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How to prepare an article for submission

Articles should be submitted as a single file readable by Microsoft Word, using a standard typeface such as Times New Roman or Arial. For standard research articles, please follow the outline below. You can also find a brief description of article types and their structures at the end of this section.

Contents

Title page

Title: a concise statement of the contents of your 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.

Author names: first name(s) and family name in full, with the author for correspondence clearly indicated. 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.

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.

Journal of Medical Microbiology prefers a structured abstract that includes the headings: Purpose, Methodology, Results, and Conclusion.

Microbiology encourages graphical abstracts to be included in all article types.

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Data Summary

Microbial Genomics is a mandatory open data journal and as such asks authors to include a section describing all supporting external data including the DOI(s) and/or accession numbers(s), and the associated URL.

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Introduction

State the objectives of the work and cite previous relevant work to set the scene. The Introduction should not constitute a full review, but should be sufficiently detailed to allow readers to interpret the rest of the article.

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Methods

Provide sufficient detail to allow your work to be repeated. Indicate the suppliers of chemicals and equipment if this may affect the results; if there are name changes between your work and submission, please ensure this is clearly indicated. We do not need suppliers’ addresses.

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Results

Please organise your Results section with enough subheadings to allow readers to gain a clear picture of the work. The section should indicate the key questions being addressed, the outcomes of experiments, and any interpretation of these results.

To help Editors and reviewers assess the reproducibility of your work, include the number of times your experiment was repeated and the type of result shown (mean, median, representative, etc.). If results are expressed as percentages, the absolute value corresponding to 100% should be stated. Indicate the variability of the results statistically wherever possible; when error terms are given, state the measure of dispersion and the number of observations. Specify the statistical techniques you used, and where necessary either describe the technique or provide a reference.

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Discussion

Your discussion should not be too long. Compare your results with previous findings without revisiting your results in full, and use subheadings where appropriate to highlight the points under discussion. It may be helpful to list the main conclusions at the end.

Where appropriate, you may wish to provide a combined Results and Discussion section.

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Author statements

Authors and contributors

We encourage all authors to sign up for ORCiD, the persistent identifier for research contributors. ORCID provides a persistent digital identifier that distinguishes you from every other researcher and supports automated linkages between you and your professional activities, ensuring that your work is recognised.

We also recommend that you include a section on authorship and contributions using the CRediT taxonomy from CASRAI, which aims to provide transparency to the contributions of researchers to published work, improving attribution, credit, and accountability. The table below summarises the roles currently included in the taxonomy: if you feel that there are additional roles which should be added, please get in touch with our Director of Publishing, who will pass the information on to CASRAI for consideration.

Contributor RoleRole Definition
ConceptualisationIdeas; formulation or evolution of overarching research goals and aims.
MethodologyDevelopment or design of methodology; creation of models.
SoftwareProgramming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components.
ValidationVerification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs.
Formal AnalysisApplication of statistical, mathematical, computational, or other formal techniques to analyse or synthesise study data.
InvestigationConducting a research and investigation process, specifically performing the experiments, or data/evidence collection.
ResourcesProvision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools.
Data CurationManagement activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later reuse.
Writing – Original Draft PreparationCreation and/or presentation of the published work, specifically writing the initial draft (including substantive translation).
Writing – Review and EditingPreparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre- or post-publication stages.
VisualisationPreparation, creation and/or presentation of the published work, specifically visualisation/data presentation.
SupervisionOversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team.
Project AdministrationManagement and coordination responsibility for the research activity planning and execution.
FundingAcquisition of the financial support for the project leading to this publication.


Conflicts of interest

You must declare any potential conflicts of interest in the article. 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, 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:

  • 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

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. For human work we also require a statement regarding informed consent.

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

If your article includes details, images, or videos relating to an individual person, you will need to have evidence of written informed consent for the publication of these details. Consent for publication must be obtained from the person, or their parent or legal guardian in the case of children under 18. If the person has died, consent for publication must be obtained from their next of kin.

You can use our consent form to obtain consent for publication, or a consent form from your own institution or region if appropriate. The consent form must state that the details/images/videos will be freely available on the internet or in print and may be seen by the general public. The consent form must be submitted with the article and will be treated confidentially.

In cases where images are entirely unidentifiable and there are no details on individuals reported within the article, consent for publication of images may not be required. The final decision on whether consent to publish is required lies with the Editor.

