Researchers should conduct their research – from research proposal to publication – in line with best practices and codes of conduct of relevant professional bodies and/or national and international regulatory bodies.
Springer Nature is committed to upholding the integrity of the scientific record. As a member of the Committee on Publication Ethics (COPE), The ISME Journal abides by COPE’s principles on how to deal with potential acts of misconduct, which includes formal investigation of all perceived transgressions.
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Requirements for all categories of articles should conform to the “Uniform Requirements for Manuscripts Submitted to Biomedical Journals,” developed by the ICMJE (www.icmje.org).
The corresponding author should list all authors and their contributions to the work. Each author must have contributed sufficiently to the intellectual content of the submission. The corresponding author must confirm that he or she has had full access to the data in the study and final responsibility for the decision to submit for publication. To qualify as a contributing author, one must meet ALL of the following criteria:
- Conceived and/or designed the work that led to the submission, acquired data, and/or played an important role in interpreting the results.
- Drafted or revised the manuscript.
- Approved the final version.
- Agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
Contributions by individuals who made direct contributions to the work but do not meet all of the above criteria should be noted in the Acknowledgments section of the manuscript. Medical writers and industry employees can be contributors. Their roles, affiliations, and potential competing interests should be included in the author list or noted in the Acknowledgments and/or Contributors section concurrent with their contribution to the work submitted. Signed statements from any medical writers or editors declaring that they have given permission to be named as an author, as a contributor, or in the Acknowledgments section is also required. Failure to acknowledge these contributors can be considered inappropriate, which conflicts with the journal’s editorial policy.
The primary affiliation for each author should be the institution where the majority of their work was done. If an author has subsequently moved, the current address may also be stated.
Changes to authorship
It is the corresponding author’s responsibility to ensure that the author list is correct, both in the manuscript file uploaded and the online submission form. Any changes to an author list, including the removal or addition of any authors, between initial submission and acceptance will require written agreement from all authors should the manuscript be considered for publication. New authors must also confirm that they fully comply with the journal's authorship requirements.
Changes to authorship (addition or removal) will not be allowed once the manuscript has been accepted for publication.
Correspondence with the Journal
The corresponding author is solely responsible for communicating with the journal and with managing communication between co-authors. It is this author's responsibility to inform all co-authors of any matters arising and to ensure such matters are dealt with promptly. Before submission, the corresponding author ensures that all authors are included in the author list, its order agreed upon by all authors, and that all are aware that the manuscript was submitted. After acceptance for publication, proofs are e-mailed to this corresponding author who should circulate the proof to all co-authors and coordinate corrections among them. The corresponding author is responsible for the accuracy of all content in the proof, in particular that names of co-authors are present and correctly spelled, and that addresses and affiliations are current.
Anonymity and Confidentiality
Editors, authors and reviewers are required to keep confidential all details of the editorial and peer review process on submitted manuscripts. Unless otherwise declared as a part of open peer review, the peer review process is confidential and conducted anonymously. All details about submitted manuscripts are kept confidential and no comments are issued to outside parties or organizations about manuscripts under consideration or if they are rejected. Editors are restricted to making public comments on a published article’s content and their evaluation.
Upon accepting an invitation to evaluate a manuscript, reviewers must keep the manuscript and associated data confidential, and not redistribute them without the journal’s permission. If a reviewer asks a colleague to assist in assessing a manuscript, confidentiality must be ensured and their names must be provided to the journal with the final report.
We ask reviewers not to identify themselves to authors without the editor's knowledge. If they wish to reveal their identities while the manuscript is under consideration, this should be done via the editor; if this is not practicable, we ask authors to inform the editor as soon as possible after the reviewer has revealed their identity. Our own policy is to neither confirm nor deny any speculation about reviewers' identities, and we encourage reviewers to adopt a similar policy.
We deplore any attempt by authors to confront reviewers or try to determine their identities. Reviewers should be aware that it is our policy to keep their names confidential and that we do our utmost to ensure this confidentiality. We cannot, however, guarantee to maintain this confidentiality in the face of a successful legal action to disclose identity.
Regardless of whether a submitted manuscript is eventually published, correspondence with the journal, referees’ reports, and other confidential material must not be published, disclosed, or otherwise publicised without prior written consent.
Communication with the Media
Material submitted must not be discussed with the media. We reserve the right to halt the consideration or publication of a paper if this condition is broken. If a paper is particularly newsworthy, the press release will be sent to our list of journalists in advance of publication with an embargo that forbids any coverage of the manuscript, or the findings of the manuscript, until the time and date clearly stated. Authors whose papers are scheduled for publication may also arrange their own publicity (for instance through their institution’s press offices), but they must strictly adhere to our press embargo and are advised to coordinate their own publicity with our press office.
