All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
The manuscript can be accepted for publication now.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
After reviewing the revised manuscript, I am pleased with the significant improvements made. The authors have effectively addressed the previous concerns, enhancing the overall quality and ensuring it meets publication standards. I fully support its publication and look forward to its contribution to our field.
NA
NA
NA
The authors have addressed all comments and suggestions well. Then they need to revise carefully the grammar and syntax of their manuscript.
The authors have addressed all comments and suggestions well. Then they need to revise carefully the grammar and syntax of their manuscript.
The authors have addressed all comments and suggestions well. Then they need to revise carefully the grammar and syntax of their manuscript.
The authors have addressed all comments and suggestions well. Then they need to revise carefully the grammar and syntax of their manuscript.
Please revise the manuscript based on the reviewers' comments accordingly.
**PeerJ Staff Note:** Please ensure that all review and editorial comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
**Language Note:** The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
Gene-panel justification thin – the 160 markers are said to be “conserved” but no selection flow or literature table is provided; please supply rationale and exclusion criteria.
No confidence intervals – AUC, F1 and other metrics are point values; 95 % CI or permutation test would strengthen statistical rigor.
Risk of class leakage – MAGs and reference genomes were annotated by the same pipeline; please clarify whether KO identifiers from test appear during feature engineering stage of training.
Over-interpretation of ANI sharing – claiming cross-host transmission from seven shared species is premature without ecological metadata or temporal sampling.
Figure resolution uneven – Fig 6 and Fig 7 fonts blur when zoomed, hard for readers; recommend higher dpi and vector export.
Raw data accessibility – raw MAG assemblies and annotation tables are not linked; deposit to ENA/Zenodo with accession numbers.
Minor language issues – several long sentences and tense shifts (e.g., Introduction lines 55-70); professional polishing will improve readability.
Method details missing – SVM kernel parameters and XGBoost tree depth are reported as “fixed” without concrete values; please list full tuned grid.
Training sample size limited – only 136 reference genomes may not sustain four ML models plus stacking; power analysis or data augmentation suggestion is needed.
External validation lacking – all performance metrics are from internal 70/30 split; please add an independent dataset to exclude optimistic bias.
This article deals with an interesting topic about machine learning and the prediction of sporulating firmicutes. The study also presents relevant results according to its hypotheses. The literature references and background are sufficient to assess the contribution of this manuscript.
The research question is well defined, relevant, and meaningful. Also, the authors have performed a rigorous investigation with high technical and ethical standards.
However, the authors failed to provide details about their bioinformatics pipelines. This type of manuscript requires transparency, and the authors should share all pipelines through a reputable repository, such as GitHub.
The conclusions of this manuscript are all well stated and linked with the original research question. It is good work, and based on that, it can be improved to be publishable at PeerJ.
Detailed comments and suggestions are in the attached file. Please revise them. I will be glad to revise the improved version of this manuscript.
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.