Instructions to Authors

Table of Contents

• How We Publish
• Peer Review Process
• Publication and Research Ethics
• Publishing Agreements and Charges
• After Publication
• Manuscript Submission
  • Article Types
    • Original Article
    • Review Article
    • Brief Communication
    • Comment
    • Perspective
    • Winogradsky Review
  • Manuscript preparation instructions
• Contact Us

How We Publish

The ISME Journal is a peer-reviewed, fully open access journal that publishes on a continuous publication model. Papers are published as they are ready into a single issue each year. Each yearly issue opens in January and closes in December. All papers published in the Journal are made freely available online under open access publishing agreements, with applicable charges. Please refer to the open access section below.

Once a paper is accepted and the publishing agreement is signed, the Journal will publish the Accepted Manuscript version of the paper (before copyediting and review of the final proof) within one week on the Advance Access page. Substantial changes to the published Accepted Manuscript may require a correction notice. The Accepted Manuscript will be removed from Advance Access when the Version of Record of the paper (after copyediting and proof review process) is published into the currently open issue. The Version of Record requires a correction notice for any changes after a paper is published, even if it is not yet placed in an issue. See the definitions of the Version of Record and other versions of the paper for more details.

Scope of the Journal

The ISME Journal is the flagship publishing venue for the International Society for Microbial Ecology, covering the diverse and integrated areas of microbial ecology. We encourage outstanding contributions that represent major advances for the study of microbial ecosystems, communities, and interactions of microorganisms in the environment. Articles in the Journal describe pioneering discoveries of wide appeal that enhance our understanding of functional and mechanistic relationships among microorganisms, their communities, and their habitats.

The broad scope of The ISME Journal encompasses the full breadth of microbial ecology research, exploring topics that include (but are not limited to):

• Climate change microbiology
• Microbial contributions to biogeochemical cycles
• Community assembly
• Engineered and synthetic microbial communities
• Host-microbiome interactions
• Microbiomes of engineered environments
• Modeling and ecological theory
• Novel microorganisms and metabolic functions
• Spatial and temporal dynamics

The ISME Journal welcomes a range of content types including original research, reviews, brief communications, perspectives, and comment articles of high significance to the microbial ecology research community.

Peer Review Process

The Journal operates single-anonymized peer review, meaning that the identity of the authors is known to the editors and to the reviewers. The identities of the reviewers are known only to the editors and are hidden from the authors, unless otherwise requested by reviewers.

Once a submitted manuscript passes initial assessment by one of the Journal’s Editor-in-Chiefs, it will then be passed to a Senior Editor for assessment. Following this assessment, the Senior Editor may send the manuscript for peer review before recommending a final decision. The Editor-in-Chief makes the final decision on the submitted manuscript. During the peer review process, a manuscript is typically sent to 2-3 reviewers. Authors may suggest potential reviewers at submission, but there is no guarantee that the suggested reviewers will be selected by the Journal. Recommended reviewers should be experts in their field and able to provide an objective assessment of the manuscript without financial or interpersonal conflicts of interest with any authors (for example, not a current collaborator or recent co-author within the past 5 years; please see COI section for further details). We encourage authors to consider reviewers from a diverse range of backgrounds, including early career researchers and those from under-represented communities.

At the time of submission, it is possible to request that specific individuals not be used as reviewers of a particular manuscript. Please do so in the cover letter that is not shown to reviewers, along with a brief explanation as to why those individuals should be excluded. However, there is no guarantee these experts will be excluded by the Journal.

Statistical methods should be rigorous and reporting of this data should be accurate and complete. Editors may request an expert statistical review of any submission containing statistical analysis.

If a manuscript is accepted for publication, reviewer comments will not be published alongside the paper.

For full details about the peer review process, see Fair editing and peer review or OUP author FAQs.

Notice for Authors

If you submitted your paper before the journal transitioned to Oxford University Press, but it was published after the transition, you might see the submission date listed as the transfer date to OUP instead of the original submission date. We are actively updating these dates through correction notices.

Manuscript transfer

Sending transfers

When a manuscript is rejected from The ISME Journal, before or after peer review, the editorial team may offer the option of transferring to ISME Communications. If this offer is accepted, all manuscript files and reviewer reports from consenting reviewers will be sent to ISME Communications. In the case of transferred manuscripts that have previously undergone peer review at The ISME Journal, it is highly recommended that authors prepare a revised manuscript and include a point-by-point response to all comments and suggestions provided by the previous reviewers. Please also include a version of the revised manuscript where changes are highlighted using the Track Changes function. The editorial team of ISME Communications may choose to seek additional peer review. A decision will be made on the manuscript based on the feedback from all reviewers and the judgment of the ISME Communications editorial team.

Screening for misconduct

Manuscripts will be screened using iThenticate to help detect publication misconduct including plagiarism and redundant publication.

Identity/activity detection

The Journal uses Editorial Manager’s Identity Confidence Check tool to build confidence in the identity of authors and reviewers.

Reviewer recognition

To promote recognition of the essential work done by reviewers, the Journal offers reviewers the option to have their reviews verified and automatically listed on their ORCID iD profile.

Reviewer locator

The Journal uses the Web of Science Reviewer Locator to assist the editors in finding appropriate reviewers.

Appeals and complaints

Authors may appeal an editorial decision. To do so, please contact the Editor-in-Chief responsible for the decision or contact the editorial office, providing as much specific detail as possible about why the original decision should be reconsidered. Every appeal will receive a response within a reasonable timeframe. Please do not resubmit the manuscript in the interim.

