Instructions to Authors
About the Journal
Launched in 1938, Journal of Applied Microbiology (JAM) is the flagship title of Applied Microbiology International, whose members benefit from free online access and discounts on open access publishing fees. Journal of Applied Microbiology aims to publish studies which represent a significant advance in the field. The journal serves as a platform to promote all aspects of applied microbiology.
Once a paper is accepted, JAM will publish a precopyedited, preproofed version of the paper online within 1 week. This is replaced by a copyedited, proofed version of the paper as soon as it is ready.
Please read these instructions carefully and follow them closely. The Editors may return manuscripts that do not follow these instructions.
Scope of the Journal
The broad scope of Journal of Applied Microbiology encompasses the full breadth of applied microbiology research, exploring topics that include (but are not limited to):
- Clinical microbiology
- Human, animal and environmental microbiomes
- Sanitation and public health microbiology
- Bacteriology, virology, mycology
- Antimicrobials, Resistance and Chemotherapy
- Applied microbial and cell physiology
- Genomics, transcriptomics, proteomics
- Environmental microbiology and biotechnology
- Veterinary microbiology
- Food microbiology
- Agricultural and plant microbiology
- Industrial microbiology
- Enzymology and protein engineering
- Marine microbiology
The following studies are generally considered out of scope:
- Microbiome, metagenomic, and genomic studies that do not go beyond descriptive findings.
- Immunological studies where microorganisms are not the focus of the work.
- Methodological studies with no demonstrated application
Find out more information about the scope of JAM.
Contents
- About the Journal
- Editorial Policies
- Submission
- Third-Party Permissions
- Manuscript Preparation: Format, Structure, and Style
- Presubmission Language Editing
- Title Page
- Abstract
- Introduction
- Materials and Methods
- Results
- Discussion
- Acknowledgements
- Funding
- CRediT
- References
- Conflict of Interest
- Supplementary Material
- Style
- Abbreviations
- Tables
- LaTeX
- Figures
- Microbial nomenclature
- Gnotobiotic animals
- Statistics
- Experimental hazards
- Production
Editorial Policies
For full details of Oxford University Press’s editorial policies, please see Publication Ethics.
Peer Review
This journal uses single-anonymised peer review. For full details about the peer review process, see Fair Editing and Peer Review.
Data Policy
Data Availability Statement
The inclusion of a Data Availability Statement is a requirement for articles published in JAM. Data Availability Statements provide a standardised format for readers to understand the availability of data underlying the research results described in the article. The statement may refer to original data generated in the course of the study or to third-party data analysed in the article. The statement should describe and provide means of access, where possible, by linking to the data or providing the required unique identifier.
The Data Availability Statement should be included in the endmatter of your article under the heading ‘Data availability’.
More information and example Data Availability Statements.
Data Citation
JAM supports the Force 11 Data Citation Principles and requires that all publicly available datasets be fully referenced in the reference list with an accession number or unique identifier such as a digital object identifier (DOI). Data citations should include the minimum information recommended by DataCite:
- [dataset]* Authors, Year, Title, Publisher (repository or archive name), Identifier
*The inclusion of the [dataset] tag at the beginning of the citation helps us to correctly identify and tag the citation. This tag will be removed from the citation published in the reference list.
Preprint Policy
You retain the right to make an Author’s Original Version (also known as a preprint) available through various channels. Making an Author’s Original Version does not prevent submission to the journal. For further information see our Online Licensing, Copyright and Permissions policies. If your paper is accepted, you will need to update the status of any preprint, including your published paper’s DOI. For details, see our Author Self-Archiving policy page.
Self-Archiving Policy
You may self-archive versions of your work on your own webpages, on institutional webpages, and in other repositories. If you want more information about the reuse rights you retain if you publish with us, please visit our Author Self Archiving Policy page.
Conflict of Interest
When submitting a paper, you and your co-authors must declare any potential conflicts of interest. You must do this by including a Conflict of Interest statement in your submitted manuscript.
A detailed definition of conflicts of interests is available.
