Compositionally aware estimation of cross-correlations for microbiome data

Ib Thorsgaard Jensen; Luc Janss; Simona Radutoiu; Rasmus Waagepetersen

doi:10.1371/journal.pone.0305032

Peer Review History

Original SubmissionOctober 18, 2023
2 Feb 2024 Decision Letter - Enrique Hernandez-Lemus, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-23-34186Compositionally aware estimation of cross-correlations for microbiome dataPLOS ONE Dear Dr. Jensen, 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, when resubmitting your manuscript take into account the following methodological suggestions as per the Reviewer's advice (Points 1 to 4 under Comments) 1、On Real Data Analysis of Atopic Dermatitis: 2、Evaluation of the Dynamic Threshold Selection Method 3、Analysis of the Impact of Data Scale on Computational Time: 4、Specific Clarification of Multiple Comparisons Correction Method Please submit your revised manuscript by Mar 18 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. 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). 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You’ll also earn an Accessible Data icon on your published paper if you deposit your data in any participating repository (https://plos.org/open-science/open-data/#accessible-data). 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: [Funding: This work was supported by the Bill and Melinda Gates Foundation and from Foreign, Commonwealth & Development Office through Engineering the Nitrogen Symbiosis for Africa (ENSA; OPP11772165). We thank Adri´an G´omez Repoll´es for assistance with the dermatitis data. We thank Thorsten Thiergart and Ruben Garrido-Oter for assistance with the plant microbiome data. We thank B Kirtley Amos and Max Gordon for critical reading. We thank Sha Zhang for supplying the data used to construct the templates for gene expression data in the simulation studies. We thank Taylor Grace FitzGerald for copy-editing] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [This work was supported by the Bill and Melinda Gates Foundation and from Foreign, Commonwealth & Development Office through Engineering the Nitrogen Symbiosis for Africa (ENSA; OPP11772165). The funders played no role in the content of this paper.] Please include your amended statements within your cover letter; we will change the online submission form on your behalf. [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: Summary In this research, the authors explore the complex domain of microbiome studies with an emphasis on deducing correlations between microbial abundances and various other variables. Addressing a notable gap in current methodologies, which primarily focus on compositional data, this paper introduces two innovative methods: SparCEV (Sparse Correlations with External Variables) and SparXCC (Sparse Cross-Correlations between Compositional data). These methods are uniquely designed to quantify correlations between OTU abundances and phenotypic variables or other compositional datasets, expanding the analytical capabilities in microbiome research. The authors have utilized a combination of real-world data analysis and comprehensive simulation studies to validate their methods. Comments 1、On Real Data Analysis of Atopic Dermatitis: "In the section analyzing real-world data on atopic dermatitis, it would be highly beneficial if the authors could present the highly correlated microbial species identified by other methods. A detailed comparison, particularly focusing on overlaps and distinctions among these methodologies, would greatly enhance our understanding of the uniqueness and effectiveness of your proposed approach." 2、Evaluation of the Dynamic Threshold Selection Method: "The dynamic threshold selection method introduced in the article seems to rely significantly on subjective judgment, such as the user-defined parameter 't'. This reliance might impact the reproducibility and objectivity of the results. I would recommend that the authors explore this method in more depth, providing a more stable criterion for dynamic threshold selection or more objective guidelines to augment the universality and reliability of the method." 3、Analysis of the Impact of Data Scale on Computational Time: "Given that the manuscript indicates similar outcomes for SparXCC and CLR transformations in Case C with large p and q values, albeit being time-consuming, a comparative analysis of the computational time across different methods as a function of data scale would be instructive. Such analysis would aid in assessing the efficiency and applicability of these methods in practical scenarios." 4、Specific Clarification of Multiple Comparisons Correction Method: "In the process of distinguishing between correlated and uncorrelated pairs, a t-test has been applied to CLR. I would urge the authors to clearly specify the exact correction method used for addressing multiple comparisons. For example, was a Bonferroni correction or a Benjamini-Hochberg procedure employed? Clarity in this aspect is crucial for assessing the statistical rigor of the study." ****** 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.0305032.r001
Revision 1