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

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References

List your references at the end of the article, numbered in the order that they appear in the text. All listed references must be cited in the text, tables, or figure legends. Where relevant and for research submitted to Microbial Genomics, please also provide a Data bibliography.

We use the Vancouver style. If your article is accepted for publication, your reference lists and citations will be reformatted to fit. Ideally, references should include a DOI to facilitate this, and to allow us to create reference links in published articles.

Example reference:

Pinheiro AM, Carreira A, Ferreira RB, Monteiro S. Fusion proteins towards fungi and bacteria in plant protection. Microbiology 2018 164: 11-19. doi: 10.1099/mic.0.000592

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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.
  • When results are expressed as percentages, the absolute value(s) corresponding to 100% must be stated.
  • Indicate the reproducibility of results.

Figure files

Figures will be required as separate files for publication. We support figures supplied in PDF, GIF, TIFF, EPS, JPEG, PNG, SVG, 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.

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.

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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…’. The latter implies more than one generic name Salmonella.

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, p15gag).

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.

Abbreviations

As a rule, you should only use an abbreviation if it will appear more than three times in your text. You should always define your abbreviations the first time they are mentioned in the Abstract and in the main text of your article, as well as in any figure or table legends. Common terms such DNA do not need to be defined.

Units

Please use SI units throughout your article where possible. If non-SI units are used, the equivalent in SI units should also be given at the first mention, e.g. 1 p.s.i. (6.9 kPa).

For compound units (e.g. micrograms per millilitre), use μg ml-1 not μg/ml.

Give concentrations as g l-1, etc. The term ‘%’ should be defined as ‘w/v’, ‘v/v’ or ‘w/w’, to avoid ambiguity.

For radioactivity, the preferred unit is becquerels (Bq).

Use relative molecular mass (Mrr) rather than ‘molecular weight’. Alternatively, use molecular mass with values quoted in daltons (Da).

You should use absorbance (A) for the quantity log(I0/I) in UV and visible absorption spectrophotometry of samples in which there is negligible scattering or reflection of light. If there is considerable scattering, as in spectrophotometric measurements of microbial biomass, use optical density (OD) or attenuance (D). Whenever A, OD or D is used, you need to specify the wavelength (in nm) of the incident light with subscript numbers (e.g. A280), the path length of the cell or cuvette and the make and model of the spectrophotometer, and the sample dilution and the diluent. Readings obtained with instruments designed for turbid samples, such as nephelometers or Klett meters, should be reported in appropriate units.

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Data

Supporting data

Supporting data provides additional, relevant, and useful information pertaining to the article. All our journals welcome supporting data, preferably deposited with data repositories such as figshare, Dryad, and Zenodo.

Microbial Genomics has partnered with Microreact, a free platform developed in the David Aanensen Research Group at Imperial College London and The Centre for Genomic Pathogen Surveillance, which provides interactive querying of the data via trees, maps, timelines and tables. Data deposited with Microreact is published in Microbial Genomics via a permanent web link.

If you prefer to provide supporting data as a supplementary material file associated with your article, please supply a single separate PDF file to be incorporated into the system-generated PDF. Excel files are also acceptable.

Microarray and other genome-wide studies

Data from microarray gene expression studies must comply with the MIAME guidelines. If your conclusions explicitly or implicitly depend on genome-wide profiling you should deposit the relevant complete data sets in a public online database such as GEO before submission, with password protection if appropriate, and provide the accession number and password with their submitted article.

Sequences

If you are making use of data from ongoing sequencing projects, you must follow the guidelines set by the project and give appropriate acknowledgement of the data source. You should show evidence that you have discussed your findings with the scientists responsible for the sequencing programme and that the organisation has approved what is being submitted.

Articles reporting new sequence data must include an accession number from one of the public databases (GenBank, EMBL, DDBJ or PIR) and you must adhere to the relevant deposition criteria for the database. If a sequence 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; you can choose to do this through figshare if you prefer. These files will not be published, but they are essential for reviewing the article. Both Microbial Genomics and International Journal of Systematic and Evolutionary Microbiology require that all sequence data be made publicly available prior to submission.

If your article reports on MLST analyses, the MLST gene sequence data for all samples presented in the article must be available.

If your article reports on insertion sequences, whether stand-alone or as part of larger sequencing projects, you should deposit the relevant information in the ISfinder database and provide the attribution number as part of your submitted article.

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.

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.

Open data and open methodology

Microbial Genomics has a mandatory open data policy. Authors are required to provide access to all supporting data, including sequencing data, which have either led to the conclusions drawn in their article or allow the procedure described in the article to be repeated. For all other journals, open data is optional and can be deposited as described in the section on Supporting data above.

