Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics

Michael T. France; Sarah E. Brown; Anne M. Rompalo; Rebecca M. Brotman; Jacques Ravel

doi:10.1371/journal.pone.0275908

Peer Review History

Original SubmissionJune 9, 2022
8 Sep 2022 Decision Letter - Andrew B. Onderdonk, Editor PONE-D-22-16695Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomicsPLOS ONE Dear Dr. Ravel, 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 Oct 24 2022 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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Additional Editor Comments: I apologize for the length of time evaluation of this manuscript has taken, but I had an exceptionally difficult time finding competent reviewers for this manuscript. I agree with the comments of the reviewer. [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: Yes ******** 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: Yes ****** 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: This work aims to identify shared bacterial strains in vaginal microbiota of reproductive-age daughters and mothers (ages 14-27, 32-51; n=39 pairs) from a metropolitan area to evaluate the hypothesis that vertical transmission is present in vaginal microbiota. Overall similarity in microbiota composition was evaluated for all volunteers with metataxonomics, and additional genome-resolved metagenomics was used to detect shared strains in a subset of families (n=22). In general, metataxonomic similarities did not exceed random expectations and the strain-level metagenomic approach indicated that less strains were shared between family members (this correlated with age; younger daughters shared more strains with their mothers) than unrelated pairs, one explanation being that biogeography might be a stronger driver for similarities in the vaginal microbiota of reproductive-age women than family relations, although some evidence for vertical transmission was present. I focus on bioinformatics aspects of the work in the evaluation. Overall, the methodology is sound and clearly reported, and the conclusions are supported by the presented material. Standard methods for bioinformatics and data analysis have been used; it is interesting to note the use of the less commonly used Yue-Clayton similarity index in the analysis. Limitations of the study are discussed adequately, and relevant literature is cited. I commend the authors for not only making the data and code available but doing this in a well organized format including an open license (GPL-3). I only have the following minor comments on this report. # Minor - Fig 1: might be useful to check if there are alternative ways to visualize the M/D relations in this figure; the comparison is complicated by the large number of colors (species) and limited overlap in M/D pairs. Perhaps showing the results per species & group level variations across all subjects (e.g. difference in the abundance between M/D?) could help to highlight the most distinguished similarity patterns. Just a suggestion to consider. - Consider using a more permissive and broadly compatible open source license, such as MIT, BSD-2-clause, or Artistic 2 (for discussion, see e.g. Morin et al. 2012 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002598). Also consider that many open source developers (including Linux kernel) have chosen to stick to GPL2. - A README file in the source code could help to navigate and interpret the material - line 182; was the Student's t test assumptions fulfilled (approximately normally distributed groups), or would a non-parametric test (Wilcoxon) be justified? ****** 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: Yes: Leo Lahti ******** [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.0275908.r001
Revision 1
23 Sep 2022 Author Response Response to reviewer’s comments Responses to comments in blue Reviewer #1: This work aims to identify shared bacterial strains in vaginal microbiota of reproductive-age daughters and mothers (ages 14-27, 32-51; n=39 pairs) from a metropolitan area to evaluate the hypothesis that vertical transmission is present in vaginal microbiota. Overall similarity in microbiota composition was evaluated for all volunteers with metataxonomics, and additional genome-resolved metagenomics was used to detect shared strains in a subset of families (n=22). In general, metataxonomic similarities did not exceed random expectations and the strain-level metagenomic approach indicated that less strains were shared between family members (this correlated with age; younger daughters shared more strains with their mothers) than unrelated pairs, one explanation being that biogeography might be a stronger driver for similarities in the vaginal microbiota of reproductive-age women than family relations, although some evidence for vertical transmission was present. I focus on bioinformatics aspects of the work in the evaluation. Overall, the methodology is sound and clearly reported, and the conclusions are supported by the presented material. Standard methods for bioinformatics and data analysis have been used; it is interesting to note the use of the less commonly used Yue-Clayton similarity index in the analysis. Limitations of the study are discussed adequately, and relevant literature is cited. I commend the authors for not only making the data and code available but doing this in a well-organized format including an open license (GPL-3). I only have the following minor comments on this report. We thank the reviewer for their time and effort in evaluating our work. # Minor - Fig 1: might be useful to check if there are alternative ways to visualize the M/D relations in this figure; the comparison is complicated by the large number of colors (species) and limited overlap in M/D pairs. Perhaps showing the results per species & group level variations across all subjects (e.g. difference in the abundance between M/D?) could help to highlight the most distinguished similarity patterns. Just a suggestion to consider. We explored additional options for how best to display Figure 1 but ultimately chose to keep the current version. A motivating reason for our decision was that the current plot allows us to display the family’s community composition and label them by number. These numbers are re-used in the network diagram and allow the reader to refer back to the family’s community composition. - Consider using a more permissive and broadly compatible open source license, such as MIT, BSD-2-clause, or Artistic 2 (for discussion, see e.g. Morin et al. 2012 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002598). Also consider that many open source developers (including Linux kernel) have chosen to stick to GPL2. We have revised the open-source license to the more permissive MIT, as suggested by the reviewer. - A README file in the source code could help to navigate and interpret the material A README file was added to the Github page to help navigate the provided material. - line 182; was the Student's t test assumptions fulfilled (approximately normally distributed groups), or would a non-parametric test (Wilcoxon) be justified? Upon further examination, the assumption of normality was not met. For this reason, we have switched to the non-parametric test as suggested by the reviewer. Note the p-value did not change. L174-176 “Sequence similarity between shared strains identified in the same family versus different families were compared using a Wilcoxon rank sum test.” L242-244 “We found strains shared within families trended to being more similar to one another than those shared between families, but this difference was not significant (Figure 5, W15.1=-136, p=0.149).” Attachments Attachment Submitted filename: mother_daughter_r2r.docx https://doi.org/10.1371/journal.pone.0275908.r002
26 Sep 2022 Decision Letter - Andrew B. Onderdonk, Editor Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics PONE-D-22-16695R1 Dear Dr. Ravel, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Andrew B. Onderdonk Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0275908.r003
Formally Accepted
29 Sep 2022 Acceptance Letter - Andrew B. Onderdonk, Editor PONE-D-22-16695R1 Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics Dear Dr. Ravel: 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. If we can help with anything else, please email us at plosone@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. Andrew B. Onderdonk Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0275908.r004

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