Enhancing in vitro ruminal digestibility of oil palm empty fruit bunch by biological pre-treatment with Ganoderma lucidum fungal culture

F. M. Y. Nur-Nazratul; M. R. M. Rakib; M. Z. Zailan; H. Yaakub

doi:10.1371/journal.pone.0258065

Peer Review History

Original SubmissionMay 10, 2021
14 Jun 2021 Decision Letter - Juan J Loor, Editor PONE-D-21-15493 Enhancing in vitro ruminal digestibility of oil palm empty fruit bunch by biological pre-treatment with Ganoderma lucidum fungal culture PLOS ONE Dear Dr. Rakib, 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 Jul 29 2021 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: http://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, Juan J Loor 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 Additional Editor Comments (if provided): [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 ******** 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: No ****** 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 work was not well set for objectives to be investigated. Many research work in this area has been reported but the authors have not made sufficient reviews with relevanct data. No new innovations have been found and reported under this experiment. Both the Abstract and Conclusion were not well wrapped up using the significant findings under this experiment. In particular, comparison of the treated OPEFB after various periods should have been stated comparatively among the treatments. The authors did not show any suggestions or recommendations to further implement the treated OPEFB in the possible feeding interventions. Reviewer #2: The study investigated the enhancing of the nutritive value of oil palm empty fruit bunch after a fungal culture treatment. This is a comprehensive and very interesting study for increasing the nutritive value after reduce the lignocellulose content by fungal degradation. The study was well-conducted with reasonable replicates. I have a question. Because Reishi is used in traditional medicine in the East, its price is high. Would it be profitable to use it to improve the nutritional value of fruit and vegetable by-products? that is, is the process very expensive? Well, when a fruit and vegetable by-product is used, it is to replace a more expensive food. And if the treatment of the by-product with Reishi is expensive, then the cost of the ration will not be lowered. have you evaluated these aspects? Could Reishi affect palatability? I have few major issues L10-L13-L153-L155-L157 …. Universiti? Check English language, please. L77 new paragraph, so tabulate L88 After Ganoderna lucidum add (G. Lucidum) L170 NEWAY is any Technology, Company, please clarify L185 Do you use DMRT abbreviation though the manuscript? If not, you do not need it. L189 SAS is Statistical Analysis System L198 I am sorry I could not find what is viz.? L303-312 correlation is R or r? Please revise the authors guidelines As I have commented previously, the study is very interesting and the description of the in vitro techniques for the production of gas and the degradability of the dry matter are adequate. But since the main objective is to use this waste byproduct in the feeding of ruminant animals, I miss the determination of some parameters and indices related to ruminal fermentation. I believe that to continue with the publication of this manuscript it should be essential to incorporate at least one table with the pH, ammoniacal nitrogen, total volatile fatty acids, and some individual VFA such us acetate, butyrate, propionate, isobutyrate, valerate and isovalerate. And ideally, it would be possible to have some odd-chain volatile fatty acid. But I think that at least these basic ones that I have indicated must be included. It is probable that the authors have already analyzed them and can incorporate them. The results and the technology are very interesting. English grammar and expression should be improved. ****** 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.0258065.r001
Revision 1
16 Jun 2021 Author Response The authors would like to thank the reviewers for their specific and helpful comments and suggestions. Please find enclosed the revised manuscript with marked changes (Revised Manuscript with Track Changes) and unmarked (Manuscript). Detail response to the reviewers can be find in 'Response to Reviewers'. Below, are the general response by the authors: Respond to editor comments: Contribution statements were added on the title page. The authors also checked throughout the manuscript to ensure the style and formatting. File naming followed the guide given. All figures were uploaded to the Preflight Analysis and Conversion Engine (PACE). Respond to Reviewer 1 comments: The comments given by Reviewer 1 are very general, and not pointing to any specific content of the manuscript. The authors believed that the study was well set, the changes in fiber composition and in vitro rumen digestibility were well described among the treatments, and new interesting innovation was reported in the study as supported by Reviewer 2. The abstract was improved, and the conclusion already summarized the findings. The authors already stated few limitations, recommendations for future research, and potential applications of the treated OPEFB in the final