Instructions for Authors
General Information
The Journal of Precision Microbiome Therapeutics (JPMT) considers manuscripts that meet the journal's scientific scope, editorial standards, ethical requirements, and reporting expectations.
Authors should ensure that manuscripts are scientifically rigorous, clearly written, appropriately referenced, methodologically transparent, and consistent with relevant reporting standards.
Submission of a manuscript implies that the authors have read and complied with these Instructions for Authors and all applicable JPMT editorial and ethical policies.
Originality and Exclusive Consideration
Manuscripts submitted to JPMT must represent original work that has not been published previously in substantially similar form and is not under consideration by another journal.
Authors must disclose any related manuscripts, preprints, conference abstracts, datasets, or publications that could create substantial overlap with the submitted work.
Duplicate publication, redundant publication, inappropriate text recycling, and undisclosed substantial overlap may result in rejection or post-publication action where appropriate.
Posting a manuscript as a preprint does not necessarily preclude consideration, provided that the authors disclose the preprint at submission and the submitted manuscript is not simultaneously under consideration elsewhere.
Authorship and Contributorship
JPMT follows internationally recognized authorship principles.
Authorship should be based on substantial contributions to the conception or design of the work; acquisition, analysis, or interpretation of data; participation in drafting the manuscript or critical intellectual revision; approval of the final version; and accountability for the work.
Individuals who contributed substantially but do not meet the criteria for authorship should be acknowledged where appropriate.
All authors must approve the submitted manuscript and agree to be accountable for the integrity of the work.
Changes to authorship after submission require a justified request and written agreement from all affected authors.
Corresponding Author
The corresponding author is responsible for communication with the journal and should ensure that:
- all authors have approved the manuscript;
- author contributions are accurately reported;
- conflicts of interest are disclosed;
- funding information is complete;
- ethical approvals are reported where applicable;
- data availability information is accurate;
- all required declarations have been completed.
Manuscript Categories
Original Research Articles
Original Research Articles should present substantial, methodologically sound findings that provide a meaningful contribution to microbiome biology, therapeutic development, precision medicine, or clinical translation.
Review Articles
Reviews should provide a critical and authoritative synthesis of the literature. Authors should identify important unresolved questions and, where appropriate, discuss methodological limitations, conflicting evidence, translational barriers, and future research directions.
Systematic Reviews and Meta-analyses
Systematic reviews should follow relevant methodological and reporting standards, including PRISMA where applicable.
Registration of systematic review protocols, such as in PROSPERO or another appropriate registry, is strongly encouraged where applicable.
Methods and Protocol Articles
Methods papers should provide sufficient detail to permit reproducibility and should explain the methodological advance, validation, limitations, and appropriate applications.
Short Communications
Short Communications should report focused findings of clear scientific significance that can be communicated more concisely than a full Original Research Article.
Perspectives
Perspectives should provide a reasoned expert analysis of emerging scientific or translational issues. They should not function as promotional material or unsupported opinion.
Editorials
Editorials are generally commissioned or invited. Unsolicited proposals may be considered at the discretion of the Editor-in-Chief.
Manuscript Structure
Unless otherwise appropriate for the article type, Original Research Articles should generally include:
- Title
- Abstract
- Keywords
- Introduction
- Materials and Methods
- Results
- Discussion
- Conclusions
- Data Availability Statement
- Funding
- Conflicts of Interest
- Author Contributions
- Ethical Approval and Consent, where applicable
- Acknowledgements
- References
Authors should avoid excessive subdivision of the manuscript and should use headings that accurately reflect the content.
Title
Titles should be concise, informative, specific, and scientifically accurate.
Titles should not exaggerate the significance of findings or imply causality when the study design only supports association.
Where appropriate, study design should be reflected in the title.
Abstract
Original Research Articles should normally include a structured abstract containing:
- Background
- Methods
- Results
- Conclusions
The abstract should accurately represent the main findings and should not contain information that is unsupported by the main manuscript.
Quantitative findings should be reported with sufficient detail to communicate the magnitude and uncertainty of the results where appropriate.
Clinical trial registration information should be included in the abstract when applicable.
Keywords
Authors should provide approximately 4–8 keywords that accurately represent the central concepts of the manuscript.
Use of established biomedical terminology, including MeSH terminology where appropriate, is encouraged.
Introduction
The Introduction should:
- establish the scientific or clinical problem;
- summarize relevant knowledge;
- identify the specific gap in knowledge;
- explain why the gap matters;
- clearly state the study objective or hypothesis.
Introductions should not become comprehensive literature reviews.
Materials and Methods
Methods must be described in sufficient detail to permit evaluation and, where reasonably possible, replication.
Authors should report:
- study design;
- study setting;
- participants or biological materials;
- inclusion and exclusion criteria;
- sample-size determination where applicable;
- experimental procedures;
- microbiome sampling procedures;
- sequencing methodology;
- laboratory methods;
- bioinformatic pipelines;
- quality-control procedures;
- statistical analyses;
- software and versions;
- databases and reference genomes;
- relevant parameters and thresholds;
- ·validation procedures;
- ethical approvals.
For computational studies, the manuscript should provide sufficient information regarding preprocessing, feature selection, model development, training, validation, testing, and performance evaluation.
Microbiome-Specific Reporting
Microbiome studies should provide sufficient methodological information to enable assessment of analytical validity.
Where applicable, authors should report:
- sample collection and storage;
- DNA/RNA extraction procedures;
- sequencing platform;
- library preparation;
- sequencing depth;
- quality-control procedures;
- taxonomic or functional profiling methods;
- reference databases and versions;
- bioinformatic software and versions;
- filtering criteria;
- ·normalization or transformation methods;
- statistical models;
- correction for multiple testing;
- relevant batch effects;
- ·negative and positive controls where appropriate;
- accession numbers for deposited sequence data.
Studies relying exclusively on compositional differences should clearly distinguish association from causation.
Artificial Intelligence and Machine Learning
Manuscripts using AI, machine learning, deep learning, generative AI, or related computational methods must provide sufficient methodological transparency to allow meaningful evaluation.
Where applicable, authors should report:
- dataset origin;
- cohort characteristics;
- preprocessing;
- feature engineering;
- model architecture;
- hyperparameters;
- training procedure;
- internal validation;
- external validation;
- test-set definition;
- performance metrics;
- confidence intervals where appropriate;
- handling of missing data;
- class imbalance;
- potential data leakage;
- interpretability methods;
- code and model availability;
- limitations and potential sources of bias.
AI models should not be evaluated only on the data used for model development.
Where feasible, independent or external validation should be provided.
AI studies should follow applicable reporting guidance, including relevant extensions available through the EQUATOR Network.
Research Reporting Guidelines
Authors are expected to use the appropriate reporting guideline for the study design.
Examples include:
- CONSORT for randomized trials;
- STROBE for observational studies;
- PRISMA for systematic reviews and meta-analyses;
- STARD for diagnostic accuracy studies;
- TRIPOD for prediction models;
- ARRIVE for animal research;
- CARE for case reports;
- SPIRIT for clinical trial protocols;
- PRISMA-P for systematic review protocols.
The appropriate guideline should be selected according to the study design rather than merely according to the scientific topic.
Human Participants
Research involving human participants must comply with applicable ethical standards and institutional or regulatory requirements.
Authors should state:
- the name of the approving ethics committee or institutional review board;
- approval or reference number where available;
- whether informed consent was obtained;
- any relevant consent exceptions approved by the ethics committee.
Clinical Trials
Clinical trials should be prospectively registered in an appropriate publicly accessible registry in accordance with applicable standards.
The registration identifier should be provided in the manuscript and, where applicable, in the abstract.
Authors should disclose discrepancies between the registered protocol and the submitted manuscript.
JPMT may request the study protocol, statistical analysis plan, or registry record during editorial assessment.
Animal Research
Studies involving animals must comply with applicable institutional, national, and international standards for animal welfare.
The manuscript should identify the relevant ethics committee and approval information.
Authors are expected to follow ARRIVE guidance where applicable.
Data Availability
JPMT strongly supports responsible data sharing and reproducibility.
Authors should provide a Data Availability Statement for all research articles.
