Fermented cereal-based Munkoyo beverage: Processing practices, microbial diversity and aroma compounds

Sydney Phiri; Sijmen E. Schoustra; Joost van den Heuvel; Eddy J. Smid; John Shindano; Anita Linnemann

doi:10.1371/journal.pone.0223501

Peer Review History

Original SubmissionJune 17, 2019
22 Aug 2019 Decision Letter - Edy de Brito, Editor PONE-D-19-16074 Fermented cereal-based Munkoyo beverage: processing practices, microbial diversity and aroma compounds PLOS ONE Dear Dr. Schoustra, 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. We would appreciate receiving your revised manuscript by Oct 06 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. 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The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for including the following Ethics Statement with your submission: 'The University of Zambia Ethics Committee approved the field work of this study'. At this time, we ask that you please revise this statement to include any associated approval number(s) and please also add this statement to the beginning of your Materials and Methods section. 3. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information. 4. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [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: Paper is, in general well writenn and experimental parts comptently done. Few suggestions/critical advices are reported below: -giving the spontaneus fermentation and the presence of microbial family harbouring pathogenic species, I'm wondering how important is safety and if pathogens (and their concentration) were identified. -fermentation process is even driven by yeast and yeast/bacteria interaction may be responsable for some identified flavour. I'm wondering if authors investigate (the yeast presence) this aspect as well. - I'm usually consider, as effective tools and when it is possible, to integrate the NGS approach with cultivable methods. Your criticisms is gratly appreciated. Line 382-390. This part is bit speculative since no antimicrobial activity was analysed as well as no vitamins concentrations determinate. Reference is mostly related to cobalamin. An example of bacteria produce K vitamin? Reviewer #2: The manuscript titled "Fermented cereal-based Munkoyo beverage: processing practices, microbial diversity and aroma compounds" is well written and scientifically sound. Hence can be accepted for publication. ****** 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0223501.r001
Revision 1
17 Sep 2019 Author Response REPLY TO REVIEWERS COMMENTS We thank the Reviewer for her/his thoughtful comments that have helped us to further improve our manuscript. Detailed responses to the points made are below. 2. Thank you for including the following Ethics Statement with your submission: 'The University of Zambia Ethics Committee approved the field work of this study'. At this time, we ask that you please revise this statement to include any associated approval number(s) and please also add this statement to the beginning of your Materials and Methods section. *REPLY: This information has been added. Our approval letter did not have a number, we have added the date of the letter and the issuing body. 3. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information. REPLY: A copy of a questionnaire has been attached. This is the original questionnaire that was used in our study. The original language of the questionnaire is English. 4. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. REPLY: we will deposit the data in an open access depository and will provide the DOI upon acceptance of the manuscript. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: Paper is, in general well written and experimental parts competently done. Few suggestions/critical advices are reported below: -giving the spontaneous fermentation and the presence of microbial family harboring pathogenic species, I'm wondering how important is safety and if pathogens (and their concentration) were identified. REPLY: The Reviewer is correct that the bacterial families/genera we found in Munkoyo are very diverse and that some families also include pathogenic bacteria. We also found that the pH of the products consistently is around pH 4 or lower. This indicates that the bacteria that lower the pH of their environment are a dominant factor in the microbiota. At this low pH, the proliferation of pathogenic bacteria is suppressed. The question of presence and survival of pathogenic bacteria is important for the further development of Munkoyo towards formalization and upscaling and should be part of future research. We have added a remark to this effect to at the end of the discussion section (starting line 403). -fermentation process is even driven by yeast and yeast/bacteria interaction may be responsible for some identified flavour. I'm wondering if authors investigate (the yeast presence) this aspect as well. REPLY: It is true yeast could inevitably be involved in the production of identified flavors. We chose not to focus on yeast in the present work since previous work on Munkoyo had revealed that yeast was not present in most Munkoyo samples that had been analysed (Schoustra et al 2013, PLOS ONE). We agree with the Reviewer that including yeast would however be of interest and we would recommend doing this in any follow-up to our present work and have added a remark to the discussion section (line 401). - I'm usually consider, as an effective tool whenever it is possible, to integrate the NGS approach with cultivable methods. Your criticisms is greatly appreciated. REPLY: We agree with the Reviewer that the use of culture based methods would be useful in the study of Munkoyo; we feel that this is especially the case in a next step of the research, namely the testing of which mixes of bacteria can generate products with properties similar to Munkoyo that is produces using spontaneous fermentation. We did not use culture based techniques in the present study since the target in this research was to initially identify all possible bacteria in the beverage, for which the use of non-culture based techniques has the highest resolution. We have added the suggestion of using culture based methods to the discussion section (starting line 396). Line 382-390. This part is a bit speculative since no antimicrobial activity was analyzed as well as no vitamins concentrations determinate. Reference is mostly related to cobalamin. An example of bacteria produce K vitamin? **REPLY: The Reviewer makes a valid comment; it is true no antimicrobial activity was analyzed and no vitamin concentration was determined in our study. However, these effects have been found in other studies and could also apply to Munkoyo given the bacterial community composition that we found. In response to comment, we have added remarks to this part of text that the antimicrobial activity and vitamin K production have been demonstrated in other studies and that this may also apply to Munkoyo (line 387 and text starting line 391). Reviewer #2: The manuscript titled "Fermented cereal-based Munkoyo beverage: processing practices, microbial diversity and aroma compounds" is well written and scientifically sound. Hence can be accepted for publication. https://doi.org/10.1371/journal.pone.0223501.r002
24 Sep 2019 Decision Letter - Edy de Brito, Editor Fermented cereal-based Munkoyo beverage: processing practices, microbial diversity and aroma compounds PONE-D-19-16074R1 Dear Dr. Schoustra, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Edy de Brito Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0223501.r003
Formally Accepted
15 Oct 2019 Acceptance Letter - Edy de Brito, Editor PONE-D-19-16074R1 Fermented cereal-based Munkoyo beverage: processing practices, microbial diversity and aroma compounds Dear Dr. Schoustra: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Edy de Brito Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0223501.r004

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