To register a complaint regarding non-editorial decisions, the Journal’s policies and procedures, editors, or staff, please contact us. Complaints will be taken seriously and will be carried forward following COPE guidelines and processes and/or sanctions will be enacted if deemed appropriate.

Publication and Research Ethics

Authorship

Authorship is limited to those who have made a significant contribution to the design and execution of the work described. Any contributors whose participation does not meet the criteria for authorship should be acknowledged but not listed as an author. For a detailed definition of authorship, please see the International Committee of Medical Journal Editors (ICMJE) definitions of authors and contributors.

The Journal does not allow ghost authorship, where an unnamed author prepares the article with no credit, or guest/gift authorship, where an author who made little or no contribution is listed as an author. The Journal follows Committee on Publication Ethics (COPE) guidance on investigating and resolving these cases. For more information, please see the OUP Publication Ethics page.

Natural language processing tools driven by artificial intelligence (AI) do not qualify as authors, and the Journal will screen for them in author lists. The use of AI (for example, to help generate or edit content, write code, or process data) should be disclosed both in cover letters to editors and in the Methods or Acknowledgements section of manuscripts. Please see the COPE position statement on Authorship and AI for more details.

After manuscript submission, no authorship changes (including the authorship list, author order, and who is designated as the corresponding author) should be made without the approval of the editor. All co-authors must agree on the change(s), and neither the Journal nor the publisher mediates such disputes. If individuals cannot agree on the authorship of a submitted manuscript, please contact the editorial office. The dispute must be resolved among the individuals and their institution(s) before the manuscript can be accepted for publication. If an authorship dispute or change arises after a paper is accepted, contact OUP’s Author Support team. COPE provides guidance for authors on resolving authorship disputes.

If authors intend to use Read and Publish funding to publish a manuscript under an open access licence, note that changing the corresponding author to access those funds is not permissible. For more information on Read and Publish funding, see the open access charges section.

ORCID iDs

Authors are encouraged to provide their ORCID iDs (Open Researcher and Contributor iDs) at submission and take advantage of the benefits of participating in ORCID. If authors do not already have an ORCID iD, they can register for free via the ORCID website.

As ORCID iDs are collected, they are included in papers and displayed online, both in the HTML and PDF versions of the publication, in compliance with recommended practice issued by ORCID.

ORCID functionality online allows users to link to the ORCID website to view an author’s profile and list of publications. ORCID iDs are displayed on web pages and are sent downstream to third parties in data feeds, where supported.

If authors have registered with ORCID, they can associate their ORCID iD with their submission system account by going to their account details, entering their ORCID iD, and validating their details. Learn more about ORCID and how to link it to an individual account.

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 may choose from the contributor roles outlined on the CRediT website and supply this information upon submission. Authors may choose multiple contributor roles for each author. Any other individuals who do not meet authorship criteria and made less substantive contributions should be listed in the manuscript as non-author contributors with their contributions clearly described. Following manuscript submission, any changes to contributor roles require the approval of the editor.

Disclosure of potential conflicts of interest

Authors

The Journal requires all authors to disclose any potential conflict of interest at the point of submission. Conflicts of interest should be clearly labeled and included in the cover letter as well as in a separate “Conflicts of interest” section at the end of the manuscript. It is the responsibility of the corresponding author to ensure that conflicts of interest of all authors are declared to the Journal.

A conflict of interest exists when the position, activities, or relationships of an individual, whether direct or indirect, financial or non-financial, could influence or be seen to influence the opinions or activities of the individual. For more information, refer to OUP’s definition of conflict of interest. The Journal follows the COPE guidance for any undisclosed conflict of interest that emerges during peer review, production, or after publication.

Peer reviewers

Individuals that have a conflict of interest relating to a submitted manuscript should recuse themselves and will not be assigned to oversee, handle, or peer review the manuscript.

If during peer review an editor, reviewer, or author becomes aware of a conflict of interest that was not previously known or disclosed they must inform the Editor-in-Chief immediately.

Editors and Editorial Board members

At initial submission, the corresponding author must declare if the Editor-in-Chief, a Senior Editor, or an Editorial Board Member of the Journal is an author of or contributor to the manuscript. Another editor without a conflict of interest will then oversee the peer review and decision-making process. If accepted, a statement will be published in the paper describing how the manuscript was handled.

Previously published material

Authors should only submit a manuscript(s) to the Journal if:

• It is original work by the corresponding author and co-author(s).
• It is not under consideration, in peer review, or accepted for publication in any other publication.
• It has not been published in any other publication.
• It contains nothing abusive, defamatory, derogatory, obscene, fraudulent, or illegal.

The submitting author must disclose in their cover letter and provide copies of all related or similar preprints, dissertations, manuscripts, published papers, and reports by the same authors (i.e., those containing substantially similar content or using the same, similar, or a subset of data) that have been previously published or posted electronically or are under consideration elsewhere at the time of manuscript submission. The submitting author must also provide a concise explanation of how the submitted manuscript differs from these related manuscripts and papers. All related previously published papers should be cited as references and described in the submitted manuscript.  Inclusion of otherwise unpublished text and data from theses/dissertations is acceptable for newly submitted manuscripts, but the author of the theses/dissertation must be included as one of the manuscript authors.

The Journal does not discourage authors from presenting their findings at conferences or scientific meetings but recommends that they refrain from distributing complete copies of their manuscripts, which might later be published elsewhere without their knowledge.

For previously published materials including tables and figures, please see the Reusing copyrighted materials section.