paragraph of the results and discussion section. Respond to Reviewer 2 comments: The authors would like to appreciate the merits given to the study and manuscript. The comments given by Reviewer 2 are specific and relevant to the study. The authors addressed most of the issues, and made necessary modification in the manuscript. The use of G. lucidum in this study was in a form of mycelial culture which is easy to multiply/culture, and not the basidiocarp (fruiting body) which is expensive. All minor errors in the manuscript as pointed by Reviewer 2 were corrected. Unfortunately, rumen fermentation characteristics data as suggested by Reviewer 2 was not recorded during the study, and the authors are unable to provide the data due to unavailability of samples to redo the in vitro experiment. The authors feel that, ruminal fermentation characteristics should be evaluated in future study for the final feed product (after the treated OPEFB is mixed with other ingredients to formulate a balanced ratio). The present study focused on improving the digestibility of OPEFB. The authors also believed that we provided sufficient data to support that the treatment of G. lucidum on OPEFB was able to reduce the fibre composition (especially lignin), and enhanced the in vitro rumen digestibility. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0258065.r002
1 Sep 2021 Decision Letter - Juan J Loor, Editor PONE-D-21-15493R1 Enhancing in vitro ruminal digestibility of oil palm empty fruit bunch by biological pre-treatment with Ganoderma lucidum fungal culture PLOS ONE Dear Dr. Rakib, 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. A FEW REVISIONS ARE STILL NEEDED. Please submit your revised manuscript by Oct 16 2021 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: http://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, Juan J Loor 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. [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 #2: 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: Partly Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 #2: 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 #2: 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: Although, the authors have addressed partly to the issues raised, some additional clarifications and modifications are still required; Line; 370-373, based on the improved nutritional value of the OPEFB by G. lucidum, the authors need to address the improvement and express the lacking parts ..and propose the potential improvement. It would be beneficial to refer to previous workers-References. Conclusions; it looks as if, the authors still discussing, rather than summarizing the significant findings under this experiment, in particular to the improvement rendered by G. lucidum, to what extent? Reviewer #2: The manuscript is now ready for publication. The authors have responded to all the questions that were raised and have completed and improved the document. ****** 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: Yes:** Metha Wanapat 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.0258065.r003
Revision 2
7 Sep 2021 Author Response The authors would like to thank the reviewers for their specific and helpful comments and suggestions. Please find enclosed the revised manuscript with marked changes (Revised Manuscript with Track Changes) and unmarked (Manuscript). Respond to Journal Requirements: The citations and references list were cross-checked, and endured complete and correct. Reference No. 23 was substituted with other reference, as the original reference was unpublished (preprints). Respond to Reviewer #1: The lacking of the G. lucidum-treated OPEFB was stated, where it contain low amount of crude protein, lipids, vitamins, and minerals. Therefore, it is necessary to incorporate the treated OPEFB with other nutrients as supplements for formulation of a balanced ration. Two additional references were added ([49,50]). The conclusions section was improved. The extent of changes in the G. lucidum treated OPEFB were specified in the conclusion section, the conclusion summarized the major findings, and answered the objectives of the study. Respond to Reviewer #2: The authors would like to thank Reviewer #2 for his/her kind contribution in reviewing this manuscript. Other issues: Previously, the rate stated was based on the number of mycelia plugs (5 mm) per 500 g OPEFB. The rate now is expressed as mg/kg of OPEFB. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0258065.r004
17 Sep 2021 Decision Letter - Juan J Loor, Editor Enhancing in vitro ruminal digestibility of oil palm empty fruit bunch by biological pre-treatment with Ganoderma lucidum fungal culture PONE-D-21-15493R2 Dear Dr. Rakib, 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, Juan J Loor Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0258065.r005
Formally Accepted
21 Sep 2021 Acceptance Letter - Juan J Loor, Editor PONE-D-21-15493R2 Enhancing in vitro ruminal digestibility of oil palm empty fruit bunch by biological pre-treatment with Ganoderma lucidum fungal culture Dear Dr. Rakib: 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. Juan J Loor Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0258065.r006

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