Taorong-type Baijiu starter: Analysis of fungal community and metabolic characteristics of middle-temperature Daqu and high-temperature Daqu

Yanbo Liu; Xin Li; Haideng Li; Huimin Zhang; Xiangkun Shen; Lixin Zhang; Suna Han; Chunmei Pan

doi:10.1371/journal.pone.0274881

Peer Review History

Original SubmissionApril 24, 2022
18 Jul 2022 Decision Letter - Mónica L. Chávez-González, Editor PONE-D-22-11830Fungal Community Compositional Diversity and Fragrance Components in Medium- and High-Temperature Taorong-Type DaquPLOS ONE Dear Dr. Liu, 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, It is requested that all comments and suggestions from reviewers be addressed and review in detail the authors' guide. Please submit your revised manuscript by Sep 01 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. 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). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. 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, Mónica L. Chávez-González, 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Thank you for stating the following financial disclosure: “Funding This work was supported by the Key Technologies Research and Development Program of Henan Province of China (202102110130), Major Science and Technology Projects of Henan Province of China (181100211400), the Scientific Research Foundation for Docotors of Henan University of Animal Husbandry and Economy (2018HNUAHEDF011) and the Key Subject Projects of Henan University of Animal Husbandry and Economy(C3060020).” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This work was supported by the Key Technologies Research and Development Program of Henan Province of China (202102110130), Major Science and Technology Projects of Henan Province of China (181100211400), the Scientific Research Foundation for Docotors of Henan University of Animal Husbandry and Economy (2018HNUAHEDF011) and the Key Subject Projects of Henan University of Animal Husbandry and Economy(C3060020).” We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that 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: “Funding This work was supported by the Key Technologies Research and Development Program of Henan Province of China (202102110130), Major Science and Technology Projects of Henan Province of China (181100211400), the Scientific Research Foundation for Docotors of Henan University of Animal Husbandry and Economy (2018HNUAHEDF011) and the Key Subject Projects of Henan University of Animal Husbandry and Economy(C3060020). “ Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. 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. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 6. Please ensure that you refer to Figure 1 in your text as, if accepted, production will need this reference to link the reader to the figure. 7. 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: It is requested that all comments and suggestions from reviewers be addressed. [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 analyzed document meets the requirements to be published as an innovation article in its area and demonstrates having an impact on the development of new research hypotheses. However, it is recommended to publish reviewing the grammatical review considerations because although the review is appreciated, the writing has spelling and writing errors and some other grammatical signs. Similar investigations were searched, and they meet the profile. observations Adscriptions Checking for double spaces and spaces after commas is required Abstract Line 24: In the results section The word largest is often overused in the text, its recommended the use of the most significant. Line 26: respectively, It appears that you have an unnecessary comma in a compound predicate. Consider removing it. Line 29: , and. Your sentence contains a series of three or more words, phrases, or clauses. Consider inserting a comma to separate the elements. Keywords Line 35: , Fungal It appears that you have improperly spaced some punctuation. Consider adding a space. Introduction Well done, only consider: Line 37: , and. Your sentence contains a series of three or more words, phrases, or clauses. Consider inserting a comma to separate the elements. Line 53: fpr change by for Line 64: It seems that you have an unnecessary comma. Consider removing the comma. Materials and Methods Line 95: iceboxes The word ice boxes seems to be miswritten. Consider replacing it. Line 97: It seems that semicolon use may be incorrect here. Consider using a comma instead of a semicolon Line 99: Consider adding a transition phrase to improve the flow of your paragraph. In addition, AMPure XP… Line 140: It appears that then may be unnecessary in this sentence. Consider removing it. Line 143: The noun phrase template seems to be missing a determiner before it. Consider adding an article. Line 149: Your sentence may be unclear or hard to follow. Consider rephrasing. (Option: The clean tags were clustered, and chimeric tags identified during this process were removed using UCHIME from USEARCH, leaving the remaining effective tags) Line 153: The phrase on the basis of may be wordy. Consider changing the wording (based on) Results Line 161: The phrase the removal of may be wordy. Consider changing the wording. (removing) Line 171: Delete