Preprints

Authors retain the right to make an Author’s Original Version (preprint) available through various channels and this does not prevent submission to the Journal. If accepted, the authors are required to update the status of any preprint, including adding the published paper’s DOI. For full details on allowed channels and updating a preprint, please see our Author self-archiving policy.

Reusing copyrighted material

Authors must obtain permission for any material used within a manuscript for which they are not the rightsholder, including quotations, tables, figures, or images. In seeking permissions for published materials, first contact the publisher rather than the author. For unpublished materials, start by contacting the creator. Copies of each grant of permission should be provided to the editorial office of the Journal. The permissions agreement must include the following:

• Nonexclusive rights to reproduce the material within the paper in The ISME Journal
• Rights for use in print and electronic format at a minimum, and preferably for use in any form or medium
• Lifetime rights to use the material
• Worldwide English-language rights

If authors have chosen to publish under an open access licence but have not obtained open access re-use permissions for third-party material contained within the manuscript, this must be stated clearly by supplying a credit line alongside the material with the following information:

• Title of content
• Author, Original publication, year of original publication, by permission of [rightsholder]
• This image/content is not covered by the terms of the Creative Commons licence of this publication. For permission to reuse, please contact the rights holder.

Our publisher, Oxford University Press, provides detailed Copyright and Permissions Guidelines, and a summary of the fundamental information.

Misconduct

Authors should observe high standards with respect to research integrity and publication ethics as set out by the Committee on Publication Ethics (COPE). Falsification or fabrication of data including inappropriate image manipulation, plagiarism, including duplicate publication of the author's own work without proper citation, and misappropriation of work are all unacceptable practices.  Allegations of ethical misconduct, both directly and through social media, are treated seriously and will be investigated in accordance with the relevant COPE guidance.

If misconduct has been established beyond reasonable doubt, this may result in one or more of the following outcomes, among others:

• If a submitted manuscript is still under consideration, it may be rejected and returned to the author.
• If a paper has already been published online, depending on the nature and severity of the infraction, either a correction notice will be published and linked to the paper, or retraction of the paper will occur, following the COPE Retraction Guidelines.
• The relevant party’s institution(s) and/or other journals may be informed.

Manuscripts submitted to the Journal may be screened with plagiarism-detection software. Any manuscript may be screened, especially if there is reason to suppose that part or all the of the manuscript has been previously published.

COPE defines plagiarism as “when somebody presents the work of others (data, words, or theories) as if they were their own and without proper acknowledgment.”

COPE defines redundant/overlapping publication as “when a published work (or substantial sections from a published work) is/are published more than once (in the same or another language) without adequate acknowledgment of the source/cross-referencing/justification, or when the same (or substantially overlapping) data is presented in more than one publication without adequate cross-referencing/justification, particularly when this is done in such a way that reviewers/readers are unlikely to realise that most or all the findings have been published before.”

COPE defines citation manipulation as “behaviours intended to inflate citation counts for personal gain, such as: excessive self-citation of an authors’ own work, excessive citation to the journal publishing the citing article, and excessive citation between journals in a coordinated manner.”

Data fabrication is defined as intentionally creating fake data or misrepresenting research results. An example includes making up data sets.

Data falsification is defined as manipulating research data with the purpose of intentionally giving a false representation. This can apply to images, research materials, equipment, or processes.

Examples include cropping of gels/images to change context and omission of selected data.

If notified of a potential breach of research misconduct or publication ethics, the Journal editor and editorial office staff may inform OUP and/or the author’s institutional affiliation(s).

Ethical research

The Journal follows Committee on Publication Ethics (COPE) guidelines on ethical oversight.  We take research integrity seriously, and all research published in the Journal must have been conducted in a fair and ethical manner. Wherever appropriate, the Journal requires that all research be done according to international and local guidelines.

Human subjects

When reporting on human subjects, authors should indicate whether the procedures followed were in accordance with the ethical standards of the Helsinki Declaration, which were developed by the World Medical Association. For non-interventional studies, where ethical approval is not required or where a study has been granted an exemption by an ethics committee, this should be stated within the manuscript with a full explanation. Otherwise, manuscripts must include a statement in the Methods section that the research was performed after approval by a local ethics committee, institutional review board and/or local licencing committee, or that such approval was not required. The name of the authorizing body and any reference/permit numbers (where available) should also be stated there. Please be prepared to provide further information to the editorial office upon request.

Human subjects must give written informed consent, or if they are minors or incapacitated, such consent must be obtained from their parents or guardians. Consent forms should cover not only study participation but also the publication of the data collected. Also, any patient or provider information should be anonymized to the extent possible; names and ID numbers should not be used in the text and must be removed from any images (e.g. X-rays, photographs). Please note that blanking out an individual’s eyes in a photograph is not an effective way to conceal their identity. In studies where verbal, rather than written, informed consent was obtained, this must be explained and stated within the manuscript. If informed consent is not required or where a study has been granted an exemption, this must be included in the Methods section along with the name of the authorizing body. The Journal does not routinely collect consent forms, but authors should be prepared to provide written consent forms signed by the participants or other appropriate documentation to the editorial office upon request. For further guidance and examples, please refer to COPE’s guidance on consent.