Human Subjects and Patient Confidentiality
Journals publishing studies using human subjects should ensure that a patient's right to privacy has not been infringed without prior consent. We encourage journals to follow the ICMJE guidelines for reporting on human subjects.
Manuscript submitted to Journal of Applied Microbiology should contain the following statements in the methods section:
- Confirmation that research was conducted in accordance with the Declaration of Helsinki.
- Statement that the study was approved by a local ethics committee, including the name of the committee and approval number. If approval was not required or was waived this should be stated.
- A statement that participants provided consent to participate in the study, or if not state why.
- If there is any identifiable information presented on participants, then consent to publish would also be required and should be stated, including that the participant has been shown the manuscript to be published.
Animal Experimentation
Where animals are used in research we expect them to have been treated in a humane manner and in line with the ARRIVE guidelines. The International Council for Laboratory Animal Science has published guidelines specifically for editors and Reviewers on how to handle submissions involving animal research. OUP supports these guidelines and, wherever possible, encourages editors and society partners to adopt them. Authors may be required to provide evidence that they obtained ethical and /or legal approval prior to conducting the research.
Manuscript submitted to Journal of Applied Microbiology should contain the following statements in the methods section:
- If international, national or institutional standards for the care and use of laboratory animals were followed.
- Statement that the study was approved by a local ethics committee, including the name of the committee and approval number. If approval was not required or was waived this should be stated.
Biosecurity
Authors of papers related to Schedule 5 biological agents should inform the Editor at the time of manuscript submission if their study has the potential for both benevolent and malevolent application. This is often referred to as “dual use research concern”. The National Science Advisory Board for Biosecurity (NSABB) guidelines state that a “dual use research of concern” can arise in relation to “research that, based on current understanding, can be reasonably anticipated to provide knowledge, products, or technologies that could be directly misapplied by others to pose a threat to public health and safety, agricultural crops and other plants, animals, the environment, or material”. Where a reviewer is concerned that an article might include information that could be a threat to security then the Editor will treat the article as possible DURC dual use research concern) and may consult a specialist reviewer. Their advice will be taken into account by the Editor in making any final decision on publication.
Antibiotic antimicrobial testing and microbial resistance
A number of methods like disc diffusion, Etest, agar dilution, broth microdilution and broth macrodilution, are suitable for in vitro antimicrobial susceptibility testing. However, the test used must be performed in accordance with an internationally accepted procedure; for example tests published by the Clinical and Laboratory Standards Institute (CLSI), the British Society for Antimicrobial Chemotherepy (BSAC), the Deutsches Institut fur Normung e.V. (DIN) and the Comité de l’Antibiogramme de la Société Francaise de Microbiologie (CA-SFM). Further guidance and interpretation of MIC 50 and MIC 90 values as well as guidance for the interpretation of multiresistance can be found in Schwarz et al. J. Antimicrobial Chemother 2010; 65: 601-604.
Submission
We will consider your manuscript as long as
- it is your own original work and does not duplicate any previously published work, including your own;
- it is not under consideration, in peer review, or accepted for publication in any journal
- it has not been published in any other journal; and
- it contains nothing abusive, defamatory, libelous, obscene, fraudulent, or illegal.
Authors should observe high ethical standards and obey publication best practices. The following are all unacceptable:
- data falsification or fabrication
- plagiarism, including duplicate publication of your own work without proper citation
- misappropriation of work
We treat any case of ethical or publication malpractice very seriously. We will address them in accordance with the Committee on Publication Ethics (COPE) guidelines. Further information about OUP’s ethical policies.
Format Free Submission
Journal of Applied Microbiology has a streamlined submission process designed to avoid unnecessary work. All submissions must include an Impact Statement.
At initial submission, manuscripts can be provided in any common document format that can be easily opened and read by others. A single PDF or Word file is usually reliable. At first submission, it is not necessary to apply formatting to match house style. Instead, simply ask: would I enjoy reading and reviewing a manuscript formatted in this way?
At revision stage, you will be asked to supply editable files that match journal formatting requirements, as well as high-resolution figures. For more information, please consult the journal’s style conventions below.
