Editorial Policy and Ethical Guidelines
As a member of the Committee on Publication Ethics (COPE), ASM adheres to its Best Practice Guidelines and expects authors to observe the high standards of publication ethics set out by COPE. ASM requirements for submitted manuscripts are consistent with the Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals, as last updated by the International Committee of Medical Journal Editors in December 2014.
Authors are expected to adhere to the highest ethical standards. The following sections of these Instructions include detailed information about ASM’s ethical standards. Failure to comply with the policies described in these Instructions may result in a letter of reprimand, a suspension of publishing privileges in ASM journals, and/or notification of the authors’ institutions. Authors employed by companies whose policies do not permit them to comply with ASM policies may be sanctioned as individuals and/or ASM may refuse to consider manuscripts having authors from such companies.
For additional information regarding ASM's ethical standards and publishing ethics in general, please visit ASM Journals' Ethics Portal. Included in the portal are ASM's policies and procedures, an author checklist, ethical guidelines and primary sources on topics in publishing ethics.
Use of Microbiological Information
The Council on Microbial Sciences (COMS) of the American Society for Microbiology affirms the long-standing position of the Society that microbiologists will work for the proper and beneficent application of science and will call to the attention of the public or the appropriate authorities misuses of microbiology or of information derived from microbiology. ASM members are obligated to discourage any use of microbiology contrary to the welfare of humankind, including the use of microbes as biological weapons. Bioterrorism violates the fundamental principles expressed in the Code of Ethics of the Society and is abhorrent to ASM and its members.
ASM recognizes that there are valid concerns regarding the publication of information in scientific journals that could be put to inappropriate use as described in the COMS resolution mentioned above. Members of the ASM Journals Board will evaluate the rare manuscript that might raise such issues during the review process. However, as indicated elsewhere in these Instructions, primary-research articles must contain sufficient detail, and material/information must be made available, to permit the work to be repeated by others. Supply of materials should be in accordance with laws and regulations governing the shipment, transfer, possession, and use of biological materials and must be for legitimate, bona fide research needs. We ask that authors pay particular attention to the NSAR Select Agent/Toxin list on the CDC website and the U.S. Government Policy for Oversight of Life Sciences Dual Use Research of Concern (March 2012).
Use of Human Subjects or Animals in Research
Authors of manuscripts describing research involving human subjects or animal experimentation must obtain review and approval or review and waiver from their Institutional Review Board (IRB) or Institutional Animal Care and Use Committee (IACUC), as appropriate, prior to manuscript submission. Authors of manuscripts that describe multisite research must obtain approval from each institution’s IRB or IACUC, as appropriate. Documentation of IRB or IACUC status must be made available upon request. In the event that institutional review boards or committees do not exist, the authors must ensure that their research is carried out in accordance with the Declaration of Helsinki, as revised in 2013, and/or the “International Guiding Principles for Biomedical Research Involving Animals,” as revised by the International Council for Laboratory Animal Science (ICLAS) and the Councils for International Organizations of Medical Sciences (CIOMS) in 2012. A statement of IRB or IACUC approval or waiver (and reason for waiver) or a statement of adherence to the Declaration of Helsinki and/or Guiding Principles must be included in the Materials and Methods section. The sex of research subjects and animals, and of materials derived directly from them (e.g., primary cell lines and clinical samples), should be included in the Materials and Methods section or Results section if these data are available.
Patient Identification
Informed consent is not needed if the patient cannot be identified from any material in a manuscript. In the absence of informed consent, identifying details, such as patient initials, specific dates, specific geographic exposures, or other identifying features (including body features in figures), can be omitted, but this must not alter the scientific meaning. Important information that is relevant to the scientific meaning should be stated so that the patient cannot be identified, e.g., by stating a season instead of the date or a region instead of a city. If a patient can be identified from the material in a manuscript, all efforts should be made to obtain informed consent to publish from patients or parents/legal guardians of minors. Informed consent requires that the patient have the opportunity to see the manuscript prior to submission if the data have not been de-identified. The written consent must state either that the patient has seen the complete manuscript or that the patient is declining to do so. Patient consent should be archived with the authors and be available upon request. A statement attesting the receipt and archiving of written patient consent should be included in the published article.