Clinical trials

Clinical trials should be registered before enrollment of the first subject in accordance with the criteria outlined by the International Committee of Medical Journal Editors (ICMJE). When reporting primary or secondary analyses from a clinical trial, follow these criteria:

• Provide the trial registration number at the end of the Abstract.
• When the trial acronym is first used in the manuscript, provide the registration number and a link to the trial registration, which should be cited as a reference.
• If data has been deposited in a public repository and/or are being used in a secondary analysis, please state at the end of the Abstract the unique, persistent data set identifier, and repository name and number.
• When submitting the manuscript, authors must disclose any protocol alterations and all posting of results of the submitted work or closely related work in registries.
• In reporting randomized clinical trials, authors must comply with published CONSORT guidelines.
• Complete the recommended checklist and be prepared to provide it to the editorial office upon request.
• Present the recommended trial flow diagram as a figure in the manuscript or as supplementary material.
• If a manuscript reports on a randomized Phase II/III trial, authors must provide a brief description of the statistical plan of the original study that includes the primary and secondary endpoints, power calculation, and sample size.

Where available, registration numbers should be provided not only for the trial authors are reporting but also for any other trial mentioned in the manuscript. When the trial acronym is first used in the manuscript, provide the registration number and a link to the trial registration, which should be cited as a reference. 

Animal subjects

Studies involving animals require approval from the relevant institutional ethics committee or institutional animal use and care committee, and the research must be conducted in accordance with applicable national and international guidelines. All such manuscripts must include a statement in the Methods section providing details of the name of the committee(s) that approved the study, as well as the permit or animal licence numbers where available. Where a study has been granted an exemption, this must be stated in the Methods section along with the name of the authorizing body. Please be prepared to provide further information to the editorial office upon request.

ARRIVE guidelines

Authors are encouraged to consult the ARRIVE guidelines recommended by the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3R).

Euthanasia or anesthesia methods

Where applicable, any euthanasia or anesthesia methods must be carried out in accordance with applicable veterinary guidelines. These methods must be described in detail in the manuscript.

Laboratory animals

Manuscripts describing research involving laboratory-based animals must include details on housing, husbandry, and steps taken to reduce suffering. In studies where experimental animals were euthanized, details must be provided on humane endpoints. Details on the planned behavioral observations or physiological measurements used to determine the humane endpoint must be described. Authors are advised to consult the NC3Rs guide on Humane Endpoints and the American Veterinary Medical Association (AVMA) Guidelines for the Humane Slaughter of Animals.

C4DISC partnership

The Journal, International Society for Microbial Ecology, and OUP aim to create a community that fosters diversity, equity, and inclusion. As part of our commitment to these principles, OUP is a proud partner of the Coalition for Diversity & Inclusion in Scholarly Communications (C4DISC). C4DISC works with organizations and individuals within the scholarly communications landscape to foster equity, inclusion, diversity, and accessibility across the publishing industry and its published outputs.

The Journal is proud to adopt the Joint Statement of Principles of C4DISC.

Inclusive language

As defined by the Linguistic Society of America, “Inclusive language acknowledges diversity, conveys respect to all people, is sensitive to differences, and promotes equal opportunities”. We encourage authors to consider using inclusive language and images when preparing their manuscript. For guidelines, please see the C4DISC Guidelines on inclusive language and images.

Accessibility

Written, visual, and audio content in a submission should be accessible to all. Please see the C4DISC guidelines for making text, images, charts, tables, and audio and video accessible.

Availability of data and materials

The Journal requires all authors, where ethically possible, to publicly release all primary and secondary data and software code (e.g., used to process primary data or to generate figures and tables) underlying any published paper as a condition of publication and be available to reviewers during the peer review process. Authors are required to include a data availability statement in their paper. Data and software underlying the research article should be available in an online source (e.g., Figshare, Zenodo) with a DOI number and authors should include a full citation in their reference list. For details of the minimum information to be included in data and software citations see the OUP guidance on citing research data and software.

Whenever possible, data should be presented in the main manuscript or additional supporting files or deposited in a public repository. Visit OUP’s Research data page for information on general repositories for all data types, and resources for selecting repositories by subject area.

Microbial strains reported in the manuscript should be deposited, before submission, to an open culture collection from where they should be made publicly available without any restrictions.

Authors may request an exception to the policy due to legal, privacy, ethical, or other limitations or restrictions. Exceptions will be made at the discretion of the Journal. Please notify the editorial office when submitting a manuscript if authors wish to request an exception. If an exception is granted, a data availability statement must still be included in the paper specifying what cannot be shared and explaining why.

Data availability statement

The inclusion of a data availability statement is required for all original articles and brief communications published in the Journal. Data availability statements provide a standardized format for readers to understand the availability of original and third-party data underlying the research results described in the paper. The statement should describe and provide means of access, where possible, by linking to the data or providing the required unique identifier.

Data availability statements can take one of the following forms (or a combination of more than one if required for multiple datasets):

1. The datasets generated during and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS].
2. The datasets generated during and/or analysed during the current study are not publicly available due [REASON WHY DATA ARE NOT PUBLIC] but are available from the corresponding author on reasonable request.
3. Data sharing not applicable to this article as no datasets were generated or analysed during the current study.
4. All data generated or analysed during this study are included in this published article [and its supplementary information files].
5. The data that support the findings of this study are available from [third party name] but restrictions apply to the availability of these data, which were used under licence for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of [third party name].

More information and example data availability statements.

SeqCode taxonomy

We encourage taxonomic names proposed based on sequence data to be validated under the SeqCode via the SeqCode Registry. Initial registration can be done during manuscript preparation. For assistance with name formation and registration, authors are encouraged to contact the SeqCode Registry curators.

Digital preservation

Content published in the Journal will automatically be deposited into digital preservation services, including CLOCKSS, the Global LOCKSS Network, and Portico. This ensures the long-term preservation of the work. Through LOCKSS, participating institutions can sustain access to content if the Journal were to otherwise be unavailable, even for a short period of time. Should the Journal ever cease to publish, or content would otherwise become permanently unavailable, long-term access to the archives of CLOCKSS and Portico would be triggered. Until such a trigger event occurs, this content is not available to the public through CLOCKSS and Portico.

