Editorial, Peer Review, Ethics and Research Integrity Policies

Editorial Independence

The Journal of Precision Microbiome Therapeutics (JPMT) is committed to editorial independence.

Editorial decisions are made on the basis of scientific quality, methodological rigor, originality, relevance to the journal's scope, research integrity, and potential contribution to the field.

Neither the publisher, commercial partners, sponsors, advertisers, nor other external parties may influence decisions regarding manuscript acceptance, rejection, peer-review selection, editorial assignment, or publication priority.

The Editor-in-Chief has primary responsibility for the scientific and editorial direction of the journal and operates independently within the journal's governance framework.

Commercial considerations must not determine editorial decisions.

The publisher is responsible for providing the infrastructure necessary for publication but does not have authority to overturn an editorial decision on scientific grounds.

Editorial Decision-Making

Manuscripts undergo an initial editorial assessment before external peer review.

The assessment may consider:

• fit with the journal's Aims and Scope;
• scientific significance;
• ·originality;
• methodological rigor;
• ethical compliance;
• reporting completeness;
• data transparency;
• statistical appropriateness;
• potential research-integrity concerns.

A manuscript may be declined without external peer review when it is clearly outside the journal's scope, lacks sufficient scientific rigor, does not meet basic reporting requirements, or is unlikely to benefit from external review.

A decision not to send a manuscript for peer review does not imply that the work is scientifically invalid; it indicates that the manuscript does not meet the journal's editorial criteria for external review.

Peer Review Policy

JPMT uses a double-anonymized peer-review model for research manuscripts unless an alternative model is explicitly stated for a particular article category. Complete anonymity cannot be guaranteed in every case; in highly specialized areas, reviewers may be able to infer authorship from the subject matter, references, self-citations, or institutional context.

Reviewers are external experts who are independent of the journal's editorial staff and, where reasonably possible, independent of the authors.

Research Articles normally receive assessment from at least two qualified external reviewers. At least one reviewer should have direct expertise in the microbiome.

Manuscripts involving substantial clinical, statistical, computational, or highly specialized methodological components may be reviewed by additional experts.

The journal may seek specialist review from:

• microbiome scientists;
• clinical investigators;
• pharmacologists;
• computational scientists;
• statisticians;
• synthetic biologists;
• regulatory or translational experts.

Peer review is advisory. Final editorial responsibility rests with the appropriate editor.

Peer Review Workflow

The standard workflow is:

Stage 1 — Technical Assessment

The editorial office verifies:

• manuscript completeness;
• article type;
• ethical declarations;
• authorship information;
• conflicts of interest;
• funding;
• data availability;
• required reporting checklists;
• plagiarism or similarity concerns;
• basic formatting and metadata.

Stage 2 — Scope Assessment

The manuscript is assessed against the journal's Aims & Scope. Particular attention is given to whether the work contributes to microbiome mechanisms, therapeutic development, precision medicine, or clinical translation.

Stage 3 — Editorial Assessment

An editor assesses:

• ·originality;
• scientific rationale;
• methodological quality;
• relevance;
• potential significance;
• reporting quality.

Stage 4 — Reviewer Selection

The editor identifies and invites independent reviewers with relevant expertise, ensuring the absence of significant conflicts of interest.

Stage 5 — External Peer Review

Appropriate independent reviewers evaluate the manuscript. Research Articles normally receive assessment from at least two qualified external reviewers. Additional experts may be invited for manuscripts involving substantial clinical, statistical, computational, or highly specialized methodological components.

Stage 6 — Statistical or Methodological Assessment

Additional specialist assessment may be requested when the manuscript contains substantial statistical modelling, machine learning, multi-omics analysis, clinical trial methodology, or other technically complex components.

Stage 7 — Revision

Authors may be invited to revise their manuscript in response to reviewer and editorial comments. Revised manuscripts may be returned to the original reviewers or, where appropriate, to additional reviewers.