How to Submit
You must submit your paper via our web-based submission system, which may be found at https://mc.manuscriptcentral.com/jamicro. If you have not published with JAM before, you will need to create an account. For more information, please see the ScholarOne FAQs and Guidelines. Questions about submitting can be sent to the editorial office at [email protected].
Article Type
This journal publishes several different article types.
Original Articles
Original Articles comprise most of the Journal and should have as their aim the development of concepts as well as the recording of facts. The manuscript should be prepared for a wide readership and as far as possible should present novel results of a substantial programme of research.
Original Articles should not exceed 34 pages and should contain the following sections in this order:
- Abstract
- Introduction
- Materials and methods
- Results
- Discussion
- Acknowledgements
- Conflict of Interest
- Data Availability
- Supplementary Data (if applicable)
Review Articles
Review articles will present a substantial survey with an adequate historical perspective of the literature on some facet of applied microbiology. We would prefer to see a distillation of early and present work within the field to show progress and explain the present interest and relevance. The manuscript should not be simply a review of past work or be concentrated largely on unpublished results.
Review Articles are invited by the Editorial Board. The journal no longer considers unsolicited review submissions. If authors wish to submit a Review Article they should complete the proposal form and email it to the Editorial Office. Proposals will be evaluated by the Editors, with authors being invited to submit if their topic is of interest to the journal. Unsolicited review submissions received without a prior approved proposal will be returned to the authors, requesting a proposal be sent first.
Review articles must normally not exceed 10,000 words (40 pages double spaced) including references, figures and tables. As references can make a heavy demand on pages available to you, it is suggested that you select key references only. The headings in Review Articles are of the author’s choice, but the manuscript should begin with a short Summary of 150-200 words. There is no requirement for Review Articles to have an Impact Statement section; this is at the discretion of the author.
Perspectives
Perspectives differ from Review Articles by giving a viewpoint on important questions that still need answering. They are future-forward and more speculative than a review article. Perspectives aim to highlight the importance of the topic covered and inspire further discussion.
Perspectives must normally not exceed 5000 words (20 pages double spaced) including references, figures and tables.
Perspectives are invited by the Editorial Board. As with Review Articles, authors wishing to submit a Perspective should first complete the proposal form.
Commentaries
Commentaries are short summaries of one or more papers which focus on a specific topic. They may summarise recent discoveries in an area, or share insights into potential future developments for that field of study, with the aim of contextualising the significance of the article being commented on and inspiring further discussion.
Commentaries must normally not exceed 2500 words (10 pages double spaced) including references, figures and tables.
Commentaries are invited by the Editorial Board. As with Review Articles, authors wishing to submit a Commentary should first complete the proposal form.
Third-Party Permissions
If you wish to reproduce any material for which you do not own the copyright—including quotations, tables, or images—you must obtain permission from the copyright holder. The permissions agreement must include the following documents:
- nonexclusive rights to reproduce the material in your article in Journal of Applied Microbiology
- both print and electronic rights, preferably for use in any form or medium
- lifetime rights to use the material
- worldwide English-language rights
Further information on obtaining permission.
Manuscript Preparation: Format, Structure, and Style
Presubmission Language Editing
If you are not confident in the quality of your English, you may wish to use a language-editing service to ensure that editors and reviewers understand your paper. Oxford University Press partners with Enago, a leading provider of author services. Prospective authors are entitled to a discount of 30% for editing services at Enago, via this link: https://www.enago.com/pub/oup.
Enago is an independent service provider, who will handle all aspects of this service, including payment. As an author you are under no obligation to take up this offer. Language editing is optional and does not guarantee that your manuscript will be accepted. Edited manuscripts will still undergo peer review by the journal.
Title Page
Please include the following:
- the title of your paper
- all author names and affiliations
- mailing address and email address of one corresponding author
- a short running head of 50 characters or less
Abstract
A brief summary of about 150-200 words, should give the major findings of the investigation under the following four headings: Aims; Methods and Results; Conclusions; Impact Statement. A list of between three and six keywords should be added.