Publishing Ethics
Authorship. ASM journals follow the criteria for authorship as outlined in the International Committee of Medical Journal Editors (ICMJE) Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals (Defining the Role of Authors and Contributors). Briefly, an author is one who makes a substantial contribution to the design, execution, and/or analysis and interpretation of experiments in addition to drafting, revising, and/or approving the initial submission and any subsequent versions of the article. All authors of a manuscript must have agreed to its submission and are responsible for appropriate portions of its content. Submission of a paper before all coauthors have read and approved it is considered an ethical violation.
Author contribution statements. As explained in the ICMJE recommendations, all persons designated as authors should qualify for authorship, and all those who qualify should be listed. ASM encourages transparency in authorship by publishing author contribution statements. Authors are strongly encouraged to include such statements in the Acknowledgments section.
Corresponding author. The corresponding author takes primary responsibility for communicating with the journal and coauthors throughout the submission, peer review, and publication processes. The corresponding author is responsible for ensuring that all coauthors have read and approved submissions, including appropriate citations, acknowledgments, and byline order. Additionally, the corresponding author and the studies’ primary investigator(s), if different, are required to have examined the raw data represented in the manuscript, affirm that such representations accurately reflect the original data, and ensure that the original data are preserved and retrievable.
Consortium authorship. A study group, surveillance team, working group, consortium, or the like (e.g., the Active Bacterial Core Surveillance Team) may be listed as a coauthor in the byline if its contributing members satisfy the requirements for authorship and accountability as described in these Instructions. The names (and institutional affiliations, if desired) of the contributing members only may be given as a separate paragraph in the Acknowledgments section. If the contributing members of the group associated with the work do not fulfill the criteria of substantial contribution to and responsibility for the paper, the group may not be listed in the author byline. Instead, it and the names of its contributing members may be listed in the Acknowledgments section.
Professional writers. “Ghost authorship” is not permitted by ASM. Professional writers should be mentioned in the Acknowledgments section, rather than be included in the byline. To avoid perceived conflicts of interest, writer affiliations and specific contributions (e.g., writing assistance, technical editing, language editing, or proofreading) must be disclosed.
Nonauthor contributions. Contributions from individuals who do not meet the ICMJE criteria for authorship should be acknowledged in the Acknowledgments section. Those who provided assistance, e.g., supplied strains or reagents or critiqued the paper, should not be listed as authors. Acquisition of funding, data collection, or general supervision of the research group does not qualify a person or persons for authorship. As mentioned above, professional writers do not meet authorship criteria and should be mentioned in the Acknowledgments section. Specific contributions for each nonauthor contributor should be included.
Byline order and changes. All authors must agree to the order in which their names are listed in the byline. Statements regarding equal contributions by two or more authors (e.g., “C.J. and Y.S. contributed equally to . . .”) are permitted as footnotes to bylines and must be agreed to by all of the authors. Achange in authorship (order of listing, addition or deletion of a name, or corresponding author designation) after submission of the manuscript will be implemented only after receipt of signed statements of agreement from all parties involved.
Authorship disputes. Disputes about authorship may delay or prevent review and/or publication of the manuscript. Should the individuals involved be unable to reach an accord, review and/or publication of the manuscript can proceed only after the matter is investigated and resolved by the authors’ institution(s) and an official report provided to ASM. ASM does not itself investigate or attempt to resolve authorship disputes but will follow institutional recommendations, as appropriate.
ORCID. ASM Journals is a member of Open Researcher and Contributor ID (ORCID) and publishes author ORCID numbers in articles. ORCID is an open, nonprofit, community-driven effort to create and maintain a registry of unique researcher identifiers; it is a transparent method of linking research activities and output to these identifiers. In the eJournalPress (eJP) submission system, authors are encouraged to use or create an ORCID number, which can be linked to manuscripts and publications for which a researcher serves as an author. This can be helpful in distinguishing authors with common names. Additional information about ORCID is available on ORCID’s website.