Self-archiving policy

Self-archiving refers to posting a copy of an authors’ work on a publicly accessible website or repository. Under certain circumstances, authors may self-archive versions of their work on their own webpages, on institutional webpages, and in other repositories. For information about the Journal's policy, and to learn which version(s) of the paper are acceptable for self-archiving, please see our Author self-archiving policy. 

Publishing Agreements and Charges

Authors, please read each section on the publishing agreement (also called a licence) and charges carefully.

Publishing agreements

After a manuscript is accepted, authors will be asked to sign a licence to publish through the Journals Licencing and Online Payments portal. The Journal is fully open access, meaning all papers in the Journal are published under an open access licence. The corresponding author will need to arrange payment of an open access charge to publish in the Journal. This charge allows all published papers to be immediately and freely available to all readers upon online publication. Editorial decisions occur prior to this step and are not influenced by payment or ability to pay.

Papers can be published under the following licence types:

• Creative Commons Attribution licence (CC BY)
• United States Government Licence
• Crown Copyright - Open Government Licence

Please see the OUP guidance on Licences, copyright, and re-use rights for more information regarding these publishing agreement options.

If you select a CC BY license, you will grant OUP a non-exclusive license. For all licenses, you, the author, retain copyright for the content and have the reuse rights described therein.

Open Government licence

The Open Government Licence is an open licencing model for content produced by employees of UK Crown bodies allowing users to copy, publish, distribute adapt and transmit the information for commercial and non-commercial purposes. For additional information see here.

Complying with funder mandates

Please note that some funders require open access publication as a condition of funding. If authors are unsure whether they are required to publish open access, please do clarify any such requirements with the funder or institution before selecting a licence. Further information on funder mandates and direct links to a range of funder policies.

Charges

Open access charges

Please note that The ISME Journal will become fully open access (OA) from 01 January 2024, with any submissions from 1st September 2023 subject to the charges detailed below.

The ISME Journal is a fully open access journal, and all articles are published in the journal under an open access licence immediately upon 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:

• Non-Member Charges for CC BY OA license: €3675
• The charge is discounted by 10% if the corresponding author is an ISME member.
• Corresponding authors based in countries and regions, that are part of the developing countries initiative are eligible for a full waiver of publishing fees in our fully open access journals. For further details, please see our APC Waiver Policy.

Authors may also apply for a waiver upon submission, which are considered on a case-by-case basis. Waiver requests should be directed to the Open Access team at [email protected].

Read and Publish

OUP has a growing number of open access agreements with institutions and consortia, which provide funding for open access publishing (also known as Read and Publish agreements). This means corresponding authors from participating institutions can publish open access, and the institution may pay the charge. Find out which institutions have an open access agreement.

To be eligible for one of OUP’s Read and Publish agreements, the corresponding author must provide their qualifying institution as their primary affiliation when they submit their manuscript. After submission, changing the corresponding author in order to access Read and Publish funding is not permissible.

Waiver policy

Corresponding authors based in countries and regions that are part of the developing countries initiative receive a full waiver of their open access charge. For further details, please see our open access waiver policy. In addition, members of the International Society for Microbial Ecology who are not covered by current Open Access agreements may apply for the Open Access Waiver Fund via the Editor-in-Chief.

Colour charges

The Journal does not charge for colour.

Page charges

The Journal does not have page charges.

Member discounts

Corresponding authors who are members of the International Society for Microbial Ecology are eligible for discounts on publication charges. Please provide the author membership number when prompted during manuscript submission.

Please see the open access charge list for more information about the open access charge discount.

After Publication

Changes to published papers

The Journal will only make changes to published papers if the publication record is seriously affected by the academic accuracy of the published information. Changes to a published paper will be accompanied by a formal correction notice linking to and from the original paper. The Journal follows the COPE guidelines on retractions.

For more information and details of how to request changes, including for authors who wish to update their name and/or pronouns, please see OUP’s policy on changes to published papers.

Authors who wish to submit a Correction to previously published content should contact the OUP Journals Corrections team, who will notify the editorial office about the Correction request. Authors should not submit Corrections through the submission systems or via any other channel of submission.

Promoting published work

Authors are the best advocates for promoting published work, and we encourage all authors to be involved in self-promotion. In sharing ideas and news about a new publication with colleagues and the public, which can help raise the profile of the published research.

Authors can best promote by:

• Sharing a published paper with colleagues. Because the Journal is open access, articles will always be freely available to all readers, and can be shared without limitations.
• Signing up for an ORCID iD to distinguish authors from other researchers with the same names, create an online profile showcasing all publications, and increase the visibility of published work.
• Using social media to promote work. To learn more about self-promotion on social media, see our social media guide for authors.

Find out how Oxford University Press promotes published content.

Manuscript Submission

How to submit

Authors must submit manuscripts via our web-based submission system, Editorial Manager. If authors have not published with The ISME Journal before, they will need to create an account. Questions about submitting manuscripts can be sent to the editorial office.

Article types

The ISME Journal publishes several different article types:

Original Article—maximum word count: 5,000

An Original Article is a substantial, in-depth, novel research study of interest to the readership of the Journal. Although the journal emphasizes discovery-based research, we are willing to consider breakthrough method papers that represent major advances for the field of microbial ecology.

Each Original Article manuscript should include:

• Unstructured Abstract—maximum word count: 250
• Key words—maximum of 10 and minimum of 3
• References—maximum of 100
• Data displays— maximum of 8 tables or figures

The maximum word count of 5,000 applies to the main body of text (excluding tables, figures, and references).

