Peer Review History

Original SubmissionJanuary 4, 2020
Decision Letter - Noreen J. Hickok, Editor

PONE-D-20-00301

Foreskin surface area is not associated with sub-preputial microbiome composition or penile cytokines.

PLOS ONE

Dear Dr. Prodger,

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.

Specifically, Reviewer 1 has detailed a weak correlation and the suggestion of submission as a short report. Alternately, additional information in a fuller manuscript would be appropriate.

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We look forward to receiving your revised manuscript.

Kind regards,

Noreen J. Hickok, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

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Reviewer #1: Partly

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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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: In this manuscript, Kigozi et al. analyzed the association between the foreskin surface area and HIV-1 risk by measuring the correlation between foreskin size and anaerobes or pro-inflammatory cytokines. While I found this work of interests, the following concerns should be raised.

1. Manuscript type. This study reports a very specific result of weak correlations between the foreskin surface area and anaerobes or pro-inflammatory cytokines. Considering the significance and the manuscript length, in this case, I would suggest the authors to format it as a “Brief report”, “Communications” or “Letter to the editor” rather than a “Research article”.

2. Technical issues. The analysis on abundance of bacteria was based-on 16S rRNA profiling, mainly on Genus-level. I strongly recommend the authors to (a) go deeper on 97% or 99% OTU level for higher precision, and (b) also from the functional aspect using 16S-based function annotation method (e.g. PICRUSt).

3. In the current results, since there is no individual genus was associated with the foreskin surface area that may influence the risk of HIV-1, is there any probability that the risk is correlated with the combination of multiple organisms? A machine-based approach / regression analysis of multiple-taxon / PCA may inspire new findings, or further confirm the current results.

4. Line #126, for specific anaerobic genera previously found to be associated with HIV-1 risk, each of them should be cited, or linked to the previous studies (e.g. listed in a table to summarize each of the genera and its citation(s)).

5. The resolution of Figure 1 should be improved.

Reviewer #2: Thank you for the opportunity to review this brief, but well-written manuscript. The study appears well-conducted and contributes novel information to the study of MMC and HIV risk. I have only minor comments:

Methods:

• It seems unusual to have ethics information at the end of the methods. If this is a journal style requirement, fine, but otherwise it is more common to lead with ethics information.

• Which R version was used? Any specific packages?

Results:

• Graphical results of numeric IL-8 analysis are mentioned in the methods but not presented.

• It’s possible that the genera previously associated with HIV risk are incorrect. Was a larger analysis conducted? I don’t necessarily advocate a fishing expedition, but given the negative results, perhaps other genera might be important here.

Discussion:

• I am not sure about the strength of the conclusions given the fact that this is a single, relatively small study. Changing “indicating” to “suggesting” on line 155 may adequately temper the language.

Supplement:

• Total bacterial load and quantitative IL8 data are not present in the spreadsheet

**********

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Reviewer #1: No

Reviewer #2: Yes: Ryan Cook

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Revision 1

We thank the reviewers for their efforts and excellent comments. Please see below responses to specific comments.

Reviewer #1: In this manuscript, Kigozi et al. analyzed the association between the foreskin surface area and HIV-1 risk by measuring the correlation between foreskin size and anaerobes or pro-inflammatory cytokines. While I found this work of interest, the following concerns should be raised.

1. Manuscript type. This study reports a very specific result of weak correlations between the foreskin surface area and anaerobes or pro-inflammatory cytokines. Considering the significance and the manuscript length, in this case, I would suggest the authors to format it as a “Brief report”, “Communications” or “Letter to the editor” rather than a “Research article”.

- We apologize for any lack of clarity. The goal of our report is not to imply that there are weak correlations between foreskin surface and either microbiome or immune parameters – rather, it is to demonstrate that there is no correlation. At scientific meetings, we are frequently questioned if there is a relationship between foreskin size and anaerobe burden, and this analysis is meant to address that question. We hope that the data presented are now clear and make a consistent story. Since the mandate of Plos One is to publish valid research regardless of whether the results are positive or negative, we hope that they will be amenable to publishing these negative results in full.

- With regards to manuscript format, Plos One does not offer the manuscript formats suggested by the reviewer. Plos One has a relatively broad definition for Research Articles (“reports the results of original primary research, including quantitative and qualitative studies, methods and software studies, systematic reviews, and other work”), with no word count minimum or maximum.