Pre- and Post-Submissions
Authors are welcome to post pre-submission versions or the original submitted version of the manuscript on a personal blog, a collaborative wiki or a recognized preprint server (such as ArXiv or BioRXiv) at any time (but not subsequent pre-accept versions that evolve following peer review).
For subscribed content, the accepted version of the manuscript, following the review process, may only be posted 6 months after the paper is published in a Springer Nature journal. A publication reference and URL to the published version on the journal website must be provided on the first page of the postprint. The published version — copyedited and in the individual Springer Nature journal format — may not be posted on any website or preprint server.
For open access content published under a creative commons license, authors can replace the submitted version with the final published version at publication as long as a publication reference and URL to the published version on the journal website are provided
If a table or figure has been published before, the authors must obtain written permission to reproduce the material in both print and electronic formats from the copyright owner and submit it with the manuscript. This follows for illustrations and other materials taken from previously published works not in the public domain. The original source should be cited in the figure caption or table footnote. Permission to reproduce material can usually be obtained through the Copyright Clearance Center.
In the interests of transparency and to help readers form their own judgments of potential bias, authors must declare whether or not there are any competing financial interests in relation to the work described. The corresponding author is responsible for submitting a competing financial interests statement on behalf of all authors of the paper. This statement must be included on the title title page, as well as within the article before the References section listed under 'Competing Interests'.
In cases where the authors declare a competing financial interest, a statement to that effect is published as part of the article. If no such conflict exists, the statement will simply read that the authors have nothing to disclose.
For the purposes of this statement, competing interests are defined as those of a financial nature that, through their potential influence on behaviour or content, or from perception of such potential influences, could undermine the objectivity, integrity or perceived value of a publication. They can include any of the following:
- Funding: Research support (including salaries, equipment, supplies, reimbursement for attending symposia, and other expenses) by organizations that may gain or lose financially through this publication. The role of the funding body in the design of the study, collection and analysis of data and decision to publish should be stated.
- Employment: Recent (while engaged in the research project), present or anticipated employment by any organization that may gain or lose financially through this publication. This includes positions on an advisory board, board of directors, or other type of management relationship.
- Personal financial interests: Stocks or shares in companies that may gain or lose financially through publication; consultation fees or other forms of remuneration from organisations that may gain or lose financially.
- Patents: Holding, or currently applying for, patents, relating to the content of a manuscript; receiving reimbursement, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript.
It is difficult to specify a threshold at which a financial interest becomes significant, but note that many US universities require faculty members to disclose interests exceeding $10,000 or 5% equity in a company. Any such figure is arbitrary, so we offer as one possible practical alternative guideline: "Declare all interests that could embarrass you were they to become publicly known after your work was published." We do not consider diversified mutual funds or investment trusts to constitute a competing financial interest.
The statement included in the submission must contain an explicit and unambiguous description of any potential competing interests, or lack thereof, for any of the authors as it relates to the subject of the report. Examples include:
- Competing Interests
The authors declare no competing financial interests
- Competing Interests
Dr Caron's work has been funded by the NIH. He has received compensation as a member of the scientific advisory board of Acadia Pharmaceutical and owns stock in the company. He also has consulted for Lundbeck and received compensation. Dr Rothman and Dr Jensen declare no potential competing interests.
Neither the precise amount received from each entity nor the aggregate income from these sources needs to be provided.
Non-financial interests that authors may like to disclose include:
- a close relationship with, or a strong antipathy to, a person whose interests may be affected by publication of the article,
- an academic link or rivalry with someone whose interests may be affected by publication of the article,
- membership in a political party or special interest group whose interests may be affected by publication of the article, or
- a deep personal or religious conviction that may have affected what the author wrote and that readers should be aware of when reading the article.
Studies involving animals and other human subjects
Research involving human subjects, human material, or human data must have been performed in accordance with the Declaration of Helsinki and must have been approved by an appropriate ethics committee. A statement detailing this, including the name of the ethics committee and the reference number where appropriate, along with a statement confirming that informed consent was obtained from all subjects, must appear in all manuscripts reporting such research.
