Peer Review History
| Original SubmissionFebruary 20, 2023 |
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PONE-D-23-04919Characterization of the anti-pathogenic, genomic and phenotypic properties of a Lacticaseibacillus rhamnosus VHProbi M14 isolatePLOS ONE Dear Dr. Duan, 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 Apr 22 2023 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:
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Kind regards, José António Baptista Machado Soares, PhD Academic Editor PLOS ONE 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 2. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. 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In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. [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 Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: 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 Reviewer #2: No Reviewer #3: Yes Reviewer #4: 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: No Reviewer #2: Yes Reviewer #3: No Reviewer #4: 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 entitled “Characterization of the anti-pathogenic, genomic and phenotypic properties of a Lacticaseibacillus rhamnosus VHProbi M14 isolate” is about to provide the characteristics of VHProbi M14 isolate. At abstract line 10, authors specify the effects of lactic acid bacteria. For example “strong inhibitory effects” should be “strong growth inhibitory effects”. Line19, It is not clear that the secondary metabolites is belong to bacteriocins? Bacteriocins is not a secondary metabolite. So authors should re-write that sentence. “The M14 strain contained 23 bacteriocin-related genes encoding for the secondary metabolites, belonging to class II bacteriocins.” Why authors mention of “bacteriostatic activity” in Line 91? It is not clear the function of bacterial suspension. It is not clear what is the advantage of this strain compared with previously identified LAB, because the test for antibacterial activity is not referenced and compared with positive control. Moreover, it is not sure the “Bacteriostatic activity test” I really to check the static or cidal activity. And, What is the difference of this LAB compare with other LAB? There are nots of unclear sentence for example “In the test against S. mutans”, “When tested against F. nucleatum,” and so on, and mistakenly written expression for example “point at line 60, OD600, CO2, IC50, membra, and sometimes missed “and”. Strain name should be abbreviated after first time use. References are not written consistently. At figure 1, What is the inhibition rate by pathogenic bacteria only control mean? Reviewer #2: In this study, the authors set out to characterize the anti-pathogenic, genomic and phenotypic properties of a novel and potential probiotic LAB. The abstract was well written, concisely overviewing the problem statement, methods, results, and conclusion. The study appears well conducted and contributes valuable data to what is already known. Before recommending it for publication, I have the following observations: 1. It is not clear how many repeated experiments (replicates) were done. Authors should include this vital piece of information. 2. For the Growth inhibition step (see line 110), authors should cite the followed method. 3. On what basis did the authors select the pathogens used in this study? Can more information about this be added to the introduction (and, if possible, the discussion) section? 4. Line 247, please change ‘346 strains of bacteria’ to ‘346 bacteria strains’ 5. Given the volume of results obtained, the discussion section can be further improved, e.g. G. vaginalis is an economic pathogen affecting women of childbearing age worldwide. Authors should discuss their findings, presenting their novel strain as an alternative to treating infections caused by this pathogen. 6. The manuscript would benefit greatly if a native English speaker could proofread it for further clarity. Reviewer #3: This manuscript describes the results of an investigation of a novel identified Lactobacillus strain with possible antimicrobial effects on various pathogens. The topic is of interest to the scientific community as the use of probiotic strains is increasing. However a few clarifications should be made before possible publication of the manuscript. 1. Introduction: Please provide a more sufficient justification of the proposed use of the new LB strain as probiotic organism. The main problem of many infections, especially in the oral cavity, is the occurence of pathogenic biofilms. Please indicate a possible way of action of the new LB strain against established biofilms containing pathogens, as a simple application on mature biofilms will only have very little effect on them. 2. p.2, l.54: ... reported a childhood reduction of dental caries...: what is meant by this phrase? Probably you mean the reduction of eary childhood caries (ECC) in patients consuming the mentioned LB strain. This is one of some parts of the manuscript which need a thourough revise of the language to provide a more easily readable manuscript. Further, some passages of the Materials and Methods section are quite long, please shorten this section of the manuscript and avoid repetitions. 3. Table 1: Why did you choose aerobic growth conditions for the P. acnes strain? The ATCC recommendation is an anaerobic culture for this strain (ATCC 6919, Cutibacterium acnes), please double check the correct nomenclature of all used microorganisms as these names change often. 