Review Reports

Response to Reviewer 1 Comments

1. Summary

We sincerely thank you for your time and expertise in reviewing our manuscript (ID: obesities-4273045). Detailed point-by-point responses are provided below, and all corresponding revisions have been clearly highlighted with red text in the resubmitted manuscript files.

2. Questions for General Evaluation

Reviewer’s Evaluation

Response and Revisions

Does the introduction provide sufficient background and include all relevant references?

Yes

Thank you for the positive feedback

Are all the cited references relevant to the research?

Yes

Appreciate the recognition.

Is the research design appropriate?

Yes

Thank you for validating the design

Are the methods adequately described?

Yes

Grateful for the affirmation

Are the results clearly presented?

Can be improved

Response 1

Are the conclusions supported by the results?

Can be improved

Response 2

Response 3

3. Point-by-point response to Comments and Suggestions for Authors

Comments 1: However, it should be noted that the conclusions are somewhat too strong for a cross-sectional NHANES analysis. The manuscript should avoid phrasing that suggests a cause-and-effect relationship, such as “protective effect”” or “reduces the risk,” and instead use terms such as “is associated with a lower likelihood.”

Response 1: Thank you for your insightful critique regarding the limitations of causal inference in cross-sectional studies. We fully agree that definitive causal claims are inappropriate for NHANES data due to the lack of temporal sequence.

In response, we have conducted a thorough revision of the manuscript to eliminate all causal terminology.

Specifically: We have replaced terms such as "protective effect," "reduced risk," and "prevented" with neutral associative phrases like "correlated with lower MetS prevalence,"​ “associated with lower likelihood of “,"was associated with a lower likelihood of,"​ and "correlate with reduced prevalence of "​ throughout the Abstract, Results, and Discussion sections in the revised manuscript with red text (e.g., Lines 30, 260, 286,328,332, 454).

Comments 2: The mediation analysis is interesting, particularly the role of the HOMA-IR index and phenotypic age, but it should be interpreted with caution because the sequence of events cannot be determined.

Response 2: We deeply appreciate your rigorous and in-depth suggestions on mediation analysis. Consistent with your comment, while the mediation analysis involving HOMA-IR and phenotypic age is noteworthy, we acknowledge that causal inferences are limited by the cross-sectional design and lack of temporality.

Therefore, we have explicitly stated in the revised Discussion (Page 14, Lines 438-444) with red text that " Second, this temporal limitation fundamentally constrains the interpretation of our mediation analysis. While we employed bootstrapping to quantify the mediated effects, cross-sectional mediation inherently lacks the sequential temporal data required to disentangle true mechanistic pathways. Consequently, the proportions mediated by insulin resistance and phenotypic aging should be viewed strictly as hypothesis-generating estimates rather than mechanistic proof. "​ We have emphasized that these findings should be viewed as exploratory rather than confirmatory.

Comments 3: You might also consider adding a summary of the figures in the discussion to make the paper easier for readers to comprehend.

Response 3: We fully acknowledge your constructive suggestion to enhance the readability and interpretability of our findings.

In accordance with your comment, we have substantially revised the paragraph of the Discussion section​ in the revised manuscript with red text (Page 12, Lines 357-366) to synthesize the key visual evidence presented in the figures and tables. This revised paragraph now explicitly summarizes the multi-scale association between DI-GM and MetS, the subgroup heterogeneity, and the mediation pathways, providing a clearer roadmap for the subsequent interpretation of our findings.

The detailed content was depicted as follows: ” Our large-scale analysis revealed a consistent inverse association between DI-GM and MetS, a finding robustly observed across both individual-status (NHANES) and global-level (GBD/GDD) data. Subgroup analyses demonstrated significant effect modification by race/ethnicity and socioeconomic status, indicating heterogeneity in this dietary-metabolic link. Utilizing mediation modeling, we identified insulin sensitivity (HOMA-IR) and phenotypic age as potential contributors accounting for a substantial proportion of this association. While these findings suggest that gut-health-promoting diets correlate with favorable metabolic profiles, interpretations must remain cautious; the cross-sectional design precludes establishing temporality, and thus these pathways should be regarded as exploratory.”

4. Response to Comments on the Quality of English Language

Point 1: The English is fine and does not require any improvement.

Response 1:  We sincerely appreciate your positive evaluation of the English language used in our manuscript. While you found the language acceptable, we have nevertheless undertaken a final thorough proofreading of the entire revised manuscript to ensure clarity and grammatical accuracy. We are confident that the current version meets the journal's standards for publication.

5. Additional clarifications

None

Response to Reviewer 2 Comments

1. Summary

We sincerely thank you for your time, expertise, and thoughtful comments regarding our manuscript (ID: obesities-4273045). Your insights have been instrumental in enhancing the clarity, rigor, and overall quality of our work. Detailed point-by-point responses are provided below, and all corresponding revisions have been clearly highlighted with red text in the resubmitted manuscript files.