For primary research manuscripts reporting experiments on live vertebrates and/or higher invertebrates, the corresponding author must confirm that all experiments were performed in accordance with relevant guidelines and regulations. The manuscript must include in the Supplementary Information (methods) section (or, if brief, within of the print/online article at an appropriate place), a statement identifying the institutional and/or licensing committee approving the experiments, including any relevant details regarding animal welfare, patient anonymity, drug side effects and informed consent. Sex and other characteristics of animals that may influence results must be described. Details of housing and husbandry must be included where they are likely to influence experimental results. The ISME Journal recommends following the ARRIVE reporting guidelines when documenting animal studies.
All clinical trials must be registered in a public registry prior to submission and the trial registry number must be included in the manuscript and provided on submission.. The journal follows the trials registration policy of the ICMJE (www.icmje.org) and considers only trials that have been appropriately registered before submission, regardless of when the trial closed to enrolment. Acceptable registries must meet the following ICMJE requirements:
- be publicly available, searchable, and open to all prospective registrants
- have a validation mechanism for registration data
- be managed by a not-for-profit organization
Examples of registries that meet these criteria include:
- ClinicalTrials.gov the registry sponsored by the United States National Library of Medicine
- the International Standard Randomized Controlled Trial Number Registry
- the Cochrane Renal Group Registry
- the European Clinical Trials Database
Randomised Controlled Trials (RCTs) must adhere to the CONSORT statement, (CONsolidated Standards Of Reporting Trials) and submissions must be accompanied by a completed CONSORT checklist (uploaded as a related manuscript file). Further information can be found at www.consort-statement.org.
When publishing identifiable images from human research participants, authors must include a statement attesting that they have obtained informed consent for publication of the images. If the participant is deceased, consent must be sought from the next of kin of the participant. All reasonable measures must be taken to protect patient anonymity. Black bars over the eyes are not acceptable means of anonymization. In certain cases, the journal may insist upon obtaining evidence of informed consent from authors. Images without appropriate consent will be removed from publication.
Cell Line Authentication
If human cell lines are used, authors are strongly encouraged to include the following information in their manuscript:
- the source of the cell line, including when and from where it was obtained,
- whether the cell line has recently been authenticated and by what method, and
- whether the cell line has recently been tested for mycoplasma contamination.
Further information is available from the International Cell Line Authentication Committee (ICLAC). We recommend that authors check the NCBI database for misidentification and contamination of human cell lines.
The Editor may seek advice about submitted papers not only from technical reviewers but also on any aspect of a paper that raises concerns. These may include, for example, ethical issues or issues of data or materials access. Occasionally, concerns may also relate to the implications to society of publishing a paper, including threats to security. In such circumstances, advice will usually be sought simultaneously with the technical peer-review process. As in all publishing decisions, the ultimate decision whether to publish is the responsibility of the editor.
The ISME Journal requires authors of papers that are sent for external review to include in their manuscripts relevant details about several elements of experimental and analytical design. This initiative aims to improve the transparency of reporting and the reproducibility of published results, focusing on elements of methodological information that are frequently poorly reported. Authors being asked to resubmit a manuscript will be asked to confirm that these elements are included by filling out a checklist that will be made available to the editor and reviewers.
Data Availability Statement and Policy
An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. The ISME Journal adheres to Springer Nature’s Data Policy Type 3. This means that a submission to the journal implies that materials described in the manuscript, including all relevant raw data, will be freely available to any researcher wishing to use them for non-commercial purposes, without breaching participant confidentiality.
It also means that a Data Availability Statement (see here for more details) must be included as part of your manuscript.
Sequences, Structures and “Omics”
Papers reporting protein or DNA sequences and molecular structures will not be accepted without an accession number to Genbank, EMBL, DDBJ, Uniprot, ProteinDataBank, or other publicly available database in general use in the field that gives free access to researchers from the date of publication.
Authors of papers describing structures of biological macromolecules must provide experimental data upon the request of Editor if they are not already freely accessible in a publicly available database such as ProteinDataBank, Biological Magnetic Resonance Databank, or Nucleic Acid Database.
Springer Nature takes seriously all allegations of potential misconduct. As a member of the Committee on Publication Ethics (COPE), The ISME Journal will follow the COPE guidelines outlining how to deal with cases of suspected misconduct. As part of the investigation, the journal may opt to do one or more of the following:
- suspend review or publication of a paper until the issue has been investigated and resolved;
- request additional information from the author, including original data or images or ethics committee or IRB approval;
- make inquiries of other titles believed to be affected;
- forward concerns to the author’s employer or person responsible for research governance at the author’s institution;
- refer the matter to other authorities or regulatory bodies (for example, the Office of Research Integrity in the US or the General Medical Council in the UK); or
- submit the case to COPE in an anonymized form for additional guidance on resolution.
