, symbol sizes, and text should be sufficient to allow for the figure to be scaled down to fit comfortably on an A4 page. All article PDFs are displayed with a single column and figure files may occupy the full complete column width.

Permissions

If you wish to use previously published figures or tables or unpublished data, it is your responsibility to obtain permission from the original copyright holder or data producer prior to submission. We accept emails, letters and Rightslink confirmation, which must be from the copyright holder. Any citations of personal communications or unpublished results must be confirmed in a cover letter.

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Discussion

Briefly compare your results with previous findings without revisiting your results in full. If necessary, list the main conclusions at the end.

If appropriate, the Results and Discussion section may be combined.

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Conflicts of interest

You must declare any potential conflicts of interest in the article. If no conflict exists, include the line "The author(s) declare that there are no conflicts of interest " under the Conflicts of interest heading.

Examples of potential financial conflicts of interest include, but are not limited to:

  • Receipt of funding or salary from an organisation that might gain or lose financially from publication of your article.
  • If you hold stocks or shares in such an organisation.
  • If you hold or are applying for a patent relating to the content of this article.

Examples of non-financial conflicts of interest might include political, religious or intellectual conflicts.

Funding information

Describe in detail the funding sources that supported this work, including the names of funding bodies and grant numbers. Any authors who are associated with specific funding sources should be named. You must also state whether anyone 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 described. If you did not receive funding for the work, include the line "This work received no specific grant from any funding agency" under the Funding information heading.

Ethical approval and consent to participate

Any experimental work with humans or animals must include a statement that the Ethical Committee of the institution in which the work was done has approved the work, including the name of the ethics committee and reference number where appropriate. For human work we also require a statement regarding informed consent to participate in the study. 

We will not accept articles in which the ethical aspects are open to doubt, and encourage all authors to consult the relevant EQUATOR guidelines for reporting experiments involving humans or animals.

Consent for publication

Consent to publish is required where personal details of an individual that may lead to their identification have been included in the article. Details include direct identifiers such as names, images and videos; or indirect identifiers that when used together may reveal the individual’s identity (e.g., gender, age, location of treatment, rare disease, socioeconomic data).

You will need to upload evidence of written consent for the publication of these details to the peer review system and you must include a sentence stating that this consent was obtained in the manuscript. For articles describing individuals under the age of 18, consent for publication must be obtained from their parent or legal guardian. If the person has died, consent must be obtained from their next of kin. You can use our Consent for Publication form to obtain consent for publication, or a consent form from your own institution or region if appropriate.

Patient or next of kin consent is required for all case reports submitted to Access Microbiology. 

We encourage authors to consult the CARE guidelines when preparing Case Reports.

Author contributions

Required for Access Microbiology and encouraged for all other journals, authors should include a section on authorship and contributions using the CRediT taxonomy, which aims to provide transparency to the contributions of researchers to published work, improving attribution, credit, and accountability. 

We encourage all authors to sign up for ORCiD, the persistent identifier for research contributors. ORCID provides a persistent identifier – an ORCID iD – that distinguishes you from other researchers and a mechanism for linking your research outputs and activities to your iD. Learn more at orcid.org

Acknowledgements

An Acknowledgements section is not compulsory. However, if materials and results were obtained from outside the authors’ laboratories (e.g. production of antibodies, properties of strains), this must be acknowledged.

If the article includes a group author in the author list, the individuals within this group should be listed here.

If you wish to acknowledge an individual, please make sure that the person consents to be named in your article.

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References

The house reference style is Vancouver. If your article is accepted for publication, your reference lists and citations will be reformatted to fit Vancouver style. Ideally, references should include a DOI to facilitate this, and to allow us to create reference links in published articles. Where websites are listed, a date when this was accessed should be provided.

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Nomenclature

Nomenclature of micro-organisms

You must use the correct name of all organisms referenced in your article, conforming with international rules of nomenclature:

Generic names are singular Latin nouns and do not take a plural form. You 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…’. 

Many microorganisms are known by their vernacular (common) names as well as by their scientific names. There are no rules governing the use of vernacular names and it is often convenient to use them; you should feel free to do so, provided you have correctly identified the microorganism the first time it is mentioned in your article. You may also add synonyms or vernacular names in parentheses when the name is first mentioned, if you wish to do so.

Chemical and biochemical nomenclature

Follow the recommendations of the International Union of Pure and Applied Chemistry (IUPAC) for chemical nomenclature, and those of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and the IUPAC–IUBMB Joint Commission on Biochemical Nomenclature for biochemical nomenclature. Similarly, follow the IUBMB system for enzyme nomenclature.

Genetic nomenclature

Take care to distinguish between genes (e.g. gag) and the proteins that they encode (e.g. Gag).

Insertion sequences should be named as given in the ISfinder Database.

Abbreviations of scientific names

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 capitalised initial letter if the context makes the meaning clear. In lists of names of species of the same genus, the genus name may be abbreviated after its first use for subsequent species in the list. If there are several generic names in the text with the same initial letter, the names should be spelled out at each occurrence.

Patent strains

If the strains under study are involved in a patent process, please make sure this is clearly indicated both in the article and in your submission cover letter. Strains other than the type strain should carry the superscript ‘PP’ if a patent is pending and ‘P’ if a patent has been issued.

Units

Please use SI units throughout your article where possible.

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Data

Full guidance for the handling, deposition and submission of supplementary and supporting data (including sequencing) can be found on our Open Data page.

Microbial Genomics and Access Microbiology 

Microbial Genomics and Access Microbiology have mandatory Open Data policies. The full guidance on what this means, and how authors can ensure compliance, can be found on our Open Data page.

Sequences

Articles reporting new sequence data must have deposited the data in one of the recommended repositories (GenBank, EMBL, DDBJ or PIR) and include an accession number. Data must be publicly available by acceptance. For more information on the minimum requirements and databases for various sequencing types,  see the Minimum data requirements section on the Open Data page.

Strains

We encourage you to deposit important strains in a recognised culture collection and to refer to the collection and strain number in the article, in line with the requirements of the Bacteriological Code: “In the case of description of new species and subspecies the culture collection number of at least two publicly accessible service collections in different countries where a subculture of the type strain has been deposited must be given” – Rule 27(3).

If you are using a strain which has been obtained from someone else, you must provide us with confirmation that you had permission to make use of the strain in the research you are reporting in the article.

For the International Journal of Systematic and Evolutionary Microbiology, you must provide evidence that types are deposited in two recognised culture collections in two different countries without restrictions. If there are any Material Transfer Agreements associated with the certificates of deposit, please include this information during submission. 

Mathematical models

If your article includes a mathematical model, you should provide appropriate details at submission so the reviewers and Editor can assess the work. If your article is accepted for publication you can choose to make your model publicly available through a data repository or as a supplementary data file.

Clinical trials

We follow the ICMJE guideline for clinical trials registration in line with the ICMJE and WHO declarations. For submission of a randomised controlled trial, please provide the registration number of the trial and the name of the trial registry in the last line of the paper’s structured abstract. Articles that report clinical trial data should contain a data sharing statement, indicating:

  • Whether you intend to share individual de-identified participant data.
  • The details of the data you intend to share.
  • Which study-related documents will be made available.
  • When and how the data will be accessible.

Clinical trials that begin enrolling participants on or after 1 January 2019 must include a data sharing plan in the trial’s registration if they wish to publish results. Any changes to the plan after registration must be disclosed in the data sharing statement when published.

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