Stage 8 — Final Decision

Possible decisions include:

• Accept;
• Minor Revision;
• Major Revision;
• Reject.

The journal may also decline further consideration when a revised manuscript does not adequately address substantive reviewer or editorial concerns.

Stage 9 — Production

Accepted manuscripts proceed to production only after all editorial, ethical, and formatting requirements have been satisfied.

Reviewer Selection

Reviewers are selected based on relevant expertise, methodological competence, availability, and absence of significant conflicts of interest.

The journal does not select reviewers solely on the basis of author suggestions. Author-suggested reviewers may be considered but are independently evaluated by the editorial team.

Reviewers should not be selected when there is a significant personal, professional, financial, institutional, or competitive conflict that could reasonably compromise impartial assessment. In particular, reviewers must not be close collaborators, colleagues at the same institution, recent co-authors, or direct competitors with a substantive conflict of interest.

Reviewer Responsibilities

Reviewers should:

• provide objective and constructive assessment;
• evaluate the scientific validity of the work;
• identify important methodological concerns;
• distinguish major from minor issues;
• avoid personal criticism;
• maintain confidentiality;
• disclose relevant conflicts of interest;
• identify potentially important omissions in the literature;
• avoid using unpublished information obtained through peer review for personal advantage.

Reviewers should not contact authors directly about the manuscript without authorization from the journal.

Confidentiality in Peer Review

Manuscripts submitted to JPMT are confidential documents.

Reviewers must not share manuscript content, data, figures, supplementary files, or editorial correspondence with unauthorized individuals.

Reviewers must not upload confidential manuscript material into external generative AI systems or other third-party platforms when doing so could compromise confidentiality or the journal's obligations to authors.

Generative AI Policy

JPMT recognizes that generative AI and AI-assisted technologies are increasingly used in research and publishing.

Authors

Authors may use AI-assisted technologies in accordance with journal policy, but authors remain responsible for the entire submitted work.

AI systems cannot be authors.

Substantive use of generative AI in manuscript preparation should be disclosed.

AI tools must not be used to fabricate or alter scientific data, generate false references, manufacture experimental results, or create misleading scientific content.

Reviewers

Reviewers must preserve manuscript confidentiality.

Reviewers must not submit confidential manuscript content to public or commercial AI systems unless explicitly permitted by the journal and appropriate safeguards are in place.

Editors

Editors must not upload confidential manuscript content, reviewer reports, or identifiable editorial correspondence into public or commercial AI systems in ways that compromise confidentiality.

Any use of AI-assisted editorial tools remains subject to human oversight and accountability.

Authorship and Contributorship

JPMT follows recognized international authorship standards, including the four criteria established by the International Committee of Medical Journal Editors (ICMJE). Authorship must be based on: substantial contributions to the conception or design of the work, or the acquisition, analysis, or interpretation of data; drafting the work or revising it critically for important intellectual content; final approval of the version to be published; and agreement to be accountable for all aspects of the work.

All authors must have made substantive contributions, participated in drafting or critical intellectual revision, approved the final manuscript, and accepted accountability for the work.

The corresponding author is responsible for ensuring that all co-authors have approved the manuscript and its submission, and for managing all correspondence with the journal. Any changes to authorship after submission must be agreed upon by all authors and approved by the editor.

The journal encourages the use of a contributor taxonomy such as CRediT where appropriate.

Honorary authorship, guest authorship, ghost authorship, and authorship purchased or exchanged for non-scientific reasons are unacceptable.

Conflicts of Interest

JPMT requires transparent disclosure of financial and non-financial conflicts of interest for:

• authors;
• reviewers;
• editors;
• editorial board members;
• guest editors.

Editors and reviewers must recuse themselves when a conflict could reasonably compromise impartiality.

Editors should not handle manuscripts in which they have a substantial personal, professional, institutional, financial, or competitive interest.

