Title: Unveiling the diagnostic and pro-inflammatory role of Crohn’s disease: insights from
16S-guided discovery and species-specific validation
Version: 1 Date: 15 Feb 2025
Reviewer's report:
General Assessment:
This manuscript investigates the association between Ruminococcus gnavus and Crohn’s
disease (CD), a topic of significant clinical relevance due to the increasing incidence of CD,
particularly in Asia. The manuscript presents interesting findings, but several revisions are
necessary to ensure scientific rigor, methodological soundness, statistical accuracy, and clarity
in figures and tables.
Scientific and Methodological Evaluation:
Strengths: The study addresses an important gap in CD research, focusing on the gut
microbiota’s role, particularly R. gnavus. The use of sequencing to identify microbiota
composition is appropriate and timely.
Limitations and Revisions Needed:
Rationale: The manuscript should elaborate on why R. gnavus was selected over other bacteria
linked to CD.
Sample Size: The cohort is relatively small, potentially limiting the power of the study.
Justification for this sample size is essential.
Inclusion/Exclusion Criteria: More detail is needed on the rationale behind these criteria to
enhance reproducibility and clarity.
Microbiota Analysis: The reference database for taxonomic classification is not specified and
should be included. A sensitivity analysis would strengthen the conclusions, demonstrating the
robustness of the results.
Functional Analysis: The study infers functional implications of R. gnavus abundance but does
not validate these claims experimentally. Functional assays or metabolomic analysis would
significantly enhance the manuscript’s impact.
Statistical Evaluation:
Multiple Testing: It is unclear whether corrections for multiple comparisons were applied.
Methods like Benjamini-Hochberg should be mentioned if used.
Effect Sizes and Confidence Intervals: Including these for key findings would provide a clearer
picture of the biological significance.
p-Values: Some p-values are reported as <0.05. Exact values should be provided for
transparency.
Figures and Tables Evaluation:
Figures:
Color Palette: Figures 2 and 4 need colorblind-friendly palettes.
Figure 3: The legend is too brief; a more detailed description of each panel is necessary.
Tables:
Supplementary Tables: Tables 1-5 are informative, but Table 3 is particularly dense. Splitting it
into smaller sections or using visual aids would improve readability.
Recommendations for Revision:
Expand the introduction to justify the choice of R. gnavus.
Provide a rationale for the sample size and detail the inclusion/exclusion criteria.
Specify the reference database and include a sensitivity analysis.
Incorporate effect sizes, confidence intervals, and clarify multiple testing corrections.
Deepen the discussion on the metabolic products of R. gnavus and their role in CD.
Revise figures for accessibility and improve table layout.
Conclusion:
The manuscript presents important findings on Ruminococcus gnavus in CD but requires minor
revisions to enhance scientific robustness, methodological clarity, and statistical precision.
Recommendation:
Minor revisions required. 
Title: Unveiling the diagnostic and pro-inflammatory role of Crohn’s disease: insights from
16S-guided discovery and species-specific validation
Version: 1 Date: 15 Feb 2025
Reviewer's report:
General Assessment:
This manuscript investigates the association between Ruminococcus gnavus and Crohn’s
disease (CD), a topic of significant clinical relevance due to the increasing incidence of CD,
particularly in Asia. The manuscript presents interesting findings, but several revisions are
necessary to ensure scientific rigor, methodological soundness, statistical accuracy, and clarity
in figures and tables.
Scientific and Methodological Evaluation:
Strengths: The study addresses an important gap in CD research, focusing on the gut
microbiota’s role, particularly R. gnavus. The use of sequencing to identify microbiota
composition is appropriate and timely.
Limitations and Revisions Needed:
Rationale: The manuscript should elaborate on why R. gnavus was selected over other bacteria
linked to CD.
Sample Size: The cohort is relatively small, potentially limiting the power of the study.
Justification for this sample size is essential.
Inclusion/Exclusion Criteria: More detail is needed on the rationale behind these criteria to
enhance reproducibility and clarity.
Microbiota Analysis: The reference database for taxonomic classification is not specified and
should be included. A sensitivity analysis would strengthen the conclusions, demonstrating the
robustness of the results.
Functional Analysis: The study infers functional implications of R. gnavus abundance but does
not validate these claims experimentally. Functional assays or metabolomic analysis would
significantly enhance the manuscript’s impact.
Statistical Evaluation:
Multiple Testing: It is unclear whether corrections for multiple comparisons were applied.
Methods like Benjamini-Hochberg should be mentioned if used.
Effect Sizes and Confidence Intervals: Including these for key findings would provide a clearer
picture of the biological significance.
p-Values: Some p-values are reported as <0.05. Exact values should be provided for
transparency.
Figures and Tables Evaluation:
Figures:
Color Palette: Figures 2 and 4 need colorblind-friendly palettes.
Figure 3: The legend is too brief; a more detailed description of each panel is necessary.
Tables:
Supplementary Tables: Tables 1-5 are informative, but Table 3 is particularly dense. Splitting it
into smaller sections or using visual aids would improve readability.
Recommendations for Revision:
Expand the introduction to justify the choice of R. gnavus.
Provide a rationale for the sample size and detail the inclusion/exclusion criteria.
Specify the reference database and include a sensitivity analysis.
Incorporate effect sizes, confidence intervals, and clarify multiple testing corrections.
Deepen the discussion on the metabolic products of R. gnavus and their role in CD.
Revise figures for accessibility and improve table layout.
Conclusion:
The manuscript presents important findings on Ruminococcus gnavus in CD but requires minor
revisions to enhance scientific robustness, methodological clarity, and statistical precision.
Recommendation:
Minor revisions required. 
Please review this paper.
user
Title: Unveiling the diagnostic and pro-inflammatory role of Crohn’s disease: insights from
16S-guided discovery and species-specific validation
Version: 1 Date: 15 Feb 2025
Reviewer's report:
General Assessment:
This manuscript investigates the association between Ruminococcus gnavus and Crohn’s
disease (CD), a topic of significant clinical relevance due to the increasing incidence of CD,
particularly in Asia. The manuscript presents interesting findings, but several revisions are
necessary to ensure scientific rigor, methodological soundness, statistical accuracy, and clarity
in figures and tables.
Scientific and Methodological Evaluation:
Strengths: The study addresses an important gap in CD research, focusing on the gut
microbiota’s role, particularly R. gnavus. The use of sequencing to identify microbiota
composition is appropriate and timely.
Limitations and Revisions Needed:
Rationale: The manuscript should elaborate on why R. gnavus was selected over other bacteria
linked to CD.
Sample Size: The cohort is relatively small, potentially limiting the power of the study.
Justification for this sample size is essential.
Inclusion/Exclusion Criteria: More detail is needed on the rationale behind these criteria to
enhance reproducibility and clarity.
Microbiota Analysis: The reference database for taxonomic classification is not specified and
should be included. A sensitivity analysis would strengthen the conclusions, demonstrating the
robustness of the results.
Functional Analysis: The study infers functional implications of R. gnavus abundance but does
not validate these claims experimentally. Functional assays or metabolomic analysis would
significantly enhance the manuscript’s impact.
Statistical Evaluation:
Multiple Testing: It is unclear whether corrections for multiple comparisons were applied.
Methods like Benjamini-Hochberg should be mentioned if used.
Effect Sizes and Confidence Intervals: Including these for key findings would provide a clearer
picture of the biological significance.
p-Values: Some p-values are reported as <0.05. Exact values should be provided for
transparency.
Figures and Tables Evaluation:
Figures:
Color Palette: Figures 2 and 4 need colorblind-friendly palettes.
Figure 3: The legend is too brief; a more detailed description of each panel is necessary.
Tables:
Supplementary Tables: Tables 1-5 are informative, but Table 3 is particularly dense. Splitting it
into smaller sections or using visual aids would improve readability.
Recommendations for Revision:
Expand the introduction to justify the choice of R. gnavus.
Provide a rationale for the sample size and detail the inclusion/exclusion criteria.
Specify the reference database and include a sensitivity analysis.
Incorporate effect sizes, confidence intervals, and clarify multiple testing corrections.
Deepen the discussion on the metabolic products of R. gnavus and their role in CD.
Revise figures for accessibility and improve table layout.
Conclusion:
The manuscript presents important findings on Ruminococcus gnavus in CD but requires minor
revisions to enhance scientific robustness, methodological clarity, and statistical precision.
Recommendation:
Minor revisions required. 
assistant