Therapeutic effect of Sanhua decoction on rats with middle cerebral artery occlusion and the associated changes in gut microbiota and short-chain fatty acids

Yiming Ni; Liangyin Cai; Xiaojun Gou; Wenjie Li; Mingmei Zhou; Ying Huang

doi:10.1371/journal.pone.0298148

Peer Review History

Original SubmissionOctober 7, 2023
23 Nov 2023 Decision Letter - Muhammad Hassham Hassan Bin Asad, Editor PONE-D-23-27233Therapeutic Effect of Sanhua Decoction on Rats with Middle Cerebral Artery Occlusion and the Associated Changes in Gut Microbiota and Short-Chain Fatty AcidsPLOS ONE Dear Dr. Zhou, 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 Jan 07 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. 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If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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 After careful review it is decided to include minor changes as recommended by the reviewers. Please go through the comments received by the reviewers and submit revised manuscript (with track changing highlighted and other revised manuscript without track changes) along with rebuttal within due date. Thank you for submitting manuscript in the Plos One. [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 Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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 is well designed and contains a comprehensive information. This covers the all aspects of the title. A few suggestions are recommended to improve the quality and streamline the contents for readers better understanding. 1. Manuscripts require to incorporate some technical literature review on previous and traditional application of Sanhua Decoction (SHD). Although some information is given, but a detail or some reported usage for other disorders. 2. Reference # 33 is cited in several times and this reference how not to be a reason for conlict of intrest. Some major portion of your results are dependendents of the findings of this reference. Pleae provide some logical reasons. 3. In methodology section manuscript contains subheadings from 2.2 - 2-4 and in result section this order and nuber is not followed exactly. however some details information is given but such heading for gene expresssion found in result section. 4. Language check is required especially for discussion section. Reviewer #2: There are a few observations to be considered before publishing: All the graphs of results and images are not clear, and the text is too small to be readable. The word "CTRL" in results from lines 199 and onwards is not mentioned in abbreviations (Page 18). Other line numbers are: 206, 221, 223, etc. The discussion is more like a review of the literature and it does not present the comparative studies of any previous data, e.g., the value of polyketide sugar as per literature was nnnn and we observed the improvement as nnn units, etc. In the discussion, references for comparison are presented, but data is absent in comparison. In conclusion, no statistical data has been presented and must be included for the scientific community. ****** 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: 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.0298148.r001
Revision 1
9 Dec 2023 Author Response Dear editor Thank you for taking your valuable time to read the revised manuscript. We have addressed the comments raised by the reviewers, and the amendments are highlighted in the manuscript in revised mode. Below this letter is our explanation on revision according to the comments of the reviewers. We hope that the revised version of the manuscript is now acceptable for publication in your journal. I look forward to hearing from you soon. With best wishes, Yours sincerely, Mingmei Zhou, MD, PhD, Associate Professor Corresponding author To Reviewer #1： Thank you for taking your valuable time to read the revised manuscript. The following is our explanation on revision according to the comments. 1. Manuscripts require to incorporate some technical literature review on previous and traditional application of Sanhua Decoction (SHD). Although some information is given, but a detail or some reported usage for other disorders. Thanks for your suggestions. Sanhua Decoction is a classic Chinese medicine prescription for IS, and we have supplemented its traditional effects in the manuscript (line 63 to 65 and 383 to 384). 2. Reference # 33 is cited in several times and this reference how not to be a reason for conlict of intrest. Some major portion of your results are dependendents of the findings of this reference. Please provide some logical reasons. Thanks for the comments. Reference # 33 analyzed the concentrations of fecal organic acids in IS patients and control subjects. They found IS was associated with decreased acetic acid and increased valeric acid. Our result showed that fecal acetic acid, and valeric acid were significantly increased in MCAO rats, and SHD reversed the changes in acetic acid. In addition, MCAO rats had significantly higher serum levels of acetic acid, and valeric acid, and valeric acid were restored after SHD administration. Literature #33 examined fecal organic acids in human patients, whereas the aim of our article was to examine SCFAs in MCAO rats and to observe the effect of SHD；and whether there are any differences or similarities with human results for better translation to clinical applications. The difference in acetic acid results may be due to diet, as acetic acid can be ingested through vinegar (apple cider vinegar, rice wine vinegar, etc.). The results for valeric acid were consistent in humans and mice. In addition, we have removed some references to literature # 33 to prevent conflict of interest. 3. In methodology section manuscript contains subheadings from 2.2 - 2-4 and in result section this order and nuber is not followed exactly. however some details information is given but such heading for gene expresssion found in result section. Thanks for the attentions. We checked and supplemented the content of 16S rRNA gene sequencing (line 173-179). 4. Language check is required especially for discussion section. Thanks for the attentions. We have reviewed and revised the full language. To Reviewer #2： Thank you for taking your valuable time to read the revised manuscript. The following is our explanation on revision according to the comments. 1. All the graphs of results and images are not clear, and the text is too small to be readable. Thanks for your suggestions. We have uploaded clear images. 2. The word "CTRL" in results from lines 199 and onwards is not mentioned in abbreviations (Page 18). Other line numbers are: 206, 221, 223, etc. Thanks for the comments. We have added "Ctrl" to the list of abbreviations. 3. The discussion is more like a review of the literature and it does not present the comparative studies of any previous data, e.g., the value of polyketide sugar as per literature was nnnn and we observed the improvement as nnn units, etc. In the discussion, references for comparison are presented, but data is absent in comparison. Thanks for the attentions. Where possible, we have supplemented the discussion with data for comparison. Regarding as polyketide sugar unit biosynthesis, the pathway was the result of our functional prediction of the gut microbiota, and we did not perform further tests for polyketide sugar. In addition, we deleted the content about the function prediction of gut microbiota in the discussion section. 4. In conclusion, no statistical data has been presented and must be included for the scientific community. Thanks for your suggestions. We have revised the conclusion section. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0298148.r002
21 Jan 2024 Decision Letter - Muhammad Hassham Hassan Bin Asad, Editor Therapeutic effect of Sanhua decoction on rats with middle cerebral artery occlusion and the associated changes in gut microbiota and short-chain fatty acids PONE-D-23-27233R1 Dear Dr. Zhou, 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. 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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: (No Response) Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) 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: (No Response) 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: (No Response) 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: Manuscript is well written and all questions and suggestions are addressed. There is no such remaining queries left to address. Reviewer #3: I have carefully examined the manuscript, considering its methodology, results, and overall structure. I am pleased to report that the work meets the standards of excellence set by PLOS ONE. The authors have addressed the reviewers observations effectively, and the conclusions drawn are well-supported by the evidence presented. But the graphs of results and images are not still clear, and the text is too small to be readable. ****** 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: Yes: Imran Ahmad ******** https://doi.org/10.1371/journal.pone.0298148.r003
Formally Accepted
8 Feb 2024 Acceptance Letter - Muhammad Hassham Hassan Bin Asad, Editor PONE-D-23-27233R1 PLOS ONE Dear Dr. Zhou, 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 Dr. Muhammad Hassham Hassan Bin Asad Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0298148.r004

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