Each submission must contain the following sections and use these terms as the section headers. Authors should ensure that their sections are also placed in the exact order shown below; authors will be asked to revise their work if the manuscript does not follow this order:

• Introduction: The Introduction should assume that the reader is knowledgeable in the field and should therefore be as brief as possible but can include a short historical review where desirable.
• Materials and Methods: This section should contain sufficient detail and cited references so that all experimental procedures can be reproduced. Methods that have been published elsewhere should be described only briefly. Please do not copy/paste method text from other publications – this is a form of plagiarism. Authors should provide the name of the manufacturer and their location for any specifically named medical equipment and instruments, and all drugs should be identified by their pharmaceutical names, and by their trade name if relevant.
• Results: The Results section should briefly present the experimental data in text, tables or figures. Tables and figures should not be described extensively in the text. Support all statements about findings with data displays included in brackets after each claim; avoid “Figure X shows” statements.
• Discussion: The Discussion should focus on the interpretation and the significance of the findings with concise objective comments that describe their relation to other work in the area. It should not repeat information found in the results. The final paragraph should highlight the main conclusion and describe the direction that future research should take.
• Results and Discussion may also be combined into one section.

Review Article—maximum word count: 5,000

Review Articles are overviews of specific topics in microbial ecology, typically making unique connections between concepts and suggesting promising directions for future research. Review Articles may be solicited by the Reviews Editor and we also welcome independent proposals and submissions.

Each Review Article should include:

• Unstructured Abstract—maximum word count: 250
• Key words—maximum of 10 and minimum of 3
• References—maximum of 100
• Data displays— maximum of 6 tables or figures

The maximum word count of 5,000 applies to the main body of text (excluding tables, figures, and references). Submissions may contain an introduction and topic-specific sections with custom section headers.

Brief Communication—maximum word count: 1,000

Brief Communications are studies that fall short of the criteria for full research papers (e.g., exciting new results with a relatively simple experimental design and without confirmatory follow-up work expected for an Original Article). The maximum word count of 1,000 applies to the main body of text (excluding tables, figures, and references).
 

Each Brief Communication should include:

• Unstructured Abstract—maximum word count: 250
• Key words—maximum of 10 and minimum of 3
• References—maximum of 20
• Data displays— maximum of 2 tables or figures

The maximum word count of 1,000 applies to the main body of text (excluding tables, figures, and references). Submissions typically do not contain sections and section headers.

Comment—maximum word count: 1,200

Comments discuss issues of particular importance for the field of microbial ecology. Comments may include highlights of significant papers, in the current issue or elsewhere, or comprise poignant opinions, responses to previously published items, or other timely information or comment.

Comments may be either solicited by the editors or offered as an unsolicited submission. If authors wish to offer an unsolicited contribution, we ask them to first contact the editorial office with their request, including a short description of the content and implications of the comment.
 

Each Comment should include:

• Key words—maximum of 10 and minimum of 3
• References—maximum of 10
• Data displays— maximum of 3 tables or figures
• Abstract is not required for this article type

The maximum word count of 1,500 applies to the main body of text (excluding tables, figures, and references). Submissions typically do not contain sections and section headers.

Perspective—maximum word count: 3,000

A Perspective is a hybrid between a commentary and a review, providing an opinion-driven perspective on a particular research topic or field of interest to the journal’s readership. Authors should present a unique and provocative view that can be supported by data and literature with the goal of sparking debate and stimulating future research directions.

Perspective articles are by invitation by the Reviews Editor. Authors wishing to contribute a perspective article are welcome to submit an unsolicited request to the Reviews Editor with an outline of the intended article. If the subject and content are deemed of interest, an invitation letter will then be extended by the editorial office.
 

Each Perspective should include:

• Key words—maximum of 10 and minimum of 3
• References—maximum of 20
• Data displays— maximum of 3 tables or figures
• Abstract is not required for this article type

The maximum word count of 3,000 applies to the main body of text (excluding tables, figures, and references). Submissions typically do not contain sections and section headers.

Winogradsky Review—maximum word count: 7,000

Winogradsky Reviews are comprehensive analyses of specific topics in microbial ecology that are by invitation only, solicited by the Reviews Editor.
 

Each piece should include:

• Unstructured Abstract—maximum word count: 250
• Key words—maximum of 10 and minimum of 3
• References—maximum of 120
• Data displays— maximum of 6 tables or figures

The maximum word count of 7,000 applies to the main body of text (excluding tables, figures, and references). Submissions may contain an introduction and topic-specific sections with custom section headers.

Manuscript preparation instructions

General guidelines on preparing a manuscript for publication can be found on OUP’s Preparing and submitting your manuscript page. Specific instructions for The ISME Journal can be found below.

Pre-submission language editing

Authors may wish to use a language-editing service before submitting to ensure that editors and reviewers understand the manuscript. Our publisher, 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, through the OUP-Enago partner page.

Enago is an independent service provider, who will handle all aspects of this service, including payment. Authors are under no obligation to take up this offer. Language editing is optional and does not guarantee that the manuscript will be accepted. Edited manuscripts will undergo the regular review process of the Journal.

Pre-submission enquiries

Our academic Editors-in-Chief cannot offer a formal pre-submission enquiry process. However, the editor team shares the following information with authors who are considering publication in The ISME Journal.

When contemplating submission to The ISME Journal one should consider:

• Is the research novel and does it represent a major advance for microbial ecology?
• Does the work fit within the ecology-focused scope of our journal? 
• Has the research been conducted with state-of-the-art approaches? 