Plagiarism. Misappropriating another person’s intellectual property constitutes plagiarism. This includes copying sentences or paragraphs verbatim (or almost verbatim) from someone else’s work, even if the original work is cited in the references. The NIH Office of Research Integrity publication “Avoiding Plagiarism, Self-Plagiarism, and Other Questionable Writing Practices: a Guide to Ethical Writing” can help authors identify questionable writing practices.
Plagiarism is not limited to the text; it can involve any part of the manuscript, including figures and tables, in which material is copied from another publication without permission and attribution. An author may not reuse his or her own previously published work without attribution; this is considered text recycling (also known as self-plagiarism).
ASM has incorporated plagiarism detection software into its journal-wide submission system in order to help editors verify the originality of submitted manuscripts. Selected manuscripts are scanned and compared with databases. If plagiarism is detected, COPE guidelines on plagiarism will be followed.
Image manipulation. Submitted figures must reflect original data. Please refer to the Image manipulation section in Illustrations and Tables for an overview of permissible manipulations, unacceptable adjustments, and required information to disclose in the figure legends of images.
ASM applies forensic imaging tools to screen selected manuscripts for inappropriate manipulation of figures. If unacknowledged and/or inappropriate image manipulations are detected, the matter will be referred to the journal’s ethics panel for consideration.
Fabrication, manipulation, and falsification of data. ASM encourages authors to consult COPE’s Code of Conduct and Best Practice Guidelines for Journal Editors. Fabrication, manipulation, and falsification of data constitute misconduct. As defined by the U.S. Department of Health and Human Services, fabrication is “making up data or results and recording or reporting them,” and falsification is “manipulating research materials, equipment, or processes, or changing or omitting data or results such that the research is not accurately represented in the research record” (42 Code of Federal Regulations, §93.103). All sources and methods used to obtain and analyze data, including any electronic preprocessing, should be fully disclosed; detailed explanations should be provided for any exclusions.
Primary publication. Manuscripts submitted to the journal must represent reports of original research, and the original data must be available for review by the editor if necessary. By submitting a manuscript to the journal, the authors guarantee that they have the authority to publish the work and that the manuscript, or one with substantially the same content, was not published previously, is not being considered or published elsewhere, and was not rejected on scientific grounds or on the basis of its general suitability for publication by another ASM journal, with the exception of mBio®. A rejection from mBio does not disqualify a manuscript from being newly submitted to another ASM journal (the rejection by mBio need not be mentioned in the cover letter). It is incumbent upon the author to acknowledge any prior publication, including his/her own articles, of the data contained in a manuscript submitted to an ASM journal. A copy of the relevant work should be submitted with the paper as supplemental material for review only. Whether the material constitutes the substance of a paper and therefore renders the manuscript unacceptable for publication is an editorial decision.
In the event that the authors’ previously published figures and/or data are included in a submitted manuscript, it is incumbent upon the corresponding author to (i) acknowledge the source of the duplication on the submission form; (ii) obtain permission from the original publisher (i.e., copyright owner); (iii) acknowledge the previous publication in the figure legend; and (iv) cite the original manuscript.
A paper is not acceptable for submission to an ASM journal if it, or its substance, has been made publicly available in the following:
- A serial, periodical, or book
- A conference report or symposium proceedings
- A technical bulletin or company white paper
- A public website (but see “Preprint policy,” below)
- Any other retrievable source
The following do not preclude submission to, or publication by, an ASM journal:
- Posting of a method/protocol on a public website
- Posting of a limited amount of original data on a personal/ university/corporate website or websites of small collaborative groups working on a problem
- Deposit of unpublished sequence data in a public database
- Preliminary disclosures of research findings as meeting posters, webcast as meeting presentations, or published in abstract form as adjuncts to a meeting, e.g., part of a program
- Posting of theses and dissertations on a personal/university-hosted website
Preprint policy. ASM Journals will consider for publication manuscripts that have been posted in a recognized preprint archive provided that upon acceptance of the manuscript for publication, the author is still able to agree to the terms of an Open Access license and pay the associated fee. It is the responsibility of authors to inform the journal at the time of submission if and where their article has been previously posted, and if the manuscript is accepted for publication in an ASM journal, authors are required to update the preprint with a citation to the final published article that includes the URL along with a link.
Conflict of Interest
All authors are expected to disclose, in the cover letter and in the appropriate field on the submission form, any commercial affiliations as well as consultancies, stock or equity interests, and patent-licensing arrangements that could be considered to pose a conflict of interest regarding the submitted manuscript. (Inclusion of a company name in the author address lines of the manuscript does not constitute disclosure.) Details of the disclosure to the editor will remain confidential. However, it is the responsibility of authors to provide, in the Acknowledgments section, a general statement disclosing financial or other relationships that are relevant to the study. Examples of potentially conflicting interests that should be disclosed include relationships that might detract from an author’s objectivity in presentation of study results and interests whose value would be enhanced by the results presented. All funding sources for the project, institutional and corporate, should be credited in the Acknowledgments section. In addition, if a manuscript concerns a commercial product, the manufacturer’s name must be indicated in the Materials and Methods section or elsewhere in the text, as appropriate, in an obvious manner.
Data and Materials
Availability of data and materials. By publishing in mSystems, the authors agree that, subject to requirements or limitations imposed by local and/or U.S. Government laws and regulations, any materials and data that are reasonably requested by others are available from a publicly accessible collection or will be made available in a timely fashion, at reasonable cost, and in limited quantities to members of the scientific community for noncommercial purposes. Similarly, the authors agree to make available computer programs and/or code, originating in the authors’ laboratory, that is the only means of confirming the conclusions reported in the article but that is not available commercially. The program(s) and suitable documentation regarding its (their) use may be provided by any of the following means: (i) as a program transmitted via the Internet, (ii) as an Internet server-based tool, or (iii) as a compiled or assembled form on a suitable medium. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner. ASM asks authors to assert this in a “Data availability” paragraph, which should appear at the end of the Materials and Methods section (or at the end of the text) of their submitted manuscript.
Therefore, a condition of publication in mSystems is that authors make data fully available and without restriction, except in rare circumstances. Data availability will be confirmed prior to publication and must be provided during the modification stage, if not before. Furthermore, data must be made available, upon request, for peer review. See Data Policy.
Data citation. To promote reproducibility, ASM expects researchers to identify and cite data sets and/or code used in their experiments and studies. These may be large or complex data sets that can include, but are not limited to, data from microarray, genomic, structural, proteomic, or video imaging analyses. Authors should cite both the data set repository and the published article in which the data set and/or code was originally described. Citations of data should be included in the reference list with persistent unique identifiers (e.g., active URLs, accession numbers, etc.). If computer code or software was created to generate results or interpret data, then a statement to that effect should be included in the “Data availability” paragraph. For cases in which the software is publicly available (e.g., FigTree to generate phylogenetic trees), the URL of the software informational page should be provided. It is preferred that authors use established, publicly available data type-specific repositories. If there is no appropriate repository available, general publicly available repositories should be used (e.g., Dryad, figshare, etc.). A list of public data repositories is available in the ASM Journals’ Ethics Portal Compendium of Resources. Examples of proper data citation are included in the “References” section of these Instructions to Authors.
Similarly, the authors agree to make available computer programs, originating in the authors’ laboratory, that are the only means of confirming the conclusions reported in the article but that are not available commercially. The program(s) and suitable documentation regarding its (their) use may be provided by any of the following means: (i) as a program transmitted via the Internet, (ii) as an Internet server-based tool, or (iii) as a compiled or assembled form on a suitable medium. It is expected that the material will be provided in a timely fashion and at reasonable cost to members of the scientific community for noncommercial purposes. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner.