We also have an optional open methodology policy supported by protocols.io. You can deposit you 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.

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.

Third-party data

Genomic data may have restrictions imposed on use in third-party publications even if the data is available on a public repository. If you are using sequence data from public repositories, you must ensure that either the data have already been published by the original owners and the relevant publication(s) are cited in your article; or you have written permission from the data owner (principal investigator or the sequencing centre), in line with the Fort Lauderdale and Toronto agreements.

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Language editing

You may wish to have your article edited before you submit it for peer review, or during revision. This is not compulsory but it may help Editors and reviewers to fully understand your article.

Many language-editing services are available, but we have partnered with Editage to provide publication-focused editing services to our authors at a 15% discount. To take advantage of this offer visit our Editage page, or if you’re an existing Editage customer, please use the code MICSOC10.

Please note that language editing does not guarantee that your article will be sent out for peer review or accepted for publication.

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Article types and structures

The tables below provide summary information about the various article types considered for publication in Microbiology Society journals. If you need further guidance, please contact the Editorial Office for the relevant journal:

Standard articles

Articles of the types described here are published in all Microbiology Society journals. The word and reference counts in the table are indicative, but not restrictive.

Article TypeDescriptionGuidance for authorsSubscription status*
Research ArticleThe study, results, and interpretations of original research. Re-analysis of published data is considered provided that novel insights are produced.3000 – 7000 words, circa 100 referencesFree to read 12 months after publication
ReviewUsually commissioned, Reviews provide a subject overview suitable for a wide audience. The text should not give undue emphasis to the authors’ work and should present controversial areas of the topic in a clear and objective way.5000 – 10,000 words, circa 150 referencesFree to read immediately
Short CommunicationAn alternative to the Research Article for describing smaller pieces of work. Suitable for reporting completed work, not preliminary findings.1000 – 3000 words, circa 50 referencesFree to read 12 months after publication
Insight ReviewUsually commissioned, Insight Reviews are an alternative to the Review for smaller, niche topics or for providing updates to earlier Reviews.1000 – 3000 words, circa 50 referencesFree to read immediately
MethodsA venue for describing novel procedures, methodologies, and techniques.1000 – 3000 words, circa 50 referencesFree to read 12 months after publication
LettersA means for readers to respond to recently published articles. Where the original article was published through OpenMicrobiology, the letter will also be Open Access.500 – 1500 words, circa 20 referencesFree to read 12 months after publication
Personal ViewUsually commissioned, Personal Views are opinion pieces exploring matters of interest to the community.500 – 1500 words, circa 20 referencesFree to read immediately
EditorialCommunications from the Editors-in-Chief and Editorial Boards of the journals.As agreed with the EditorFree to read immediately

* All eligible for immediate Open Access through our OpenMicrobiology option.

Specialist articles

Some of our journals have one or two specialist article types, as described here. With a focus on systematics, International Journal of Systematic and Evolutionary Microbiology naturally has multiple additional specialist article types, described in full on the Journal’s scope page.

Article TypeDescriptionGuidance for authorsJournals
ICTV Profile or Microbe Profile*Usually commissioned, these are concise, review-style articles providing overviews of the classification, structure, and properties of viruses or microbes1000 – 1500 words, circa 5 referencesJournal of General Virology and Microbiology
Microbiology Society Prize Lecture**Summary article of a Prize Lecture presented at the Society’s Annual Conference.As agreed with the Editor.As agreed with the Prize winner and Editor
BioResource***For highlighting research that is recognised as a significant resource with potential long-term impact. Focused on accurate descriptions of the data and samples, with emphasis on significance and accessibility.3000 – 7000 words, circa 100 referencesMicrobial Genomics
Outbreak Report***Descriptions of basic epidemiology with a genomics approach taken; results and an ‘Outcome’ box summarising the take-home points arising from the investigation. Analysis methods must be fully documented, including all parameters and reference sequences used.3000 – 7000 words, circa 100 referencesMicrobial Genomics
Cases***Case Reports, Case Series and Case Reviews describing interesting diagnoses, investigation and/or treatment of infectious diseases in humans or animals are all considered.1000 – 3000 words, circa 50 referencesAccess Microbiology

*Published as Open Access under OpenMicrobiology.

**Free to read immediately after publication. Open Access available with OpenMicrobiology.

***Published in Open Access journals under OpenMicrobiology.

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