respectively. Line 222: Change: Monascus can produce various enzymes during the growth process, and their high enzymatic esterifying activity can catalyze the synthesis of acids and alcohols that are significant sources of fragrance in liquors Funding Line 347: Doctors Reviewer #2: ABSTRACT The full title is confusing, the Taorong-Type Daqu, it is liquor flavor and Daqu is a type or fermentation, it must be written in English which is the language of the article and improve writing of the title to link the objective with the liquor. Must be understood in English by all readers. Maybe Fermented liquor flavor Taorong type Daqu or something. The same for the Short title Clarify in methods molecular identification of microorganism communities and characterization of the volatile components of the fermentation liquor Taorong flavor type Daqu Keywords, should not be words included in the title INTRODUCTION Review writing errors and spaces in text Unify the format of references in terms of spaces, score, etc. METHODOLOGY Clarify that a fermentation liquor that was used, is a micro-ecological product enriched with communities of microorganisms called Daqu Taorong- flavor or something and then name this Taorong-flavored Daqu. First explain, what were the temperatures medium and high The subtitle Total DNA extraction and quantitative pcr…. it is suggested to change to molecular identification of microorganism communities of taorong-flavored daqu liquor fermentation by PCR system RESULTS reference the table in the text first goes the explanation, discussion of results and then the table separate discussions from conclusions, discuss in the results ****** 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: Roberto Arredondo-Valdés Reviewer #2: Yes: MIRIAM DESIREE DAVILA MEDINA ******** [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.0274881.r001
Revision 1
3 Aug 2022 Author Response Dear Editor and Reviewers: Thank you again for your letter and for the reviewers' comments concerning our manuscript. Those comments are all valuable and very helpful for revising and improving our paper, as well as the important guiding significance to our researches. We have studied comments carefully and have made correction which we hope meet with approval. The main corrections in the paper and the responds to the reviewer 's comments are as following: Journal 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf It has been modified. 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. It has been modified. 3. Thank you for stating the following financial disclosure: “Funding This work was supported by the Key Technologies Research and Development Program of Henan Province of China (202102110130), Major Science and Technology Projects of Henan Province of China (181100211400), the Scientific Research Foundation for Docotors of Henan University of Animal Husbandry and Economy (2018HNUAHEDF011) and the Key Subject Projects of Henan University of Animal Husbandry and Economy(C3060020).” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. It has been modified. I have added after the funding “all awarded to YL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This work was supported by the Key Technologies Research and Development Program of Henan Province of China (202102110130), Major Science and Technology Projects of Henan Province of China (181100211400), the Scientific Research Foundation for Docotors of Henan University of Animal Husbandry and Economy (2018HNUAHEDF011) and the Key Subject Projects of Henan University of Animal Husbandry and Economy(C3060020).” We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that 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: “Funding This work was supported by the Key Technologies Research and Development Program of Henan Province of China (202102110130), Major Science and Technology Projects of Henan Province of China (181100211400), the Scientific Research Foundation for Docotors of Henan University of Animal Husbandry and Economy (2018HNUAHEDF011) and the Key Subject Projects of Henan University of Animal Husbandry and Economy(C3060020). “ Please include your amended statements within your cover letter; we will change the online submission form on your behalf. I have removed Funding in the manuscript. please show it elsewhere. 5. 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. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. Relevant data has been uploaded to NCBI database，and the accession numbers is PRJNA861706. 6. Please ensure that you refer to Figure 1 in your text as, if accepted, production will need this reference to link the reader to the figure. It has been modified. 7. 