Research Misconduct

JPMT considers the following examples of research or publication misconduct:

• fabrication;
• falsification;
• plagiarism;
• substantial unattributed text reuse;
• duplicate publication;
• redundant publication;
• inappropriate image manipulation;
• data manipulation;
• fraudulent authorship;
• undisclosed conflicts;
• peer-review manipulation;
• citation manipulation;
• interference with editorial processes;
• concealment of relevant ethical concerns.

Suspected misconduct may be investigated before or after publication.

Where appropriate, JPMT may seek clarification from authors, institutions, ethics committees, funders, or other relevant organizations.

Allegations and Whistleblowing

Concerns regarding possible research or publication misconduct may be submitted to the editorial office.

The journal will treat credible allegations seriously and will seek appropriate evidence before reaching an editorial conclusion.

Where confidentiality is necessary, information will be handled appropriately.

The journal will not tolerate retaliation against individuals who raise concerns in good faith.

Ethical Oversight

Research involving humans, human biological materials, animals, identifiable personal data, or other ethically sensitive materials must comply with applicable ethical and regulatory requirements. Authors must provide appropriate ethics approval and consent information. The journal may request supporting documentation.

Human Research

Research involving human participants must comply with the ethical standards set out in the Declaration of Helsinki and applicable national regulations. Authors must obtain approval from an appropriate research ethics committee prior to commencing the study and must provide written informed consent from all participants (or their legal guardians for minors or incapacitated individuals). The privacy and confidentiality of participants must be protected, and identifiable personal information, photographs, recordings, or quotations should not be published without explicit consent for publication. Manuscripts reporting human research must include a statement of ethical approval in the Methods section. Particular attention should be given to the protection of vulnerable populations.

Animal Research

Studies involving animals must be conducted in accordance with relevant institutional, national, and international standards for animal welfare. Authors must obtain approval from the relevant institutional ethics committee or animal care and use committee and must report the name of the approving committee in the manuscript. Research should be designed to minimise suffering and to use alternatives to animal testing where possible, in line with the 3Rs principles (Replacement, Reduction, Refinement). Authors reporting animal studies should follow the ARRIVE reporting guidelines. The journal may request evidence of ethical approval or a statement explaining why approval was not required.

Informed Consent

Where identifiable information, images, or other potentially identifiable material concerning individuals is published, appropriate consent for publication must be obtained unless a valid ethical or legal exception applies.

The journal may request evidence of consent.

Clinical Trial Registration

JPMT expects applicable clinical trials to be registered prospectively in a public trials registry acceptable to the International Committee of Medical Journal Editors (ICMJE), such as those listed on the WHO International Clinical Trials Registry Platform or ClinicalTrials.gov, before the enrolment of the first participant. The trial registration number must be included in the abstract and at the end of the manuscript.

Registration information should be included in the manuscript. The journal may request clarification of discrepancies between the registered study and the submitted report.

Authors reporting randomised controlled trials should follow the CONSORT reporting guidelines, and the CONSORT checklist and flow diagram should be submitted with the manuscript.

The journal may make limited exceptions only where scientifically and ethically justified, and the circumstances must be transparently documented.

Data Availability and Reproducibility

JPMT supports responsible sharing of data and analytical resources.

Authors should make relevant data, code, workflows, protocols, and other supporting materials available whenever ethically, legally, and practically possible.

For microbiome and multi-omics research, authors should provide appropriate accession numbers and repository information.

For computational and AI studies, authors should provide sufficient information to permit independent assessment and, where possible, reproduction.

Statistical and Computational Integrity

Editors may request specialist statistical or computational review.

Models should be appropriately validated, and authors should clearly distinguish exploratory analyses from confirmatory analyses.

Potential overfitting, data leakage, selective reporting, inappropriate normalization, pseudoreplication, inappropriate multiple testing, and inadequate validation will be considered during editorial assessment.

Reporting Guidelines

JPMT encourages and, where appropriate, requires the use of recognized reporting guidelines relevant to the study design. Examples include CONSORT for randomised controlled trials, STROBE for observational studies, PRISMA for systematic reviews and meta-analyses, and ARRIVE for animal studies. Other design-specific guidelines may also apply.

The editorial office may request completed reporting checklists during submission.

The checklist is considered a reporting aid and does not replace scientific or editorial assessment.

Appeals

Authors may appeal an editorial decision when they believe that:

• a significant factual error occurred;
• the manuscript was assessed using materially incorrect information;
• a substantial procedural problem affected the decision.

An appeal should provide a concise, evidence-based explanation.

Disagreement with the scientific judgment of reviewers, without a substantive basis, does not by itself constitute grounds for appeal.

Appeals are normally considered by an editor who was not responsible for the original decision where feasible.

Complaints

Complaints concerning editorial procedures, reviewer conduct, editorial decisions, conflicts of interest, or publication ethics may be submitted to the editorial office.

Complaints involving the Editor-in-Chief may be directed to an independent senior editorial or publisher-level contact designated by the journal's governance structure.

Complaints will be handled confidentially where appropriate and investigated in accordance with the nature of the concern.

Corrections

JPMT will publish corrections when a published article contains an error that affects the accuracy or interpretation of the scientific record but does not invalidate the overall work.

Corrections should clearly identify the affected content and explain the correction.

Retractions

An article may be retracted when there is compelling evidence that the findings are unreliable because of major error, fabrication, falsification, plagiarism, serious ethical violations, or other circumstances that substantially compromise the integrity of the published record.

Retractions will be clearly identified and linked to the original article.

The original record will not normally be removed.

Expressions of Concern

When serious concerns arise but an investigation cannot yet be completed, the journal may publish an Expression of Concern.

This mechanism is intended to alert readers while preserving the integrity of the editorial and investigative process.

Post-Publication Discussion

JPMT supports responsible scientific discussion after publication.

Substantive concerns regarding published work may be evaluated by the editorial team.

Where appropriate, the journal may publish correspondence, corrections, editorials, expressions of concern, or retractions.

Special Issues

Special Issues are subject to the same scientific, ethical, and peer-review standards as regular journal content.

Guest Editors must disclose relevant conflicts of interest.

Guest Editors may recommend reviewers but must not compromise reviewer independence.

Guest Editors must not guarantee acceptance of submissions.

Manuscripts submitted by Guest Editors, members of the Editorial Board, or individuals with close professional relationships to Guest Editors must be handled independently.

Editorial Board Responsibilities

Editorial Board members are expected to contribute actively to the journal.

Depending on their role, responsibilities may include:

• handling manuscripts;
• reviewing manuscripts;
• advising on editorial policy;
• developing special issues;
• promoting rigorous scientific standards;
• identifying emerging areas of importance;
• supporting international author and reviewer diversity.

Editorial Board membership is not honorary and does not imply preferential publication.

The journal periodically reviews board composition, activity, expertise, geographic representation, conflicts of interest, and alignment with the journal's scientific scope.

Editorial Independence from the Publisher

The Publisher provides the journal's publishing infrastructure, administrative support, production services, and commercial operations.

The Publisher does not determine scientific acceptance or rejection.

The Editor-in-Chief and delegated editors retain authority over editorial decisions.

Any contractual relationship between the Publisher and the editorial leadership should explicitly protect editorial independence.

Advertising and Commercial Activities

Advertising, sponsorship, commercial partnerships, and other revenue-generating activities must be clearly separated from editorial decision-making.

Commercial relationships must not influence the selection, peer review, acceptance, rejection, or presentation of scholarly content.

Digital Preservation

The journal will maintain an appropriate digital preservation strategy to protect the scholarly record against loss of content or interruption of publishing operations.

The journal will identify its preservation and archiving arrangements transparently on the website.

Accessibility and Non-Discrimination

JPMT is committed to fair and respectful participation in scholarly publishing.

Editorial decisions are based on scientific and ethical considerations and are not influenced by nationality, geographic origin, ethnicity, religion, sex, gender, disability, institutional prestige, political views, or other characteristics unrelated to the scientific merit of the work.