24 Apr 2024 Author Response Response to editor: 1. The manuscript has been edited to comply with the PLOS One style guidelines. Specifically, headings has been changed to sentence case and their font sizes has been adjusted, the main text has been changed to double space paragraph format, and the ”Support information” section has been moved down after the references. Additionally, addresses have been removed from author affiliations and changes in author affiliations since the time of the original submission have been incorporated. 2. Implementations of the methods SparCEV and SparXCC are now available as an R-package at https://github.com/IbTJensen/CompoCor. Everything else necessary to replicate the results of the paper is available at https://github.com/IbTJensen/Microbiome-Cross-correlations. 3. See reply to Editor Point 2. 4. We have removed the funding information from the Acknowledgments section in the manuscript. Please add the following to the funding statement: ”Ib Thorsgaard Jensen and Rasmus Waagepetersen were supported by research grant VIL57389 from Villum Fonden.” Response to reviewer: 1. We have now added a more thorough discussion on the differences between the results found by SparCEV, CLR and log-TSS. Additionally, a supplementary table provides the results with all three methods on all families (this table was also included in the previous version, but it was not mentioned in the text. This has now been rectified.). 2. Inspired by this comment, we made a refinement to the estimation procedures. Specifically, we implemented an iterative procedure similar to the one utilized by SparCC, which both SparCEV and SparXCC are based on. We had initially written this off after initially seeing poor results, but after more thorough investigation, we found that it can help alleviate the bias caused by the sparsity assumption. This obviates the need for the parameter t. We have rerun all the simulation studies and included this new iterative approach. In some cases we see a substantial gain in accuracy, while in others we see a decrease in accuracy (in cases where the sparsity assumption is almost exact). We also provide practical guidance for assessing whether or not the iterative procedure is appropriate on a given dataset. The iterative procedure makes use of user-specified thresholds, t, t1 , and t2 to select ”weakly correlated OTUs/genes” (no connection to the t from the previous version of the manuscript). However, we believe these are of a different nature than the t from the previous version of the manuscript for the following reasons: Firstly, SparCC, which is already widely used in the microbiome literature, uses a similar procedure with a similar user-specified parameter. Secondly, we suggest a bootstrap approach to select them in a data-driven way. Thirdly, we suggest a diagnostic plot to assess whether or not SparCEV/SparXCC with the iterative procedure provides an improvement over SparCEV/SparXCC without it on a given dataset. In contrast, the t from the previous version of the manuscript could neither be selected nor evaluated for a specific dataset. 3. An analysis of the running time is now included in the manuscript. Additionally, we explored a different approach for the mathematical derivation of SparXCC. A different way to express the covari- ances was formulated, and it was easily shown to be equivalent to the formulation from the previous manuscript. Using this formulation substantially speeds up SparXCC. Additionally, with the iterative procedure SparXCC can provide substantially better results than CLR in some cases, even when p and q are large, which we believe justifies the greater running time. 4. Throughout the manuscript, all p-values are corrected for multiple testing with Benjamini- Hochberg (except in the plant microbiome data example, where we follow the method employed in the original paper for the purposes of comparison). This has now been clearly indicated in every instance. Attachments Attachment Submitted filename: Response to reviwers.pdf https://doi.org/10.1371/journal.pone.0305032.r002
23 May 2024 Decision Letter - Enrique Hernandez-Lemus, Editor Compositionally aware estimation of cross-correlations for microbiome data PONE-D-23-34186R1 Dear Dr. Jensen, 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 Editorial Manager® 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, Enrique Hernandez-Lemus, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. 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 ****** 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 ****** 6. 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 authors have adeptly incorporated my feedback. I am pleased with the revisions made to the manuscript. Consequently, I wholeheartedly endorse its publication. ****** 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 #1: No ******** https://doi.org/10.1371/journal.pone.0305032.r003
Formally Accepted
19 Jun 2024 Acceptance Letter - Enrique Hernandez-Lemus, Editor PONE-D-23-34186R1 PLOS ONE Dear Dr. Jensen, 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 Prof. Enrique Hernandez-Lemus Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0305032.r004

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