If the answer to these questions is yes, the study may well be appropriate for The ISME Journal, regardless of the system being studied.

Cover letter

Authors should provide a cover letter that includes the affiliation and contact information for the corresponding author. Authors should briefly discuss the importance of the work and explain why it is considered appropriate for the diverse readership of the journal. The cover letter should confirm the material is original research, has not been previously published and has not been submitted for publication elsewhere while under consideration. If the manuscript has been previously considered for publication in another journal, please include the previous reviewer comments and author rebuttal, to help expedite the decision by the Editorial team. The cover letter should also include a Competing Interest/Conflict of Interest statement.

Title page

Please include the following:

• Title of the paper: brief, informative, of 150 characters or less (including spaces). Good titles should concisely state the main discovery of the research without emphasizing methodology
• A short title of the paper of 40 characters or less (including spaces), to be used as a running head
• All full author names and affiliations
• Mailing address and email address of one corresponding author

Abstracts

Text abstracts must be written in English and should be designed to summarise the essential features of the paper in a logical and concise sequence. Abstracts should be unstructured, have a maximum length of 250 words and must not contain reference citations or abbreviations. They are required for all article types except for Comments and Perspectives.

Graphical abstracts and featured images

Authors of all article types may submit either a graphical abstract or featured image, in addition to the text abstract. The graphical abstract or featured image should clearly summarize the focus and findings of the article and will be published as part of the article online and in the PDF. The graphical abstract or featured image should be submitted for peer review as a separate file, selecting the appropriate file-type designation in the journal’s online submission system. The file should be clearly named, e.g. graphical_abstract.tiff or featured_image.tiff. See this page for guidance on appropriate file format and resolution for graphics. Colour graphical abstracts or featured images are encouraged. Textual statements should be kept to a minimum.

In the absence of a graphical abstract or featured image file, Figure 1 of the manuscript will be used alongside the paper by default.

Acknowledgments

Acknowledgments should be clearly labelled and included under a separate subheading at the end of the manuscript. These should be brief, and should include sources of support including sponsorship (e.g., university, charity, commercial organisation) and sources of material (e.g. novel drugs) not available commercially. Land acknowledgments relevant to samples analyzed in the study may be included here if appropriate. Authors should use this section to acknowledge field stations, marine laboratories, or other facilities that supported the work, as appropriate.

Study funding

Authors must fully declare all funding information relevant to the study, including specific grant numbers, under a separate subheading on the title page. If the funder is listed in the Crossref funder registry, the funder name should appear exactly as it appears in that database. Where grants were received by specific members of the author group, they should be identified by initial.

Style

The journal follows Oxford SciMed style. Please refer to these requirements when preparing the manuscript. More information on the style guide is available here. UK spelling and Oxford commas should be used throughout, except in quotations and in references.

Abbreviations

Please define nonstandard abbreviations at the first occurrence and then place the abbreviation in parentheses after the full item. Very common abbreviations need not be defined (e.g., PCR, RNA). Other common abbreviations include: gram g; litre l; milligram mg; kilogram kg; kilojoule kJ; megajoule MJ; weight wt; seconds s; minutes min; hours h. Do not add “s” for plural units. Terms used less than three times should not be abbreviated.

Statistical methods: For normally distributed data, mean (SD) is the preferred summary statistic. Relative risks should be expressed as odds ratios with 95% confidence interval. To compare two methods for measuring a variable the method of Bland & Altman (1986, Lancet 1, 307–310) should be used; for this, calculation of a p value only is not appropriate.

Units: Use metric units (SI units) as fully as possible. Preferably give measurements of energy in kiloJoules or megaJoules with kilocalories in parentheses (1 kcal = 4.186kJ). Use % throughout.

Native language author names

If the paper is published, the author name(s) will be displayed online in Latin-alphabet characters as provided to us in the manuscript. If authors wish for an alternative name also to be displayed (e.g., Chinese-character versions, other names used), please include that name in parentheses, immediately after the Latin-character name in the manuscript. Note that alternatives names will be presented as supplied on our website and in the article PDF, but may not be presented in other locations where the published article appears, such as Pubmed. 

Tables

Tables should only be used to present essential data; they should not duplicate what is written in the text. Authors must number all tables (e.g., Table 1, Table 2, Table 3) and reference them within the text. Tables should be supplied in an editable format (e.g., Microsoft Word), and not embedded as an image file. Authors must place all tables at the end of the main text. Avoid excessive formatting such as the use of colour and shading, which are not replicated in the published web version, and the use of tabbed spacing to indicate alignment. Ensure that any formatting or superscript symbols such as asterisks are explained in the table footnote. Provide units in column or row headers rather than in the table body. Like data should read down (not across) and tables should not be included within figures.

Figures

Figures should be submitted in one of the following file formats: .jpeg, .jpg, .png, .tiff, .pdf, or .eps. Images prepared as .bmp, .gif, or .doc/.docx files will not be accepted. Authors must include figure titles, legends, and captions within the manuscript file; they should not be included in the image files.

Figure files should be named simply to match their citation (e.g., fig1.tiff, fig2.eps). Authors must submit each figure as a single individual image file. Submit all panels of a multi-panel figure as one single figure file. Each panel should be labelled with a single capital letter (e.g., A, B, C, D – no brackets or periods) in the upper-left corner of each panel. Please also ensure that authors have permission to re-use or adapt any third-party image materials.

Images of maps, charts, graphs, shapes, and diagrams are best rendered digitally as geometric forms called vector graphics. Vector images use mathematical relationships between points and the lines connecting them to describe an image. Because these file types do not use pixels, resolution does not apply to vector images. Save vector images as .eps or .pdf files and embed the fonts.