Where appropriate, authors should deposit:
- sequencing data;
- genomic data;
- proteomic or metabolomic datasets;
- relevant clinical datasets where legally and ethically permissible;
- analytical code;
- computational workflows;
- model specifications.
Data should be deposited in an appropriate recognized repository whenever possible.
Human data must be shared only in accordance with applicable consent, privacy, ethical, legal, and regulatory requirements.
Code and Computational Reproducibility
For computational manuscripts, authors are encouraged to provide source code, workflow descriptions, software versions, and relevant configuration files in an appropriate repository.
Where code cannot be publicly released, authors should explain the restriction.
Statistical Reporting
Statistical methods must be appropriate for the study design and data structure.
Authors should report:
- sample size;
- statistical tests;
- assumptions where relevant;
- effect estimates;
- measures of uncertainty;
- exact or appropriately reported P values;
- multiplicity adjustments where appropriate.
P values should not be presented as the sole evidence of scientific importance.
Research Integrity
JPMT does not tolerate fabrication, falsification, plagiarism, image manipulation, data manipulation, duplicate publication, citation manipulation, peer-review manipulation, authorship fraud, or other forms of research or publication misconduct.
Suspected misconduct may be investigated before or after publication.
Where necessary, JPMT may contact the authors' institution, funder, ethics committee, or other appropriate body.
Plagiarism and Text Overlap
Submitted manuscripts may be screened using appropriate similarity-detection and research-integrity tools.
Similarity reports are not interpreted mechanically. Editorial assessment considers the nature, location, extent, and context of overlapping text.
Unattributed copying of ideas, text, figures, tables, data, or other intellectual material is unacceptable.
Image Integrity
Images must accurately represent the underlying data.
Authors must not manipulate images in a manner that obscures, removes, adds, or misrepresents scientific information.
Any legitimate image processing applied to experimental data must be disclosed where appropriate and applied consistently to relevant samples.
Original image files may be requested during editorial review or research-integrity investigation.
Conflicts of Interest
All authors must disclose financial and non-financial relationships or activities that could reasonably be perceived as relevant to the submitted work.
Potential conflicts may include:
- employment;
- consultancy;
- research funding;
- patents;
- equity interests;
- honoraria;
- advisory roles;
- personal relationships;
- intellectual or academic interests;
- commercial relationships.
A conflict does not necessarily prevent publication, but it must be transparently disclosed and appropriately managed.
Funding
All sources of financial and material support must be disclosed.
The role of the funder in study design, data collection, analysis, interpretation, manuscript preparation, and publication decisions should be stated.
Generative AI and AI-Assisted Technologies
Generative AI tools may be used as editorial or writing assistance only in accordance with JPMT policy.
AI systems cannot be listed as authors because they cannot assume responsibility for the accuracy, integrity, originality, and accountability required of authorship.
Authors remain fully responsible for the submitted content, including any text, references, analyses, figures, tables, or interpretations produced or assisted by AI.
Substantive use of generative AI in manuscript preparation should be disclosed according to the journal's AI policy.
Authors must not use AI tools to fabricate references, data, citations, experimental results, or scientific claims.
Preprints
JPMT may consider manuscripts previously deposited as preprints, provided that the authors disclose the preprint during submission.
Authors should ensure that the submitted manuscript clearly identifies and appropriately cites the preprint where required.
References
References should be accurate, relevant, and directly support the statements for which they are cited.
Authors should avoid excessive citation of their own work, citation stacking, and irrelevant references.
References should not be included merely to increase citation counts.
Corrections and Retractions
The journal maintains the integrity of the published record.
Corrections, expressions of concern, retractions, and other post-publication notices may be issued when necessary.
The journal will distinguish between honest errors, which may require correction, and misconduct requiring stronger action.
Submission Declaration
By submitting a manuscript to JPMT, the authors confirm that:
- the manuscript is original;
- it is not simultaneously under consideration elsewhere;
- all listed authors meet the journal's authorship requirements;
- all authors have approved the submitted version;
- relevant conflicts of interest have been disclosed;
- funding has been accurately reported;
- ethical approval and consent information is accurate;
- data availability information is truthful;
- any substantive use of AI has been disclosed;
- the manuscript complies with applicable research-integrity standards.