Please note that, in keeping with the journal’s policy of the confidentiality of peer review, if sharing of information with third parties is necessary, disclosure will be made to only those Editors who the Editor believes may have information that is pertinent to the case, and the amount of information will be limited to the minimum required.
Papers must be original and not published or submitted for publication elsewhere. This rule also applies to non-English language publications..
Springer Nature allows and encourages prior publication on recognized community preprint servers for review by other scientists before formal submission to a journal. The details of the preprint server concerned and any accession numbers should be included in the cover letter accompanying manuscript submission. This policy does not extend to preprints available to the media or that are otherwise publicized outside the scientific community before or during the submission and consideration process.
Springer Nature also allows publication of meeting abstracts before the full contribution is submitted. Such abstracts should be included with the journal submission and referred to in the cover letter accompanying the manuscript. Again this policy does not extend to meeting abstracts and reports available to the media or which are otherwise publicised outside the scientific community during the submission and consideration process.
Plagiarism is when an author attempts to pass off someone else's work as his or her own. Duplicate publication, sometimes called self-plagiarism, occurs when an author reuses substantial parts of his or her own published work without providing the appropriate references. This can range from getting an identical paper published in multiple journals, to 'salami-slicing', where authors add small amounts of new data to a previous paper.
Plagiarism can be said to have clearly occurred when large chunks of text have been cut-and-pasted. Minor plagiarism without dishonest intent is relatively frequent, for example, when an author reuses parts of an introduction from an earlier paper. Journal editors judge any case of which they become aware (either by their own knowledge of and reading about the literature, or when alerted by referees) on its own merits.
Springer Nature is a member of Similarity Check (formerly CrossCheck), a multi-publisher initiative used to screen published and submitted content for originality. The ISME Journal uses Similarity Check to detect instances of overlapping and similar text in submitted manuscripts. To find out more about visit the Similarity Check website.
If a case of plagiarism comes to light after a paper is published, the Journal will conduct a preliminary investigation, utilising the guidelines of the Committee on Publication Ethics. If plagiarism is proven, the Journal will contact the author's institute and funding agencies as appropriate. The paper containing the plagiarism may also be formally retracted or subject to correction.
Data Fabrication & Falsification
Falsification is the practice of altering research data with the intention of giving a false impression. This includes, but is not limited to, manipulating images, removing outliers or “inconvenient” results, or changing, adding or omitting data points. Fabrication is the practice of inventing data or results and recording and/or reporting them in the research record. Data falsification and fabrication call into question the integrity and credibility of data and the data record, and as such, they are among the most serious issues in scientific ethics.
Some manipulation of images is allowed to improve them for readability. Proper technical manipulation includes adjusting the contrast and/or brightness or colour balance if it is applied to the complete digital image (not parts of the image). The author should notify the Editor in the cover letter of any technical manipulation. Improper technical manipulation refers to obscuring, enhancing, deleting and/or introducing new elements into an image. See Image Integrity & Standards below for more details.
Image Integrity and Standards
Images submitted with a manuscript for review should be minimally processed (for instance, to add arrows to a micrograph). Authors should retain their unprocessed data and metadata files, as editors may request them to aid in manuscript evaluation. If unprocessed data is unavailable, manuscript evaluation may be stalled until the issue is resolved.
A certain degree of image processing is acceptable for publication, but the final image must correctly represent the original data and conform to community standards. The guidelines below will aid in accurate data presentation at the image processing level:
- Authors should list all image acquisition tools and image processing software packages used. Authors should document key image-gathering settings and processing manipulations in the Methods section.
- Images gathered at different times or from different locations should not be combined into a single image, unless it is stated that the resultant image is a product of time-averaged data or a time-lapse sequence. If juxtaposing images is essential, the borders should be clearly demarcated in the figure and described in the legend.
- Touch-up tools, such as cloning and healing tools in Photoshop, or any feature that deliberately obscures manipulations, is to be avoided.
- Processing (such as changing brightness and contrast) is appropriate only when it is applied equally across the entire image and is applied equally to controls. Contrast should not be adjusted so that data disappear. Excessive manipulations, such as processing to emphasize one region in the image at the expense of others (for example, through the use of a biased choice of threshold settings), is inappropriate, as is emphasizing experimental data relative to the control.
For gels and blots, positive and negative controls, as well as molecular size markers, should be included on each gel and blot – either in the main figure or an expanded data supplementary figure. The display of cropped gels and blots in the main paper is encouraged if it improves the clarity and conciseness of the presentation. In such cases, the cropping must be mentioned in the figure legend.