2. Questions for General Evaluation

Reviewer’s Evaluation

Response and Revisions

Does the introduction provide sufficient background and include all relevant references?

Can be improved

Response 4

Are all the cited references relevant to the research?

Yes

Appreciate the recognition.

Is the research design appropriate?

Yes

Response 5

Are the methods adequately described?

Can be improved

Response 5

Are the results clearly presented?

Yes

Response 6

Are the conclusions supported by the results?

Can be improved

Response 8

3. Point-by-point response to Comments and Suggestions for Authors

Comments 1: Title: No major concerns.

Response 1: We sincerely appreciate your positive feedback regarding the manuscript title. We are pleased that it accurately reflects the scope and focus of our study.

Comments 2: Abstract: The abstract is informative and well structured. However, it is recommended that the study design be explicitly stated. In addition, minor revisions are needed to reduce causal language and ensure consistency with the observational nature of the study.

Response 2: We sincerely appreciate the reviewer’s positive feedback on the Abstract’s informativeness and structure.

In response to the suggestions:

(1) Study design clarification: We have explicitly stated the study design as a cross-sectional observational study in the Abstract (Page 1, Lines 16-17).

(2) Causal language revision: We have carefully revised the Abstract to replace causal terms with observational language (Page 1, Lines 23,25,30-32), ensuring consistency with the study’s observational nature.

Comments 3: Keywords: Avoid repeating the words and terms mentioned in the title.

Response 3: We sincerely appreciate your helpful suggestion to refine the keywords. We have replaced "Insulin Resistance" and "Phenotypic Age" with "Impaired Insulin Sensitivity"​ and "Biological Age"​ respectively (Page 1, Lines 34). This substitution enhances terminological precision while aligning with your recommendation to avoid redundancy with the title terms.

Comments 4: INTRODUCTION: The introduction provides a solid and up-to-date theoretical background. However, the section is excessively long for an observational study. (1) Greater conciseness is recommended, together with a stronger and more focused presentation of the scientific gap. (2) Although the research gap is identifiable, it is diluted within a lengthy and highly descriptive paragraph. A more direct and objective formulation would strengthen the scientific rationale of the study. (3) Furthermore, the justification could be more compelling by explicitly emphasizing the potential contribution of the findings to nutritional recommendations and clinical practice guidelines.

Response 4: We sincerely appreciate your constructive feedback on the introduction, which has helped us sharpen the focus and scientific rationale of our manuscript. We have revised the section accordingly, as detailed below:

(1) Addressing excessive length and strengthening the scientific gap

We have streamlined the Introduction by removing redundant background descriptions. The revised section now focuses exclusively on: (1) the core theoretical frameworks linking diet, gut microbiota, and metabolic health; and (2) key unresolved questions in observational nutrition research. Details are shown in the revised manuscript (Page 2, Lines 41–60).

(2) Improving directness and objectivity in presenting the research gap

We have restructured this paragraph to present the research gap objectively and directly, and have revised the relevant content accordingly in the manuscript (Page 2, Lines 62–71). (3) Enhancing the justification for nutritional and clinical contributions

We have added Lines 76–79 to explicitly emphasize practical implications in the revised manuscript (Page 2).

Comments 5: METHODS

 (1) The cross-sectional design is not explicitly stated and should be clearly identified at the beginning of the section.

(2) It would be important to include a subsection or a more detailed description of bias control procedures, particularly regarding the potential selection bias resulting from extensive participant exclusions and the handling of missing data.

(3) The absence of information regarding sample size justification or statistical power adequacy represents a relevant methodological limitation that should be clarified by the authors.

Response 5: We sincerely appreciate your rigorous evaluation of our methodology.

We have addressed each concern as follows:

(1) Explicit statement of the cross-sectional design

We have added a clear declaration of the study design in the first sentence of the Methods section (Page 2, Line 82-83): ” This cross-sectional study leveraged data from seven consecutive NHANES cycles (2005–2018), utilizing publicly accessible datasets to evaluate metabolic health outcomes.” This description ensures immediate clarity regarding the study’s temporal framework.

(2) Enhanced description of bias control procedures

A new subsection titled “(2) Covariate Selection and Bias Mitigation”​ (Page 5, Lines 194–201) has been added to explicitly address: “To mitigate potential selection bias from missing data, participants with incomplete key variables were excluded (Fig. 1). Baseline characteristics were rigorously compared between included and excluded participants (Supplementary Table S2). To address residual missingness, multiple imputation by chained equations (MICE) was performed, generating five imputed datasets; estimates were pooled via Rubin’s rules to ensure robust statistical inference (32, 33). Finally, comprehensive sensitivity analyses were conducted to confirm the robustness of the findings.”

(3) Clarification of sample size and statistical power

We have added a “(1) Sample Size and Power”​ subsection (Page 5, Lines 186–190):”An a prioripower analysis using G*Power (v3.1.9.2) indicated that 82 participants were required to detect a medium effect (Cohen's d = 0.5) with 80% power (α = 0.05). Our analytic sample of 20,800 participants vastly exceeded this threshold, providing ample power to detect even small effect sizes and ensuring robust, generalizable estimates.”

These revisions strengthen the methodological transparency and rigor of the manuscript. We hope they address your concerns satisfactorily.

Comments 6: RESULTS However, some points require attention. Greater objectivity in the presentation of findings is recommended, focusing primarily on reporting observed results rather than their interpretation.

Response 6: We fully agree with your point that the Results section should prioritize objective reporting of observed data over interpretation. Accordingly, we have removed interpretative/speculative phrasing​ that previously appeared in the Results section, and updated description was observed in the revised manuscript (Page 9, Lines 288-289; Page 10, Lines 304-307; Page 11, Lines 315-317,333-335), so the RESULTS now strictly report statistical findings and data patterns as observed.

Comments 7: DISCUSSION:

 (1) However, there is an excessive degree of causal interpretation considering the proposed study design, particularly when describing insulin resistance and phenotypic age as established biological mediators and when proposing changes to clinical guidelines.

(2) Greater caution in interpretation is recommended, together with a reduction in causal statements and a strengthening of the limitations section. In particular, the authors should discuss the implications of the cross-sectional design, the limitations of mediation analyses in studies of this nature, potential sources of bias, and issues related to data handling.

Response 7: We sincerely appreciate your insightful critique regarding the causal interpretation of our findings. We fully acknowledge that the original manuscript overstepped the inferential boundaries of a cross-sectional design.

In response, we have undertaken a rigorous revision to temper causal language, reframe our interpretations, and substantially expand the Limitations section.

(1) Mitigation of causal interpretation and revision of mediator/guideline claims

We have systematically purged causal terminology and speculative claims regarding clinical translation: (Page 12, Lines 353-355,361-363; Page 13, Lines 400-408; Page 14, Lines 438-444, 454-458).

(2) Strengthening of the Limitations section

We have expanded the Limitations section (Page 14, Lines 433–452) by adopting a multidimensional perspective to assess the impact of study design, analytical methods, measurement tools, and confounding factors on the robustness of our findings.

Collectively, these revisions indeed ensure that the manuscript presents a balanced, cautious, and methodologically transparent account of our findings, aligning strictly with the evidentiary limits of observational research. We thank you for your holding us to this high standard of scientific rigor.

Comments 8: CONCLUSION:

The conclusion is concise, consistent with the study objective, and summarizes the main findings appropriately. However, given the lack of temporality inherent to the study design, the inferences presented should be interpreted with caution.

It is recommended that the conclusion be reformulated using association-based language rather than causal terminology. In addition, a brief statement highlighting the need for longitudinal and prospective studies to confirm the proposed mechanisms and clinical applicability of the findings should be included.

Response 8: We sincerely appreciate your positive assessment of the conclusion’s conciseness and alignment with the study objectives. We fully agree that the inherent lack of temporality in our cross-sectional design necessitates cautious interpretation.

We have carefully revised the conclusion to address both concerns explicitly stated in the revised CONCLUSION (Page 14, Lines 454-460) with red text.

Comments 9: REFERENCES The bibliography is adequately updated for the scope of the manuscript, with a substantial proportion of recent references supporting the scientific background and discussion. Overall, the reference list is appropriate for the topic under investigation.

Response 9: We sincerely appreciate your positive evaluation of the REFERENCE list. We confirm that the bibliography is intentionally curated to balance recent, cutting-edge studies with foundational works, ensuring both currency and scholarly depth for the manuscript’s scope. Thank you for recognizing its appropriateness.

4. Response to Comments on the Quality of English Language

Point 1: The English is fine and does not require any improvement.

Response 1:  We sincerely appreciate your positive evaluation of the English language used in our manuscript. While the reviewer found the language acceptable, we have nevertheless undertaken a final thorough proofreading of the entire revised manuscript to ensure clarity and grammatical accuracy. We are confident that the current version meets the journal's standards for publication.

5. Additional clarifications

We would like to clarify two additional revisions:

(1) We have systematically reorganized the data and provided statistical descriptions for both included and excluded populations in Supplementary Table S2​ of the updated supplementary materials.

(2) Regarding the previously noted lack of structural clarity in Section 2.8 (Statistical Analysis), we have further polished and refined the content. The section is now reorganized under clear subsections to improve readability (Page 5, Lines 186–190).