Culture deposition. mSystems, expects authors to deposit strains used in therapeutic-activity assessments and studies of mechanisms of action, resistance, and cross-resistance in publicly accessible culture collections and to refer to the collections and strain numbers in the text. Since the authenticity of subcultures of culture collection specimens that are distributed by individuals cannot be ensured, authors should indicate laboratory strain designations and donor sources as well as original culture collection identification numbers.
Authentication of cell lines. Cell line misidentification or contamination can adversely impact the validity of research findings. Authors should describe the source along with the date and method used for authentication of any cell lines used in manuscripts submitted to this journal. Cell lines used less than 6 months after receipt from a cell bank that performs authentication do not require reauthentication, but the source and method of authentication should be reported in the Materials and Methods section.
Accessibility of mass spectrometry data. Proteomics, metabolomics, or imaging mass spectrometry and related data must be accessible through hyperlinks so that reviewers can rapidly assess accessibility. Currently accepted data repositories are MassIVE, which is a part of ProteomeXchange, at http://massive.ucsd.edu/ProteoSAFe/static/massive.jsp (proteomics), GNPS at http://gnps.ucsd.edu (metabolomics, natural products, and imaging mass spectrometry data), MetaboLights at https://www.ebi.ac.uk/metabolights/, and OpenMSI at https://openmsi.nersc.gov/openmsi/client/ (imaging mass spectrometry data). For reference spectra, we encourage deposition into GNPS (http://gnps.ucsd.edu), MassBank of Japan at http://www.massbank.jp/?lang=en, or MassBank of North America at http://mona.fiehnlab.ucdavis.edu. Other available data repositories may be acceptable, and we encourage database repository administrators or authors of papers to contact the journal for additional appropriate databases that should be listed. Only databases that make all the data accessible via hyperlinks and are downloadable, including reference libraries, are considered acceptable repositories.
Nucleotide and amino acid sequences. Newly determined nucleotide and/or amino acid sequence data must be deposited and GenBank/ENA/DDBJ accession numbers must be included in the manuscript no later than the modification stage of the review process. It is expected that the sequence data will be released to the public no later than the publication (online posting) date of the article. As part of the publication process, accession numbers will be linked from the article to GenBank, which will prompt the release of any previously unreleased sequences. Authors are encouraged to comply with community metadata standards, such as the “Minimal Information about any (X) Sequence” (MIxS) checklist (http://gensc.org/projects/mixs-gsc-project/), when submitting to Gen- Bank, ENA, or DDBJ.
The accession numbers should be included in a separate paragraph with the lead-in "Accession number(s)" at the end of the Materials and Methods section (for Research Articles) or at the end of the text (for other formats). If conclusions in a manuscript are based on the analysis of sequences and a GenBank/ENA/DDBJ accession number is not provided at the time of the review, authors should provide the annotated sequence data as supplemental material for review only.
It is expected that, when previously published sequence accession numbers are cited in a manuscript, the original published article(s), as well as a citation of the database where the accession number is deposited, will be included in the References section. Authors are also expected to do elementary searches and comparisons of nucleotide and amino acid sequences against the sequences in standard databases (e.g., GenBank) immediately before manuscripts are submitted and again at the proof stage.
Analyses should specify the database, and the date of each analysis should be indicated as, e.g., 6 January 2018. If relevant, the version of the software used should be specified.
See “Presentation of Nucleic Acid Sequences” for nucleic acid sequence formatting instructions. Links to the databases mentioned above are found here: DNA Data Bank of Japan (DDBJ); European Nucleotide Archive (ENA); and GenBank, National Center for Biotechnology Information.