2. Technical issues. The analysis on abundance of bacteria was based on 16S rRNA profiling, mainly on Genus-level. I strongly recommend the authors to (a) go deeper on 97% or 99% OTU level for higher precision, and (b) also from the functional aspect using 16S-based function annotation method (e.g. PICRUSt).

- Thank you for this suggestion. Data are shown to the 97% OTU level, as recommended.

3. In the current results, since there is no individual genus was associated with the foreskin surface area that may influence the risk of HIV-1, is there any probability that the risk is correlated with the combination of multiple organisms? A machine-based approach / regression analysis of multiple-taxon / PCA may inspire new findings, or further confirm the current results.

- In response to this excellent suggestion we conducted decision tree analyses to evaluate potential associations of combinations of bacterial taxa with surface area. For this analysis, we also expanded to use the full set of bacterial taxa found in the sub-preputial space, as opposed to limiting to those taxa previously associated with circumcision. Only one taxon (an OTU with 80% similarity to Gallicola) was identified as positively associated with surface area. Forcing an expansion of tree depth did not identify any informative or significant combinations of multiple organisms. The one taxon identified as being associated with surface area was only marginally informative (r=0.280), and although the association had a significant Spearman correlation, this taxon had a mean proportional abundance of less than 0.1% and is unlikely to be of biological relevance.

4. Line #126, for specific anaerobic genera previously found to be associated with HIV-1 risk, each of them should be cited, or linked to the previous studies (e.g. listed in a table to summarize each of the genera and its citation(s)).

- The relevant citation had been added.

5. The resolution of Figure 1 should be improved.

- This figure has been uploaded as a high-resolution tiff, and we hope that the reviewer is now able to view it in a high res format.

Reviewer #2: Thank you for the opportunity to review this brief, but well-written manuscript. The study appears well-conducted and contributes novel information to the study of MMC and HIV risk. I have only minor comments.

- Thank you for the kind comments.

Methods:

• It seems unusual to have ethics information at the end of the methods. If this is a journal style requirement, fine, but otherwise it is more common to lead with ethics information.

- These have now been placed at the start of the Methods, as suggested.

• Which R version was used? Any specific packages?

- The R version used was R Development Core Team, Version 3.3.1. This information has now been added to the Methods section (lines 116-118).

Results:

• Graphical results of numeric IL-8 analysis are mentioned in the methods but not presented.

- Thank you, the methods have been corrected (line 112).

• It’s possible that the genera previously associated with HIV risk are incorrect. Was a larger analysis conducted? I don’t necessarily advocate a fishing expedition, but given the negative results, perhaps other genera might be important here.

- Our prior publication demonstrated eight genera associated with HIV risk in uncircumcised men, but the reviewer is correct that the analysis was limited to genera that had previously demonstrated to be reduced by circumcision. To determine if other taxa are associated with surface area, we performed additional analyses expanding to use the full set of bacterial taxa found in the sub-preputial space. Only one taxon (an OTU with 80% similarity to Gallicola) was identified as being marginally informative in predicting surface area (positive association, r=0.280). Although the association had a significant Spearman correlation, this taxon had a mean proportional abundance of less than 0.1% and is therefore unlikely to be of biological relevance.

Discussion:

• I am not sure about the strength of the conclusions given the fact that this is a single, relatively small study. Changing “indicating” to “suggesting” on line 155 may adequately temper the language.

- We have tempered the wording, as suggested.

Supplement:

• Total bacterial load and quantitative IL8 data are not present in the spreadsheet

- Our apologies for the oversight, those data have now been added.

Attachments
Attachment
Submitted filename: Response to reviewers.docx
Decision Letter - Noreen J. Hickok, Editor

PONE-D-20-00301R1

Foreskin surface area is not associated with sub-preputial microbiome composition or penile cytokines.

PLOS ONE

Dear Dr. Prodger,

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.

Specifically, I have asked you to expand your discussion to place it more securely in the context of the field, especially your previous work.

We would appreciate receiving your revised manuscript by Jun 08 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
  • A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
  • An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Noreen J. Hickok, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

These findings are of significance because they (1) show no correlation between foreskin size and anaerobic bacterial load and (2) because they are on update on your previous findings that DID suggest a correlation. Could you please address your previous studies and succinctly point out the assumptions/analyses/small sample sizes that led you to draw your previous conclusions...and how they differ from your current study. Also, please address the issue that these are all adults who are being circumcised to lower their chances of contracting AIDS yet they don't have AIDS and they presumably have been sexually active. Is it possible that these subjects are also skewed? Thus, please bring the paper into context on the level of subject selection and previous studies.

