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Dear Dr. Zhang,
The reviewers have concluded that your manuscript, "Exploration of severe early childhood caries microbiota through a novel developed nutrient-enriched microbiological medium, high-throughput 16S rRNA sequencing, and culturomics," is suitable for publication. Congratulations on this achievement!
[# PeerJ Staff Note - this decision was reviewed and approved by Konstantinos Kormas, a PeerJ Section Editor covering this Section #]
Dear Dr Wang,
After carefully considering the feedback from the reviewers, we believe that the manuscript is close to being suitable for publication. However, the reviewers have requested minor revisions, including addressing specific comments and adjusting the citations to avoid overlapping with the main text. Once these refinements are made, the manuscript will be in a strong position for publication.
We look forward to receiving the revised version at your earliest convenience.
Best regards,
Authors need to revise the citations since they are overlapped with the main text.
No comments
No comments
The recommended changes have been implemented satisfactorily. Additional comments and tracked changes indicated in the manuscript document.
Significantly improved. A few minor comments need to be attended to linked to error of omission in the materials and methods section, but appearing in the results section. These are indicated in the manuscript document also.
The recommended changes were implemented satisfactorily.
No comment.
Dear Dr Wang,
Thank you for submitting the revised version of your manuscript. We appreciate your efforts to improve the content, and we have observed significant enhancements in the work.
However, the reviewers and I believe the manuscript still requires a thorough final proofreading to ensure clarity, coherence, and overall quality before it can be considered for publication.
We look forward to receiving the revised version.
Best regards,
Marisa Fabiana Nicolás
Academic Editor
PeerJ Life & Environment
None
None
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Authors have addressed well all comments and suggestions.
Authors have addressed well all comments and suggestions.
Authors have addressed well all comments and suggestions.
Authors have addressed well all comments and suggestions.
Following a careful evaluation by the reviewers, it has become clear that your work presents significant contributions to the field of microbiota associated with S-ECC. The reviewers recognized the advancement provided by the creation of an innovative microbiological medium and highlighted the importance of your findings in understanding and treating severe early childhood caries.
However, the reviewers also identified some areas that require substantial improvements before the manuscript can be considered for publication. I would like to highlight the most critical points raised by the reviewers:
Reviewer 1:
- Enhancements in statistical analysis, visualization, keyword optimization, research logic, and experimental detail are necessary to strengthen the credibility of the study.
- Suggestions to improve figures and methodology to make the results more comprehensible and robust.
Reviewer 2:
- Complete revision of references to provide more context and background from the field.
- Need to share raw data to enable the replicability of results.
- The Materials and Methods section needs to be expanded and improved to provide sufficient details about the methods used in the study.
Reviewer 3:
- The methodology needs to be described in more detail to ensure the reproducibility of the study.
- Lack of statistical analyses and in-depth interpretations in some sections.
- Strengthening the discussion to link the results to the study objectives and explore the microbial interactions underlying S-ECC.
- Based on these considerations, I would like to invite you to revise the manuscript according to the reviewers' suggestions. I suggest that you carefully address each point raised and provide detailed explanations, and where appropriate, additional data or analyses to support your conclusions.
I sincerely hope that you will find these recommendations helpful in improving your work, and I look forward to receiving the revised version of the manuscript. If you require further clarification on the suggested revisions, please do not hesitate to contact me.
Best regards,
**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.
This study dives into the S-ECC microbiota through a fresh nutrient-enriched microbiological medium (NEMM), combining high-throughput 16S rRNA sequencing with culturomics. The creation of NEMM marks a significant stride, possibly allowing for the growth and investigation of bacteria linked to severe early childhood caries (S-ECC) that were previously uncultivable. The experimental setup is solid, blending culturomics with sequencing to offer a detailed picture of the S-ECC microbiota. Yet, the statistical analysis could use some tweaking, especially concerning multiple comparisons to bolster the research's credibility. Furthermore, making the figures more understandable and elaborating on the methodology would enhance the paper's contributions. Overall, the research sheds light on the S-ECC microbiota, hinting at future studies and clinical implications.
1. Although the manuscript features various figures to depict the data, some could be made clearer. For example, using stacked column charts to show bacterial abundance might not effectively highlight the differences among groups, particularly when dealing with many bacterial taxa. A suggestion is to add heatmaps or principal component analysis (PCA) plots for a clearer differentiation in microbial communities among sample groups.
2. The manuscript's chosen keywords should mirror the research's core elements. Currently, the keywords might not entirely represent the study's novel aspects, such as the new medium (NEMM) creation and its effect on uncultured bacteria. Adding "novel microbiological medium," "uncultured bacteria," and "culturalomics" is recommended to emphasize these innovative contributions.
3. The reasoning behind developing a new nutrient-enriched microbiological medium (NEMM) is evident, yet the manuscript could better explain how this new medium stands out from existing options beyond the SHI medium. Specifically, a more thorough discussion on the decision-making behind the medium's composition and its expected superiority in cultivating S-ECC microbiota would reinforce the research logic.
4. The manuscript provides an overview of the sample collection process but lacks detailed information on controlling variability in sample collection (e.g., time of day, dietary influences). Including details on how these factors were standardized or their potential impacts on the results would improve the manuscript's experimental design section.
5. While the manuscript describes anaerobic and normoxic culture conditions, it could offer more details on why these specific conditions were chosen and how they were consistently maintained throughout the study. This includes any steps taken to ensure uniform culture conditions across all experiments.
1. The manuscript could use more insights on statistical power calculations and sample size justifications. Considering the microbiota analysis's complexity, it's essential to ensure the study can accurately spot differences across groups. It's advised to add a part that explains how the sample size was decided, including any presumptions about effect sizes and variance in the microbiota data.
2. The section on statistical analysis mentions T-tests for comparing species abundance but leaves out the adjustment for multiple comparisons. With the microbiota data's high dimensionality, likely, numerous tests were conducted. It's suggested to adopt a stricter correction approach, like the False Discovery Rate (FDR) or Bonferroni correction, for adjusting p-values for multiple comparisons. This adjustment needs to be clearly outlined and justified in the methodology section.
The authors present clear and unambiguous English. However, they need to revise all references because they do not provide enough field background and context.
Also, they do not share any raw data, which is worrying because we cannot replicate their results.
The authors should have described their methods in more detail. Thus, the materials and methods section of this manuscript must be improved.
Authors must revise their statistical test since gut microbiome data are compositional.
Detailed comments and suggestions are in the attached file; please revise them.
The authors submitted an article titled: ‘Exploration of S-ECC microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics’ for revision.
The study seeks to explore the oral microbiota of S-ECC in children using two types of media in two forms (liquid and solid). A commonly used medium (SHI) and a novel medium which they developed in their laboratory were used to enhance culturing of previously uncultured bacteria associated with S-ECC. The authors compared the efficacy of the media under anaerobic and normoxic conditions and collected biofilms from the cultured media at various intervals over a period of 28 Days. They compared their findings clinical samples. The developed medium seems efficient and yielded a higher bacterial load, with higher abundance observed and lastly, previously uncultured bacteria in SHI media were cultivable with NEMM. This was confirmed through high-throughput 16S rRNA sequencing. The authors achieved their aim successfully, interpreted their results and discussed their findings.
The article structure and format was mostly adhered to with some technical issues that need to be revisited.
The research question is well defined, there have been previous studies that investigated the oral microbiome of S-ECC however the novelty in this study includes development of an enrichment media with the aim of enhancing the yield.
Generally, the reproducibility of this study is questionable, simply because the methodology is not described in detail and important aspects are omitted. This can be addressed accordingly as suggested in the manuscript document and the additional comments, in order to ensure reproducibility.
While the results are interpreted in detail, the statistical analyses and thorough interpretation thereof are missing in some sections. The authors simply grazed through the surface. Furthermore the discussion and conclusion focus on the developed medium and its properties, neglecting the microbial community contained in the samples and how the microbes interact to lead to development of dental caries. Therefore, authors need to work on strengthening the discussion in order to sum up the findings and tie them back to the study aim which was to explore the microbiota associated with S-ECC.
Overall, there seems to be a language barrier issue. It is prominent throughout the whole document. I suggest the authors seek the assistance of a fluent English speaker or language practitioner to help with proper sentence construction, grammar and correct use of language.
Most of the comments are annotated in the main manuscript document, however a file with additional comments is uploaded with the manuscript.
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