PONE-D-21-16611

Development and Characterization of an Oral Microbiome Transplant Among Australians for the Treatment of Dental Caries and Periodontal Disease: A Study Protocol.

PLOS ONE

Dear Dr. Nath,

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.

In addition to clarification of the results throughout, both reviewers found the concept of the 'super donor' to be poorly described, if not ill conceived. Due to the plasiticity in microbiome between individuals, it is likely to the authors' benefit to more carefully consider this idea.

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Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions?

The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field.

Reviewer #1: Partly

Reviewer #2: Yes

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2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses?

The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory.

Reviewer #1: Partly

Reviewer #2: Yes

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3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable?

Descriptions of methods and materials in the protocol should be reported in sufficient detail for another researcher to reproduce all experiments and analyses. The protocol should describe the appropriate controls, sample size calculations, and replication needed to ensure that the data are robust and reproducible.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Have the authors described where all data underlying the findings will be made available when the study is complete?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. 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: Yes

Reviewer #2: No

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5. 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

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics.

You may also provide optional suggestions and comments to authors that they might find helpful in planning their study.

(Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This manuscript aims to develop and characterize an Oral Microbiome Transplant (OMT) for the treatment of caries and periodontal disease. Supragingival plaque samples would be collected from healthy participants to find donors suitable for microbial transplantation. Based on the current protocol, a novel in vitro flow cell model combined with microscopic examination and DNA sequencing were be used to describe the composition and functions of the donors. Hydrogels would be used to deliver microbiota for OMT. The effectiveness of OMT would be assessed using caries and periodontitis animal models. Although the current research would provide preliminary results of the feasibility of oral microbiome transplant, I still see some major areas of concern that I think need to be addressed before this manuscript is ready for primetime.

1. What is the specific definition of “super donor”? Authors mentioned that it is prudent to understand the variation and functions of a healthy oral microbiome and hence define a “super donor”, however, authors never presented data in support of any of these claims.

2. In Rodent periodontitis model, why not use silk-ligature for induction of experimental periodontitis? Also, why not include the application of a broad-spectrum antimicrobial agent before OMT?

3. “The use of hydrogel for OMT delivery provides a unique opportunity to seed the micro-organisms onto the surface of teeth for a prolonged period” Any data to support these claims?

4. Safety concerns in the application of OMT are similar to those for oral probiotics, as transplanted biofilms should possess a high degree of genetic stability. It is critical to determine whether oral biofilms should be transplanted directly from donors to patients, or pre-treated with methods that eliminate pathogenic organisms prior to transplantations. How can these problems be solved according to the current protocol?

5. In OMT, transplanted biofilms must exhibit the capacity to effectively endure the selective pressure of the environment. Why do authors choose hydrogels to deliver microbiota for OMT? Please specify in the text.

6. The discussion part should focus more on the advantages of this experimental method

Reviewer #2: The protocol seems to make sense, however the concept of the super donor seems a bit naive at this point. None knows what is the "healthiest" microbiota is and how is it supposed to be characterized. The idea of an in vitro "factory" for the beneficial microbiota is very interesting. The weakness of the protocol is that it artificially induces caries and periodontitis in rats and then attempts "fixing" it. It would be much more interesting to test the OMT with naturally occurring periodontitis in dogs or humans directly. Of note, before COVID, we were able to obtain an IRB approval for a direct human-to-human OMT for volunteer couples. (Our study did not move forward due to COVID) Perhaps the authors of the paper may consider something along these lines as an addition to their protocol. This is because if OMT could be shown to work in principle in a simple setting, there will be a strong motivation to continue with the "super donor".

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Reviewer #1: No

Reviewer #2: Yes: ALEXANDER POZHIKOV

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Attachments

Attachment

Submitted filename: 0628plosone.docx

Development and Characterization of an Oral Microbiome Transplant Among Australians for the Treatment of Dental Caries and Periodontal Disease: A Study Protocol.

PONE-D-21-16611R1

Dear Dr. Nath,

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.

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Kind regards,

Christopher Staley, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions?

The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field.

Reviewer #2: Yes

Reviewer #3: No

**********

2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses?

The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory.

Reviewer #2: Yes

Reviewer #3: No

**********

3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable?

Descriptions of methods and materials in the protocol should be reported in sufficient detail for another researcher to reproduce all experiments and analyses. The protocol should describe the appropriate controls, sample size calculations, and replication needed to ensure that the data are robust and reproducible.

Reviewer #2: Yes

Reviewer #3: No

**********

4. Have the authors described where all data underlying the findings will be made available when the study is complete?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. 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 #2: Yes

Reviewer #3: No

**********

5. 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 #2: Yes

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics.

You may also provide optional suggestions and comments to authors that they might find helpful in planning their study.

(Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: My major concern was the use of the hydrogel and the definition of the "super donor". Although one may argue if the hydrogel use is warranted, the authors gave a satisfactory rationale. Still, I would leave a room for other potential modes for delivering the OMT other than a hydrogel.

Reviewer #3: The authors are strongly encouraged to perform the proposed study!!!

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7. 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 #2: Yes: Alexander Pozhitkov

Reviewer #3: No