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.
Thanks for addressing all comments and congrats!
[# PeerJ Staff Note - this decision was reviewed and approved by Valeria Souza, a PeerJ Section Editor covering this Section #]
I thank the authors for addressing the points raised in my previous review. I would recommend the manuscript for publication pending some final editorial polishing (especially consistent writing, e.g. line 75, twenty-two and 20; italic and normal p). I hope that these preliminary findings will encourage more in-depth studies in the future, particularly involving larger Vietnamese cohorts with their specific environmental and lifestyle contexts.
No comment.
No comment.
no comment
no comment
no comment
The authors' responses have adequately addressed my concerns. The current version meets the standards for publication in Peer J. However, in future research, one point requires consideration: the authors should investigate whether the differential analysis results remain consistent after adjusting for key covariates (e.g., age, sex, BMI, smoking status, adverse event, family history, etc.). Confirming the robustness of findings would strengthen the validity and generalizability of the conclusions.
Please address all reviewers' comments.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff 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.
The authors presented an interesting investigation of gut microbiota profiles in Vietnamese patients with rheumatoid arthritis, addressing a timely and important research question in the context of autoimmune disease pathogenesis and providing novel data from an underrepresented population. The manuscript is generally clear, methodologically sound, and well-structured. The raw data were deposited at NCBI PRJNA1295194; however, the linked SRA data are not accessible yet.
Minor comments for reproducibility:
1. For participant recruitment, please specify related conditions and define restricted diets to reduce ambiguity.
2. The versioning of cutadapt and the parameters of taxonomic classification were not mentioned.
1. Please clarify whether all stool samples were collected before any RA treatment, as medication can strongly influence microbiota composition. Otherwise, is there a maximum time for delivery when collecting at home?
2. I'd like to see more information on the distribution of sample depths. Then I'm wondering if using alternative approaches for normalization that keep all reads and normalize data mathematically would have a considerable impact on the findings.
1. Non-parametric tests on raw relative abundance data can be misleading because they confuse relative shifts with true biological changes. A taxon may “appear” to increase or decrease simply because another taxon changed, not because its absolute abundance did. Other methods like ANCOM (or variants), ALDEx2, etc., could be considered.
2. I would expect to see a compositional measurement trajectory from control to low, mediate, and high disease activity in the main text and figures.
3. The manuscript could include a cautionary note about interpreting the findings, given the small cohort size, as microbiome variability is high.
4. The discussion section provides strong links to prior studies. However, it remains unclear whether the observed enrichment reflects protective, compensatory, or pathogenic mechanisms. The limitation of genus-level resolution might also be discussed.
Minor comments:
1. Using a non-parametric test for age instead of a t-test. (line 126)
2. Principal coordinates (but not coordinate) analysis for PCoA. (line 120)
3. Number of permutations in PERMANOVA.
-
-
-
This is a well-written and concise study, appropriately framed as a pilot investigation given the sample size. The findings are compelling and consistent with the growing body of evidence on gut dysbiosis in rheumatoid arthritis (RA). Linking microbial profiles to clinical parameters such as DAS28 and serological markers further enhances the clinical relevance of the work. The focus on the Vietnamese population represents a particular strength, providing valuable data for global studies. Additionally, the use of multiple diversity metrics and rigorous statistical methods strengthens the validity of the observations.
Key concerns:
1. The sample size remains small, limiting statistical power—especially for subgroup analyses.
2. 16S rRNA gene sequencing provides taxonomic resolution only to genus level; functional inferences (e.g., "toxic metabolites") are speculative without metagenomic/metabolomic data.
3. No adjustment for confounders like diet, antibiotics, or RA medications—critical factors that may influence gut microbiota.
4. Associations with clinical parameters are descriptive and do not imply causation.
5. To enhance clarity and impact, the manuscript might benefit from incorporating selected supplementary figures into the main text.
6. No significance indicators (e.g., *, **) are shown in Figure 2C.
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.