Images of photographs, paintings, or scans can be provided as raster images. Raster images should be saved as uncompressed .tiff files to avoid quality loss. Both .jpg and .png file formats are acceptable for raster images but may result in a lower resolution. 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 colour half-tones: 300dpi
• Minimum resolution for grayscale half-tones: 600dpi
• Minimum resolution for combination half-tones and line art: 600-900dpi
• Minimum resolution for monochrome line art (complex or finely drawn): 1200dpi

Graphs, Histograms and Statistics: Plotting individual data points is preferred to just showing means, especially where N<10. If error bars are shown, they must be described in the figure legend. Axes on graphs should extend to zero, except for log axes. Statistical analyses (including error bars and p values) should only be shown for independently repeated experiments and must not be shown for replicates of a single experiment. The number of times an experiment was repeated (N) must be stated in the legend.

Please also consider accessibility when designing each figure, so that all images can be easily understood by colour-blind and visually impaired readers. Guidelines for preparing different image-types, including recommendations for colour palettes, colour contrast, image layout, and text accessibility.

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. 

LaTeX

Information on LaTeX files and formatting is available. For authors preparing their manuscripts using LaTeX, Overleaf RASTI LaTeX class files are available; these simulate the appearance of the journal page. Authors are encouraged to use these, although papers prepared using other class files can also be accepted.

References

Authors may format references in any readable style at submission, though if an author/date system is used then this may be queried by the production team for a resupply. Authors are responsible for the accuracy of reference information.

• Reference style: see New Hart’s Rules/Oxford SciMed numbered references
• References are listed in numerical order.
• Journal article: Kennedy T, Jones R. Effect of obesity on esophageal transit. Am J Surg 1985;149:177–81.
  • Please include the full DOI link where available.
• Book: Long HC, Blatt MA, Higgins MC et al. Medical Decision Making. Boston: Butterworth-Heinemann, 1997.
• Book chapter:  Manners T, Jones R, Riley M. Relationship of overweight to haitus hernia and reflux oesophagitis. In: Newman W (ed.), The Obesity Conundrum. Amsterdam: Elsevier Science, 1997, 352–74.
• Websites: Public Health Laboratory Service. Antimicrobial Resistance in 2000: England and Wales. http://www.hpa.org.uk./infections/topics_az/antimicrobial_resistance/amr.pdf (7 January 2004, date last accessed).

When there are 4 or more authors, list the first author name followed by et al.

• Page spans are elided (e.g., 213-5 and 137-87, 1185-2042).
• Latin phrase ibid is discouraged
• In-text citations: numbers in square brackets before punctuation [1, 3–5].

Supplementary material

Authors must submit supplementary data or supplementary material at the same time as the main manuscript. Supplementary material should enhance the written article without being necessary to understand it and must be cited in the text of the main manuscript.

• Supplementary material will be available online only and will not be copyedited or typeset.
• 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.
• Supplementary items should be submitted as clearly-labeled files that are separate from the main manuscript file(s).
  • Documentation and online appendices should be submitted in PDF file format.
  • Data files should be submitted in a .zip file format.
• Supplementary material may be hosted on OUP’s website or at one of our preferred partner sites, such as Dryad. Material hosted elsewhere (e.g. the author’s personal or institutional website, Google Docs, YouTube) is not allowed as links may expire.

When submitting Supplementary Information, authors are required to include a text summary (no more than 50 words) to describe the contents of each file and identify the types of files (file formats) submitted.

Open Science Badges

The ISME Journal supports Open Science Badges to acknowledge open science practices. These badges are offered as incentives to share data and materials and preregister research, and signal to the reader that the content has been made available in a persistent location. These badges will feature in the published article. When submitting a manuscript, authors should indicate the desired badge, and include a completed Open Science Badge application form and eligibility will be confirmed upon acceptance.

The four badges are as follows:

• Open Materials Badge: This will be granted to authors who deposit research materials needed to reproduce the reported procedure and analysis in an Open Access repository; for example, the Open Science Framework (for other repositories please consult the Registry of Research Data Repositories). Open materials criteria can be found here, and a link should be given in the submitted paper with a link to the deposited materials.
• Open Data Badge: This will be awarded to authors who deposit their data in an Open Access repository (either an entire dataset or part of it, or a transformed dataset, as long as an independent researcher can reproduce the reported results). Criteria for Open Data Badges can be found here, and a link to the deposited data should be included in the paper.
• Preregistered Badge: This is awarded for having a preregistered design. A preregistered design includes: (1) Description of the research design and study materials including planned sample size, (2) Description of motivating research question or hypothesis, (3) Description of the outcome variable(s), and (4) Description of the predictor variables including controls, covariates, independent variables (conditions). When possible, the study materials themselves are included in the preregistration. More information on Preregistered Badges can be found here. 
• Preregistered Plus Analysis Plan Badge: This is awarded for having a preregistered research design (described above) and an analysis plan for the research and reporting results according to that plan. An analysis plan includes specification of the variables and the analyses that will be conducted. More information on Preregistered Plus Analysis Plan Badges can be found here.

Please note that for all four badges, manuscripts should contain a link to data, materials, or preregistered research in the Open Science Framework or other recognized repository.

Contact Us

For questions regarding submission and review, including appeals, individuals can reach the editorial office by email at [email protected].

After a paper has been sent to production, authors can contact [email protected] for questions regarding the production process or publication. Please see the Changes to Published Papers section if authors need to request a substantive correction to their published paper.