4. Discussion: This section needs major revisions as it is mainly a repetition of the results. Please avoid any unnecessary repetitions. Some ideas for improving this section may include a discussion of possible clinical protocols for the use of the new LB strain, as well as some suggestions what further research should be carried out before an in-vivo application is possible. Reviewer #4: The manuscript “Characterization of the anti-pathogenic, genomic and phenotypic properties of a Lacticaseibacillus rhamnosus VHProbi M14 isolate” is well written, and the study is generally presented with a good design for drawing the conclusions made by the authors. The author isolated and identified a novel LAB strain from cheese that showed the capability to inhibit a series of human pathogens including Streptococcus mutans and Fusobacterium nucleatum. The study brings new results for the LAB characterization that supports earlier studies related to the exploration of clinical probiotics. Still, the manuscript could benefit from some language polishing. I have some minor comments for changes that may be considered during a revision process. If more information is provided as described below, I recommend that the manuscript can be published in Plos One. Introduction Line 44: “and produce lactic acid ….” Line 47-51: The information on other genera is irrelevant to the main context as you did not investigate these bacteria and their interbacterial relationship in the current study. Line 60- 61: Reference. Line 67: “in the prevention of oral diseases…” Line 69: “a strong inhibition effect” or “the strongest inhibition effect” M&M The research question is well defined, relevant, and meaningful. Line 85: where were the S. mautans strains from? Obtained from commercial providers or isolated by the authors? Line 97: The provider of the “Big Dye TM Terminator Cycle Sequencing Ready Reaction kit” Line 104-108: It’s good to see you have tested a wide range of pathogens that are related to various diseases. However, it would be better to provide more background information in the section of Introduction on these target pathogens. Line 111: again, where did you get the strain of F. nucleatum? Line 164: the reference for Oxford cup agar diffusion assay Results Line 247-249: what were those isolated LAB? Why did not show the result? Line 259-260: How close? What was the similarity? Line 271-272: “because….” This sentence should be move to the discussion section. Line 283: reductions of the adhesion index were significant Discussion Line 375: these bacteriocin-related genes were… Line 376: Did you isolate these L. rhamnosus strains? ********** 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 Reviewer #2: Yes: Smith Etareri Evivie Reviewer #3: No Reviewer #4: 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. |
| Revision 1 |
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PONE-D-23-04919R1Characterization of the anti-pathogenic, genomic and phenotypic properties of a Lacticaseibacillus rhamnosus VHProbi M14 isolatePLOS ONE Dear Dr. Duan, 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 May 11 2023 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. We look forward to receiving your revised manuscript. Kind regards, José António Baptista Machado Soares, PhD Academic Editor PLOS ONE Additional Editor Comments: Dear authors, Congratulations for the revised manuscript. Please address the minor comments added by Reviewer 1, as follow: Please add SD in the figure and clarify the test of “Bacteriostatic activity test against other pathogens” because it was not realized a static or bactericidal activity. [Note: HTML markup is below. Please do not edit.] 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: (No Response) Reviewer #3: 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 Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #3: 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 Reviewer #3: 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 Reviewer #3: 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: I still wonder because authors said “Bacteriostatic activity test against other pathogens”, but that is just to test antibacterial effects not for whether static or cidal activity. So, authors should change that. Authors need to add SD in the figure. Reviewer #3: (No Response) ********** 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 Reviewer #3: 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. |
| Revision 2 |
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PONE-D-23-04919R2Characterization of the anti-pathogenic, genomic and phenotypic properties of a Lacticaseibacillus rhamnosus VHProbi M14 isolatePLOS ONE Dear Dr. Duan, 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 May 21 2023 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:
If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, José António Baptista Machado Soares, PhD Academic Editor PLOS ONE Journal Requirements: 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. Additional Editor Comments: Dear authors, Please address the minor commentors of the reviewer that I also agree, more exactly: "I still wonder because authors said “Bacteriostatic activity test against other pathogens”, but that is just to test antibacterial effects not for whether static or bactercidal activity. So, authors should change that. Authors need to add SD in the figure." I believe that after this minor change, that the next version will be suitable for publication. Thank you and best regards, António [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.] 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. |
| Revision 3 |
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Characterization of the anti-pathogenic, genomic and phenotypic properties of a Lacticaseibacillus rhamnosus VHProbi M14 isolate PONE-D-23-04919R3 Dear Dr. Duan, 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, José António Baptista Machado Soares, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-23-04919R3 Characterization of the anti-pathogenic, genomic and phenotypic properties of a Lacticaseibacillus rhamnosus VHProbi M14 isolate Dear Dr. Duan: 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. José António Baptista Machado Soares Academic Editor PLOS ONE |
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