Introduction
A balance must be struck between the pure and applied aspects of the subject.
Materials and Methods
Ensure that the work can be repeated according to the details provided. By submission of a manuscript, the authors consent that biological material, including plasmids, viruses and microbial strains, unobtainable from national collections will be made available to members of the scientific community for non-commercial purposes subject to national and international regulations governing the supply of biological material. In the case of a new diagnostic PCR, you should consider the need for an internal amplification control (JAM 2004 96(2):221; available here).
Results
Well-prepared tables and figures must be a cardinal feature of the 'Results' section because they convey the major observations to readers who scan a paper. Information provided in tables and figures should not be repeated in the text but focus attention on the importance of the principal findings of the study. In general, journal papers will contain between one and six figures and tables.
Discussion
This must not recapitulate the results and authors must avoid the temptation of preparing a combined 'Results and Discussion' section.
Acknowledgements
The acknowledgements section should include details of any non-financial support. Contributors who do not qualify as authors should be acknowledged and their particular contribution described.
Funding
All sources of funding for the work reported, for all the authors, must be acknowledged in a separate section titled ‘Funding.’ Please fully cite any relevant funding information, including specific grant numbers. If no funding was received you should include a statement clarifying this.
CRediT
The Journal uses the contributor roles taxonomy (CRediT), which allows authors to describe the contributor roles in a standardized, transparent, and accurate way. Authors should choose from the contributor roles outlined on the CRediT website and supply this information upon submission. You may choose multiple contributor roles per author. Any other individuals who do not meet authorship criteria and made less substantive contributions should be listed in your manuscript as non-author contributors with their contributions clearly described.
References
You may format references in any readable style at submission. You are responsible for the accuracy of reference information.
Conflict of Interest
If no conflict of interest exists, then 'no conflict of interest declared' should appear within this section. Otherwise, authors should list all pertinent commercial and other relationships that may be perceived as a potential source of conflict of interest. Further information on the types of interest that should be declared can be found in ICMJE guidelines.
Supplementary Material
You must submit supplementary data or supplementary material at the same time as the main manuscript.
- Supplementary material must be cited in the text of the main manuscript.
- Supplementary material will be available online only and will not be copyedited.
- Style and formatting of supplementary material should be consistent with that of the manuscript.
- Supplementary material should be formatted to function on any internet browser.
- If it is at all possible, Supplementary material files should be no larger than 15MB each.
Style
The journal follows Oxford SCIMED style. Please refer to these requirements when preparing your manuscript. More information is available here. US spelling should be used throughout, except in quotations and in references.
Abbreviations
Please define nonstandard abbreviations at the first occurrence. Authors can use this list of common abbreviations used in the Journal.
Tables
You must number all tables (e.g., table 1, table 2, table 3) and reference them in the text. You must place all tables at the end of the main text. Please submit all tables in an editable format. Do not submit tables as an image file.
LaTeX
Information on LaTeX files and formatting can be found at: https://academic.oup.com/journals/pages/authors/preparing_your_manuscript.
Figures
You must include figure titles and legends within the manuscript file—they should not be included in the image file.
You must submit each figure as an individual image file. Submit all panels of a multipanel figure on a single page as one file. For example, if the figure has 3 panels, the figure should be submitted as one file. Each panel should be labeled as a letter (A, B, C, D, etc.) in the upper-left corner of each panel.
Images of photographs or paintings can be provided as raster images. Common examples of raster images are .tif/.tiff, .raw, .gif, and .bmp file types. The resolution of raster files is measured by the number of dots or pixels in a given area, referred to as “dpi” or “ppi.”
- minimum resolution required for printed images or pictures: 350dpi
- minimum resolution for printed line art: 600dpi (complex or finely drawn line art should be 1200dpi)
- minimum resolution for electronic images (i.e., for on-screen viewing): 72dpi
Images of maps, charts, graphs, and diagrams are best rendered digitally as geometric forms called vector graphics. Common file types are .eps, .ai, and .pdf. Vector images use mathematical relationships between points and the lines connecting them to describe an image. These file types do not use pixels; therefore resolution does not apply to vector images.
Figures prepared as .doc/.docx or .jpeg/.jpg files will not be accepted.
Figure accessibility and alt text
Incorporating alt text (alternative text) when submitting your paper helps to foster inclusivity and accessibility. Good alt text ensures that individuals with visual impairments or those using screen readers can comprehend the content and context of your figures. The aim of alt text is to provide concise and informative descriptions of your figure so that all readers have access to the same level of information and understanding, and that all can engage with and benefit from the visual elements integral to scholarly content. Including alt text demonstrates a commitment to accessibility and enhances the overall impact and reach of your work.
Alt text is applicable to all images, figures, illustrations, and photographs.
Alt text is only accessible via e-reader and so it won’t appear as part of the typeset article.
Detailed guidance on how to draft and submit alt text.
Microbial nomenclature
The Latin binomial name of micro-organisms, plants and animals (other than farm animals) must be given at first mention in the text; thereafter the generic name will be abbreviated in such a way that confusion is avoided when dealing with several genera all beginning with the same letter, viz. Pseudomonas, Proteus, Pediococcus, etc. (see list of abbreviations above). Subspecies are italized (Corynebacterium diphtheriae subsp. mitis); groups and types are printed in Roman and designated by capital letters or Arabic figures (e.g. Staphylococcus aureus group A). Common names will not have an initial capital letter nor will they be underlined in the manuscript, viz. pseudomonad, salmonellas. The specific name will be given in full in the captions to tables and figures. Major ranks are written in Roman with an initial capital (e.g. Enterobacteriaceae).
Gnotobiotic animals
The terminology for describing the environmental status of animals in gnotobiotic experiments has established itself by usage. Germ-free implies freedom from any detectable microorganisms or viruses and it is limited by the tests used to detect contaminants. Conventional animals have a full complement of associated microbes. Open conventional animals are housed in a standard animal house. Isolator conventional animals are maintained in isolators and associated with full flora. Ex-germ-free animals are those with an associated flora which have become conventional.
Statistics
Tests must be presented clearly to allow a reader with access to the data to repeat them. Statistical tests used in the study should be clearly indicated in the Materials and Methods section. It is not necessary to describe every statistical test fully, as long as it is clear from the context what was done. In particular, null hypotheses should be clearly stated.
Authors are urged to give consideration to the assumptions underlying any statistical tests used and to assure the reader that the assumptions are at least plausible. Authors should be prepared to use nonparametric tests if the assumptions do not seem to hold.
Experimental hazards
Chemical or microbiological hazards that may be involved in the experiments must be explained. Authors should provide a description of the relevant safety precautions adopted or cite an accepted 'Code of Practice'.
Production
Manuscript Charges
Author Services
You can pay open access charges on the same Author Services site you used to sign your licence to publish. You can pay immediately online or request an invoice by email or post. You may also refer the charges to an institutional prepayment account. Any applicable discounts can also be applied prior to payment.
You can pay your open access charges immediately after you sign your licence.
Open Access Charges
Journal of Applied Microbiology offers the option of publishing under either a standard licence or an open access licence. Please note that some funders require open access publication as a condition of funding. If you are unsure whether you are required to publish open access, please do clarify any such requirements with your funder or institution.
Should you wish to publish your article open access, you should select your choice of open access licence in our online system after your article has been accepted for publication. You will need to pay an open access charge to publish under an open access licence.
Details of the open access licences and open access charges.
OUP has a growing number of Read and Publish agreements with institutions and consortia which provide funding for open access publishing. This means authors from participating institutions can publish open access, and the institution may pay the charge. Find out if your institution is participating.
Toll-free link
All corresponding authors will be provided with a free access link to their article upon publication. The link will be sent via email to the article’s corresponding author who is free to share the link with any co-authors. Please see OUP’s Author Self-Archiving policy for more information regarding how this link may be publicly shared depending on the type of license under which the article has published.
