Exploring bioactive compound origins: Profiling gene cluster signatures related to biosynthesis in microbiomes of Sof Umer Cave, Ethiopia

Abu Feyisa Meka; Gessesse Kebede Bekele; Musin Kelel Abas; Mesfin Tafesse Gemeda

doi:10.1371/journal.pone.0315536

Peer Review History

Original SubmissionAugust 27, 2024
27 Aug 2024 Author Response https://doi.org/10.1371/journal.pone.0315536.r001
30 Sep 2024 Decision Letter - Richa Salwan, Editor PONE-D-24-37159 Exploring Bioactive Compound Origins: Profiling Gene Cluster Signatures Related to Biosynthesis in Microbiomes of Sof Umer Cave, Ethiopia PLOS ONE Dear Dr. Feyisa, 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 Nov 14 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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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. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://doi.org/10.1007/s42452-024-06110-x In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. 4. 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In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. [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: N/A ****** 3. 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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: Work done by author is good. Title of the manuscript acceptable as work done by author Abstract: all things mention clearly in the abstract. explained everything well Introduction: well written Material and methods: all the procedure used during work step wise clearly mentioned Results and discussion: all the data clearly written in graphical manner with photographs. and discussed very well Reviewer #2: Dear Authors, The MS PONE-D-24-37159 entitled Exploring Bioactive Compound Origins: Profiling Gene Cluster Signatures Related to Biosynthesis in Microbiomes of Sof Umer Cave, Ethiopia can be accepted for publication after minor corrections. What is eDNA? In figure 2 Qualitaty correct type mistake. Revise figure there should be connectivity and flow of information in the form of steps Line 119 amplified through PCR …. Mention complete details about the methodology how DNA was amplified? Line 119 An effective concentration what it that mention in unit At what place instrument used for quantification is nanaodrop whereas at other place it is qubit? There should be uniformity Authors should data to public repository ****** 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: Vivek Sharma ******** [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.0315536.r002
Revision 1
4 Oct 2024 Author Response Dear Editors: We would like to thank you for your invitation to resubmit the revised manuscript. We have addressed each point raised, and we believe that the revisions have improved the quality and clarity of our manuscript. Response for Editors 1. Additional permits information in the Methods section. o Response: Permission was not required for the collection of sedimentary rock samples. However, we announce the Bale district administration orally because our study was not applied on humans or animals. 2. Address overlapping text with previous publication (https://doi.org/10.1007/s42452-024-06110-x). o Response: We have revised the manuscript to avoid overlap and appropriately cited any relevant material. The text has been rephrased, and the necessary citations have been included. Changes in the Manuscript: Specifically, some parts of the methods, results and discussion sections have been revised to avoid self-plagiarism. Please see the highlighted parts. 3. Competing interests. o Response: We have submitted the competing interests online as per the journal's guidelines. 4. Captions for the Supporting Information. o Response: We have added captions for all the Supporting Information files of the manuscript and updated the in-text citations accordingly. Change in Manuscript: Captions were added to the Supporting Information section. 5. Provide original uncropped and unadjusted images for blot or gel results. 6. Response: We have provided original, uncropped and adjusted images of the gel results. Response to Reviewer 1 Dear Reviewer, We would like to thank you for your valuable comments and suggestions. We have addressed each point raised, and we believe that the revisions have improved the quality and clarity of our manuscript. Below are our responses to each comment, as well as the changes made to the manuscript. Reviewer #1: 1. Title of the manuscript is acceptable; abstract and introduction are well-written. o Response: Thank you for your positive feedback. 2. Materials and methods: all the procedures are clearly mentioned. o Response: We appreciate your comments, even though we have made slight modification to this section as per Reviewer 2. 3. Results and discussion: data is clearly written and well-discussed. o Response: Thank you for your acknowledgment. We believe these revisions address your concerns and significantly improve the quality of our manuscript. We are confident that the changes we have made have improve our findings and the clarity of our presentation. Please let us know if there are any other areas that require further attention. Thank you again for your constructive feedback. Response to Reviewer 2 Dear Reviewer, We would like to thank you for your valuable comments and suggestions. We have addressed each point raised, and we believe that the revisions have improved the quality and clarity of our manuscript. Below are our responses to each comment, as well as the changes made to the manuscript. Reviewer #2: 1. What is eDNA? o Response: We have added a definition of eDNA in the methodology section to clarify this term for readers who may not be familiar with it. Change in Manuscript: “Environmental DNA (eDNA)” refers to DNA collected from environmental samples such as soil. 2. In Figure 2, "Qualitaty" should be corrected to "Quality." o Response: We have corrected the type error in Figure 2 and ensured clarity and flow in the figure. The revised figure now shows a more logical progression of information, with steps clearly indicated. Changes in the Manuscript: Figure 2 has been updated. 3. Line 119: Amplified through PCR – please provide complete details of the methodology. o Response: We have revised this section to include the complete details of the PCR process, including the reagents, thermal cycling conditions, and specific primers used. Change in Manuscript: "eDNA was amplified using PCR with standard PCR protocol" 4. "An effective concentration" – please mention in units. o Response: We have revised the manuscript to mention the concentration in specific units. Change in Manuscript: "50 ng/μL purified environmental DNA was used for ……………………" 5. Uniformity between Nanodrop and Qubit measurements. o Response: We have ensured consistency in referring to the quantification instrument and clarified where the Nanodrop and Qubit instruments were used. 6. Data should be deposited in a public repository. Response: We have submitted all raw data to the NCBI Sequence Read Archive (SRA) under accession number PRJNA1082540, and a supplementary file was submitted with the manuscript. The data can be accessed at the following link: (https://www.ncbi.nlm.nih.gov/sra/PRJNA1082540). We believe these revisions address your concerns and significantly improve the quality of our manuscript. We are confident that the changes we have made have improve our findings and the clarity of our presentation. Please let us know if there are any other areas that require further attention. Thank you again for your constructive feedback. Attachments Attachment Submitted filename: Response to Reviewers (PLOS ONE).docx https://doi.org/10.1371/journal.pone.0315536.r003
27 Nov 2024 Decision Letter - Richa Salwan, Editor Exploring Bioactive Compound Origins: Profiling Gene Cluster Signatures Related to Biosynthesis in Microbiomes of Sof Umer Cave, Ethiopia PONE-D-24-37159R1 Dear Dr. Abu Feyisa Feyisa 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Richa Salwan Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0315536.r004
Formally Accepted
Acceptance Letter - Richa Salwan, Editor PONE-D-24-37159R1 PLOS ONE Dear Dr. Feyisa, 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. Richa Salwan Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0315536.r005

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