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[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Revision 2

Dear Dr. Hickok

Our group has previously published two independent analyses using data collected during the randomized controlled trial of circumcision in Uganda: one showing an association between foreskin surface area and risk of HIV acquisition (Aids 2009), and a second analysis showing associations between penile anaerobes, pro-inflammatory cytokines, and HIV risk (MBio 2017). However, our group (and, to our knowledge, no other group) has previously assessed the relationship between foreskin surface area and penile anaerobes and/or pro-inflammatory cytokines. Therefore, the analyses presented in the current manuscript are not an update on any previous findings. I apologize for this lack of clarity, and have altered the wording in the introduction in lines 79-80 to try to address this issue.

Another concern raised was the possibility of selection bias for enrollment of men who had been exposed to HIV but remained uninfected. At the time of enrollment in the trial there was no evidence that circumcision reduced HIV risk, and thus enrollment was performed at a community level without selection based on sexual activity or prior HIV exposure. Additionally, the present analyses were performed on samples collected at trial initiation, and thus no additional selection bias was introduced by a requirement of remaining HIV negative throughout the trial period. This has now been clarified on lines 93-95.

I hope that we have adequately addressed your two remaining concerns, and have uploaded a new version of the manuscript with these changes tracked. Thank you for considering our manuscript for publication in Plos One.

Sincerely,

Jessica Prodger

Attachments
Attachment
Submitted filename: response to comments.docx
Decision Letter - Noreen J. Hickok, Editor

PONE-D-20-00301R2

Foreskin surface area is not associated with sub-preputial microbiome composition or penile cytokines.

PLOS ONE

Dear Dr. Prodger,

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.

I am afraid that I am asking you to look at your discussion again and to expand this section as detailed below.

We would appreciate receiving your revised manuscript by Jun 13 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
  • A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
  • An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Noreen J. Hickok, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

I am sorry, but I still ask you to expand your Conclusions/Discussion section. In your introduction, you state,

"We previously reported that on the penis both the density of specific anaerobic bacterial genera

67 and local levels of pro-inflammatory cytokines are associated with increased risk of HIV-1

68 seroconversion in uncircumcised men [5, 6]. Additionally, the abundance of anaerobic genera

69 on the penis correlates positively with local concentrations of these cytokines [5]. One possible

70 interpretation for these findings is that anaerobic bacteria increase HIV-1 risk by driving penile

71 inflammation. Mucosal inflammation is a demonstrated risk factor for cervico-vaginal HIV-1

72 acquisition, and is associated with an increased number and relative susceptibility of HIV-1

73 target cells in the mucosa [7, 8], altered dendritic cell sampling [9], and decreased epithelial

74 barrier function [10, 11].

75 An epidemiologic study showed that a larger foreskin surface area is also associated with an

76 increased risk of HIV-1 seroconversion [12]. Since coverage of the glans on the non-erect penis

77 is variable and dependent on foreskin size, a deeper foreskin fold from a larger foreskin could

78 result in a less aerobic environment that might preferentially promote anaerobic bacterial growth

79 and induce inflammation. However, it has not yet been explored if foreskin size is associated

80 with penile microbiome composition and local inflammation."

I ask that you indicate any weaknesses in your study as well as putting these studies into the context of the other studies that you have cited. Some explanation of what they found and what you found, other than it is not what you found, is needed. Please expand this section so as to increase its relation to the publications in the field.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Revision 3

We have significantly expanded the discussion, and hopefully have now placed our findings within the context of previous publications in the field (lines 156 – 170). We have also included a section detailing what we believe to be the two most important limitations of our study: the lack of direct measurements of (i) depth of foreskin fold, and (ii) HIV target cell density (lines 182 – 192). To our knowledge, no other publications have previously investigated the relationship between foreskin size (or fold depth) and penile microbiome composition or penile immune outcomes.

Decision Letter - Noreen J. Hickok, Editor

Foreskin surface area is not associated with sub-preputial microbiome composition or penile cytokines.

PONE-D-20-00301R3

Dear Dr. Prodger,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Noreen J. Hickok, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Formally Accepted
Acceptance Letter - Noreen J. Hickok, Editor

PONE-D-20-00301R3

Foreskin surface area is not associated with sub-preputial microbiome composition or penile cytokines.

Dear Dr. Prodger:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

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.

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Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Noreen J. Hickok

Academic Editor

PLOS ONE

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