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. It has been modified. Response to Reviewer #1: Abstract Line 24: In the results section The word largest is often overused in the text, its recommended the use of the most significant. It has been modified. Line 26: respectively, It appears that you have an unnecessary comma in a compound predicate. Consider removing it. It has been modified. Line 29: , and. Your sentence contains a series of three or more words, phrases, or clauses. Consider inserting a comma to separate the elements. It has been modified. Keywords Line 35: , Fungal It appears that you have improperly spaced some punctuation. Consider adding a space. It has been modified. Introduction Well done, only consider: Line 37: , and. Your sentence contains a series of three or more words, phrases, or clauses. Consider inserting a comma to separate the elements. It has been modified. Line 53: fpr change by for It has been modified. Line 64: It seems that you have an unnecessary comma. Consider removing the comma. It has been modified. Materials and Methods Line 95: iceboxes The word ice boxes seems to be miswritten. Consider replacing it. It has been modified. Line 97: It seems that semicolon use may be incorrect here. Consider using a comma instead of a semicolon It has been modified. Line 99: Consider adding a transition phrase to improve the flow of your paragraph. In addition, AMPure XP… It has been modified. Line 140: It appears that then may be unnecessary in this sentence. Consider removing it. It has been modified. Line 143: The noun phrase template seems to be missing a determiner before it. Consider adding an article. It has been modified. Line 149: Your sentence may be unclear or hard to follow. Consider rephrasing. (Option: The clean tags were clustered, and chimeric tags identified during this process were removed using UCHIME from USEARCH, leaving the remaining effective tags) It has been modified. Line 153: The phrase on the basis of may be wordy. Consider changing the wording (based on) Results It has been modified. Line 161: The phrase the removal of may be wordy. Consider changing the wording. (removing) It has been modified. Line 171: Delete respectively. It has been modified. Line 222: Change: Monascus can produce various enzymes during the growth process, and their high enzymatic esterifying activity can catalyze the synthesis of acids and alcohols that are significant sources of fragrance in liquors It has been modified. Funding Line 347: Doctors It has been modified. Response to Reviewer #2: ABSTRACT The full title is confusing, the Taorong-Type Daqu, it is liquor flavor and Daqu is a type or fermentation, it must be written in English which is the language of the article and improve writing of the title to link the objective with the liquor. Must be understood in English by all readers. Maybe Fermented liquor flavor Taorong type Daqu or something. The same for the Short title Clarify in methods molecular identification of microorganism communities and characterization of the volatile components of the fermentation liquor Taorong flavor type Daqu Keywords, should not be words included in the title Revised and improved the title, new title: Taorong-type Baijiu Starter: Analysis of Fungal Community and Metabolic Characteristics of Middle-Temperature Daqu and High-Temperature Daqu. Redefined keywords: Correlation, Baijiu starter, Flavor ingredient, Microbial community. INTRODUCTION Review writing errors and spaces in text Unify the format of references in terms of spaces, score, etc. The above notes have been modified. METHODOLOGY Clarify that a fermentation liquor that was used, is a micro-ecological product enriched with communities of microorganisms called Daqu Taorong- flavor or something and then name this Taorong-flavored Daqu. First explain, what were the temperatures medium and high The medium-temperature Daqu (The incubation temperature is between 50°C and 60°C, and the maximum does not exceed 60°C) and high-temperature Daqu (The incubation temperature is above 60°C, and the maximum temperature can reach 70°C) were marked D-Z and E-G, respectively. The subtitle Total DNA extraction and quantitative pcr…. it is suggested to change to molecular identification of microorganism communities of taorong-flavored daqu liquor fermentation by PCR system It has been modified. RESULTS reference the table in the text first goes the explanation, discussion of results and then the table separate discussions from conclusions, discuss in the results It has been modified. We tried our best to improve the manuscript and made some changes in the manuscript. These changes will not influence the content and framework of the paper. We appreciate for Editor and Reviewers' warm work earnestly, and hope that the correction will meet with approval. If there are any shortcomings in the article, please tell me immediately, and I will seriously revise it again.Once again, thank you very much for your comments and suggestion. Thank you and best regards. Yours sincerely, Yanbo Liu E-mail: yanboliu@hnuahe.edu.cn Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0274881.r002
7 Sep 2022 Decision Letter - Mónica L. Chávez-González, Editor Taorong-type Baijiu Starter: Analysis of Fungal Community and Metabolic Characteristics of Middle-Temperature Daqu and High-Temperature Daqu PONE-D-22-11830R1 Dear Dr. Yanbo Liu 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, Mónica L. Chávez-González, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0274881.r003
Formally Accepted
26 Sep 2022 Acceptance Letter - Mónica L. Chávez-González, Editor PONE-D-22-11830R1 Taorong-type Baijiu Starter: Analysis of Fungal Community and Metabolic Characteristics of Middle-Temperature Daqu and High-Temperature Daqu Dear Dr. Liu: 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. Mónica L. Chávez-González Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0274881.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .