Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseases

Cristian Roca; Alaa A. Alkhateeb; Bryson K. Deanhardt; Jade K. Macdonald; Donald L. Chi; Jeremy R. Wang; Matthew C. Wolfgang

doi:10.1371/journal.pone.0301016

Peer Review History

Original SubmissionDecember 20, 2023
29 Jan 2024 Decision Letter - Farah Al-Marzooq, Editor PONE-D-23-40989Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseasesPLOS ONE Dear Dr. Wolfgang, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Mar 14 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). 3. Thank you for stating the following financial disclosure: “C.R., D.L.C and M.C.W. were funded in part by support from the National Institute of Dental and Craniofacial Research, NIH (U01DE030418), and J.R.W. was funded by NIH K01 DK119582.” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. 5. We notice that your supplementary figures are uploaded with the file type 'Figure'. Please amend the file type to 'Supporting Information'. Please ensure that each Supporting Information file has a legend listed in the manuscript after the references list. 6. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript titled 'Saliva Sampling Method Influences Oral Microbiome Composition and Taxa Distribution Associated with Oral Diseases,' submitted to PLOS ONE, compares the oral microbiome composition using simulated and unstimulated saliva sampling methods. In general, this study is well-conducted, and the figures are good. However, there are many areas that require attention before it can be accepted for publication. Major comments: 1. Considering the significance of stimulated and unstimulated saliva sampling methods for this paper, the authors are required to provide some background on these methods in the introduction. 2. Including a figure illustrating the study design can enhance readers' understanding of the study. 3. The authors are required to provide the accession number for the deposited raw reads. Minor comments: 1. The writing for stimulated saliva sampling collection should be clearer in methods. 2. In lines 155-156, where it is mentioned, 'Taxa were assigned based on matching ASVs to the Human Oral Microbiome database v.15.23 (27),' the authors are advised to provide the criteria used for taxa classification. 3. The authors mentioned ANCOM analysis in line 160; they are advised to provide the full name of it and include a citation. 4. The authors used PC1 and PC3 for PC plots, whereas it is more common to use PC1 and PC2 for such plots. It is advised to consider a three-dimensional figure if the authors wish to retain PC3. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0301016.r001
Revision 1
15 Feb 2024 Author Response We would like to thank the editor and reviewer for their insightful comments and valuable suggestions. We have addressed all comments and believe that it has resulted in a more concise and improved manuscript. Journal requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf The manuscript has been re-organized to comply with the journal requirements for the main text and the authors affiliations. 2. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). Additional details on the ethics statement were added in the Methods so that it clarifies whether a written or verbal consent/assent was obtained from the study participants (lines 108-115). 3. Thank you for stating the following financial disclosure: “C.R., D.L.C and M.C.W. were funded in part by support from the National Institute of Dental and Craniofacial Research, NIH (U01DE030418), and J.R.W. was funded by NIH K01 DK119582.” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. A statement about the role of the funders of the study was added to the author’s contribution section (lines 349-351) and the cover letter. 4. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. The ethics statement was moved to the Materials and Methods section and deleted from its previous position (lines 108-115). 5. We notice that your supplementary figures are uploaded with the file type 'Figure'. Please amend the file type to 'Supporting Information'. Please ensure that each Supporting Information file has a legend listed in the manuscript after the references list. The file type was corrected, and a legend of each supporting information figure is now present in the manuscript after references (lines 472-504). 6. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. References have been revised. Some references have been added to comply with the reviewer’s comments. Reviewer #1 (Comments for the Author): Reviewer #1: The manuscript titled 'Saliva Sampling Method Influences Oral Microbiome Composition and Taxa Distribution Associated with Oral Diseases,' submitted to PLOS ONE, compares the oral microbiome composition using simulated and unstimulated saliva sampling methods. In general, this study is wellconducted, and the figures are good. However, there are many areas that require attention before it can be accepted for publication. Major comments: 1. Considering the significance of stimulated and unstimulated saliva sampling methods for this paper, the authors are required to provide some background on these methods in the introduction. The introduction has been amended to now include background information on stimulated and unstimulated saliva samples (lines 70-78). 2. Including a figure illustrating the study design can enhance readers' understanding of the study. A flow diagram has been added as Figure S1 in the supporting information to clarify the participants selection and study design. 3. The authors are required to provide the accession number for the deposited raw reads. The accession number for the raw sequences and the metadata have been added to the text (lines 334-338). Minor comments: 1. The writing for stimulated saliva sampling collection should be clearer in methods. A clarification for the stimulated saliva collection was included in the methods section (lines 124-127). 2. In lines 155-156, where it is mentioned, 'Taxa were assigned based on matching ASVs to the Human Oral Microbiome database v.15.23 (27),' the authors are advised to provide the criteria used for taxa classification. Details related to the taxonomic classification were added to the text (lines 172-174). 3. The authors mentioned ANCOM analysis in line 160; they are advised to provide the full name of it and include a citation. The full name for ANCOM and the respective citation was added to the text (lines 178-179). 4. The authors used PC1 and PC3 for PC plots, whereas it is more common to use PC1 and PC2 for such plots. It is advised to consider a three-dimensional figure if the authors wish to retain PC3. Regarding Figure 1, there was a typographical error, and it already presented PC1 and PC2. The error was corrected. All remaining figures were revised to show PC1 and PC2. In addition, the plots for PC1 and PC3 were included as a supplementary figure (Fig. S7). Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0301016.r002
11 Mar 2024 Decision Letter - Farah Al-Marzooq, Editor Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseases PONE-D-23-40989R1 Dear Dr. Wolfgang, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at http://www.editorialmanager.com/pone/ and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Farah Al-Marzooq, MD, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0301016.r003
Formally Accepted
20 Mar 2024 Acceptance Letter - Farah Al-Marzooq, Editor PONE-D-23-40989R1 PLOS ONE Dear Dr. Wolfgang, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Farah Al-Marzooq Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0301016.r004

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