Proper use of locus tags as systematic identifiers for genes. To comply with recommendations from the International Nucleotide Sequence Database (INSD) Collaborators and to avoid conflicts in gene identification, researchers should implement the following two fundamental guidelines as standards for utilization of locus tags in genome analysis, annotation, submission, reporting, and publication. (i) Locus tag prefixes are systematic gene identifiers for all of the replicons of a genome and as such should be associated with a single genome project submission. (ii) New genome projects must be registered with INSD, and new locus tag prefixes must be assigned in cooperation with INSD to ensure that they conform to the agreed-upon criteria.
Structural determinations. Coordinates for new structures of macromolecules must be deposited in the Protein Data Bank and assigned identification codes must be included in the manuscript no later than the modification stage of the review process. It is expected that the coordinates will be released to the public no later than the publication (online posting) date of the article.
Authors are encouraged to send coordinates with their original submission so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph with the lead-in "Accession number(s)" at the end of the Materials and Methods section for Research Articles and at the end of the text for other formats.
The URLs for coordinate deposition are http://deposit-1.wwpdb.org/deposition/ and http://www.rcsb.org/pdb/home/home.do#Category-deposit.
Gene expression data. The entire set of supporting gene expression data, as well as genomic or metagenomic data sets, must be deposited in the appropriate public database (e.g., GEO, ArrayExpress, or CIBEX) and the assigned accession number(s) must be included in the manuscript no later than the modification stage of the review process. It is expected that the data will be released to the public no later than the publication (online posting) date of the article.
Authors are encouraged to send the relevant data with their original submission so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph with the lead-in "Accession number(s)" at the end of the Materials and Methods section for Research Articles and at the end of the text for other formats.
Links to the databases mentioned above are found here: Gene Expression Omnibus (GEO); ArrayExpress; and Center for Information Biology Gene Expression Database (CIBEX).
MycoBank. New scientific names of fungi along with key nomenclatural and descriptive material must be deposited in MycoBank and the assigned accession number(s) must be included in the manuscript no later than the modification stage of the review process. It is expected that the data will be released to the public no later than the publication (online posting) date of the article. Authors are encouraged to send the relevant data with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph with the lead-in "Accession number(s)" at the end of the Materials and Methods section for Research Articles and at the end of the text for other formats.
Copyright
Copyright of all material published in mSystems Research Articles remains with the authors. The authors grant the American Society for Microbiology a nonexclusive license to publish their work if it is accepted. Upon publication, the work becomes available to the public to copy, distribute, or display under a Creative Commons Attribution License (CC BY 4.0). The corresponding author must sign the mSystems Warranty and Provisional License to Publish on behalf of all coauthors. Authors can sign the license electronically during submission.
Supplemental material is also covered by the mSystems Research Articles License to Publish (see “Supplemental Material”).
Permissions
The corresponding author is responsible for obtaining permission from both the original author and the original publisher (i.e., the copyright owner) to reproduce or modify figures and tables and to reproduce text (in whole or in part) from previous publications.
Permission(s) must be obtained no later than the modification stage. The original signed permission(s) must be identified as to the relevant item in the ASM manuscript (e.g., “permissions for Fig. 1 in mSystems00123-18”) and submitted to the mSystems production editor on request. In addition, a statement indicating that the material is being reprinted with permission must be included in the relevant figure legend or table footnote of the manuscript. Reprinted text must be enclosed in quotation marks, and the permission statement must be included as running text or indicated parenthetically.
It is expected that the authors will provide written assurance that permission to cite unpublished data or personal communications has been granted. For supplemental material intended for posting by ASM (see “Supplemental Material”), if the authors of the mSystems manuscript are not also the owners of the supplemental material, the corresponding author must send to ASM signed permission from the copyright owner that allows posting of the material, as a supplement to the article, by ASM. The corresponding author is also responsible for incorporating in the supplemental material any copyright notices required by the owner.
Warranties and Exclusions
Articles published in this journal represent the opinions of the authors and do not necessarily represent the opinions of ASM. ASM does not warrant the fitness or suitability, for any purpose, of any methodology, kit, product, or device described or identified in an article. The use of trade names is for identification purposes only and does not constitute endorsement by ASM.