- Quantitative comparisons between samples on different gels/blots are discouraged; if this is unavoidable, the figure legend must state that the samples derive from the same experiment and that gels/blots were processed in parallel. Vertically sliced gels that juxtapose lanes that were not contiguous in the experiment must have a clear separation or a black line delineating the boundary between the gels. Loading controls (e.g. GAPDH, actin) must be run on the same blot. Sample processing controls run on different gels must be identified as such, and distinctly from loading controls
- Cropped gels in the paper must retain important bands.
- Cropped blots in the body of the paper should retain at least six band widths above and below the band.
- High-contrast gels and blots are discouraged, as overexposure may mask additional bands. Authors should strive for exposures with gray backgrounds. Immunoblots should be surrounded by a black line to indicate the borders of the blot, if the background is faint.
- For quantitative comparisons, appropriate reagents, controls and imaging methods with linear signal ranges should be used.
Microscopy adjustments should be applied to the entire image. Threshold manipulation, expansion or contraction of signal ranges and the altering of high signals should be avoided. If ‘pseudo-colouring’ and nonlinear adjustment (for example ‘gamma changes’) are used, this must be disclosed. Adjustments of individual colour channels are sometimes necessary on ‘merged’ images, but this should be noted in the figure legend.
We encourage inclusion of the following with the final revised version of the manuscript for publication:
- In the Methods section, specify the type of equipment (microscopes/objective lenses, cameras, detectors, filter model and batch number) and acquisition software used. Although we appreciate that there is some variation between instruments, equipment settings for critical measurements should also be listed.
- The display lookup table (LUT) and the quantitative map between the LUT and the bitmap should be provided, especially when rainbow pseudo-colour is used. It should be stated if the LUT is linear and covers the full range of the data.
- Processing software should be named and manipulations indicated (such as type of deconvolution, three-dimensional reconstructions, surface and volume rendering, 'gamma changes', filtering, thresholding and projection).
- Authors should state the measured resolution at which an image was acquired and any downstream processing or averaging that enhances the resolution of the image.
Correction and Retraction Process
Publishable amendments that affect the publication record and/or the scientific accuracy of published information will receive a DOI and be published in the journal. Five categories of amendments are relevant for peer-reviewed material – detailed below.
All five correction types are bi-directionally linked to the original published paper.
Erratum or Publisher Correction. Notification of an important error made by the journal that affects the publication record or the scientific integrity of the paper, or the reputation of the authors or of the journal.
Corrigendum or Author Correction. Notification of an important error made by the author(s) that affects the publication record or the scientific integrity of the paper, or the reputation of the authors or the journal.
Retraction. Notification of invalid results that affect the reliability of a previously published article. The original article is marked as retracted but remains available to readers, and the retraction statement notifying readers of the invalidity of the published paper is bi-directionally linked to the original published paper.
Addendum. Notification of additional information about a paper. Addenda are published when the editors decide that the addendum is crucial to the reader's understanding of a significant part of the published contribution. Addenda include Editorial Expression of Concern, which is an editorial statement alerting our readership to serious concerns with the published paper. Editorial Expressions of Concern are typically updated with another amendment once further information is available.
Editor's Note. An editor's note is a statement from editors notifying readers of issues related to the published paper. It is an online update made only to the HTML version of record of the published article. Editor's notes are typically updated with another amendment once further information is available.
All correction requests should be submitted to the editorial office.
Decisions about corrections are made by the Editor (sometimes with peer-reviewers' advice) and this sometimes involves author consultation. Requests to make corrections that do not affect the paper in a significant way or impair the reader's understanding of the contribution (a spelling mistake or grammatical error, for example) are not considered.
In cases where co-authors disagree about a correction, the editors will take advice from independent peer-reviewers and impose the appropriate correction, noting the dissenting author(s) in the text of the published version.
If there is suspicion of misconduct, the journal will carry out an investigation following COPE guidelines. Following an investigation, if the allegation raises valid concerns, the author will be contacted and given an opportunity to address the issue. If misconduct is established beyond reasonable doubt, this may result in the Editor implementing one of the following measures:
- If the article is still under consideration, it may be rejected and returned to the author.
- If the article has already been published online, depending on the nature and severity of the infraction, either a correction will be published alongside the article or, in severe cases, complete retraction of the article will occur. The reason for the correction or retraction must be given.
- In either case, the author’s institution or funding agency may be informed.