Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey

Zirui Ray Xiong; Mario Cobo; Randy M. Whittal; Abigail B. Snyder; Randy W. Worobo

doi:10.1371/journal.pone.0266470

Peer Review History

Original SubmissionJanuary 26, 2022
4 Mar 2022 Decision Letter - Filippo Giarratana, Editor PONE-D-22-02605Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honeyPLOS ONE Dear Dr. Zirui Ray Xiong, 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. ACADEMIC EDITOR:Dear Authors, improve the paper with the suggestion of the Reviewer 1. Please submit your revised manuscript by 18 April 2022. 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. 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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. Additional Editor Comments: Dear Authors, improve the paper with the suggestion of the Reviewer 1. [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: N/A 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: Introduction - Line 45: In the medical field, ……… and safe to use. Is not clear, please rewrite this sentence - Line 53 in the introduction, delete the dot after infection. - Line 86: replace antioxidant by compounds - Line 89: the sentence “B. subtilis H215 was isolated from raw honey that was inhibitory to Byssochlamys fulva H25” need to be revised. - Line 91: the ref “Lee, Churey (16)” must be corrected as the journal instructions. - Line 99: please change The potential application of these natural products from microbial source by The potential application of these microbial natural products Results - 121: The first sentence should be revised - Line 123: please change this sentence “These 12 isolates were identified by 16S rRNA sequencing; all isolates were Bacillus spp.” by The 16S rDNA sequence of these 12 isolated strains showed a highest identity to that of several B. subtilis spp. - Line 124: change the sentence “by ……were summarized respectively” in Table 1 and 2. - Table 1: this table should be placed in material and methods - As described in table 2, I don’t understand why you have chosen only Co29 and Co30? and not isolates from clove honey like Co5 and Co-6?. These later have better antifungal activity. - Legend of table 2 should be improved - m/z in italic -line 165: “Based on results from previous studies, we presumed that the ions with m/z value of 1043.55 and 1057.57 were C14 and C15 iturin A [M+H]+, respectively: please add references and the formula of the identified compound. Indeed, precise that C14 was at ion with m/z value of 1057.57 was assigned to C15 iturin A [M+H]+. Ion with m/z value of 1079.55 was assigned to C15 iturin A [M+Na]. - C14 or C15? Please clarify -Last paragraph page 11: add the figure number -Figure legend (line 182): “was” and not “were” -Line 209 to 210: sentence should be revised -line 401-402: sentence should be revised Materials and methods - Please add a title “Antifungal assays” before the paragraph in line 448 Additionally, the authors should check their English writing. It should be improved. Reviewer #2: The paper “Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey” provides interesting results about the isolation, characterization and potential application of iturin A with antifungal effect. The experiments were well defined and the results are clear. Moreover, the application of a genomic approach showed interesting findings on the detection and identification of secondary metabolites. Other studies documented the effect of iturin A, however this article can provide a suitable contribution on this specific topic. ****** 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.0266470.r001
Revision 1
10 Mar 2022 Author Response We thank the editor for the opportunity to submit a revised version of our manuscript “Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey”. We appreciate the feedback from the reviewers, and we have revised our manuscript based on the reviewers’ suggestions. We address the specific issues in a detailed response below. Reviewer #1: Introduction - Line 45: In the medical field, ……… and safe to use. Is not clear, please rewrite this sentence We have re-written the sentence for better clarity. - Line 53 in the introduction, delete the dot after infection. We have made the suggested change. - Line 86: replace antioxidant by compounds We have made the suggested revision. - Line 89: the sentence “B. subtilis H215 was isolated from raw honey that was inhibitory to Byssochlamys fulva H25” need to be revised. We have revised the sentence for better clarity. - Line 91: the ref “Lee, Churey (16)” must be corrected as the journal instructions. We appreciate the reviewer’s comment and have corrected the reference as required by the journal. - Line 99: please change The potential application of these natural products from microbial source by The potential application of these microbial natural products We have made the suggested change. Results - 121: The first sentence should be revised We have re-written the sentence for better clarity. - Line 123: please change this sentence “These 12 isolates were identified by 16S rRNA sequencing; all isolates were Bacillus spp.” by The 16S rDNA sequence of these 12 isolated strains showed a highest identity to that of several B. subtilis spp. We have re-written the sentence as suggested for better clarity. - Line 124: change the sentence “by ……were summarized respectively” in Table 1 and 2. We have re-written the sentence to avoid confusion. - Table 1: this table should be placed in material and methods We have rearranged the table order and put the original table 1 in the supporting information. - As described in table 2, I don’t understand why you have chosen only Co29 and Co30? and not isolates from clove honey like Co5 and Co-6?. These later have better antifungal activity. We appreciate the reviewer’s comment. As we mentioned in the manuscript (Line 130-132), the isolates Co29 and Co30 were the only two isolates that were able to produce and excrete antifungal compounds to the extracellular environment. Consequently, these two isolates were selected for the following experiments. - Legend of table 2 should be improved We have re-written the legends for better clarity. - m/z in italic We have made the suggested change. -line 165: “Based on results from previous studies, we presumed that the ions with m/z value of 1043.55 and 1057.57 were C14 and C15 iturin A [M+H]+, respectively: please add references and the formula of the identified compound. Indeed, precise that C14 was at ion with m/z value of 1057.57 was assigned to C15 iturin A [M+H]+. Ion with m/z value of 1079.55 was assigned to C15 iturin A [M+Na]. We appreciate the reviewer’s comment and have added two references on Line 164-165. The molecular formula of the identified compound is also included on Line 165-166. - C14 or C15? Please clarify We thank the reviewer’s comment, but we think our phrasing is clear. The peak with m/z value of 1043.55 was C14 iturin A [M+H]+; m/z 1057.57 was C15 iturin A [M+H]+; m/z 1079.55 was C15 iturin A [M+Na]+ (Line 165-166, Fig 3 legend, S1 Fig legend). -Last paragraph page 11: add the figure number We appreciate the reviewer’s comment, but the paragraph mentioned by the reviewer was a summary of the genome sequencing data and there were no associated figures. -Figure legend (line 182): “was” and not “were” We have made the suggested change. -Line 209 to 210: sentence should be revised We have re-written the sentence for better clarity. -line 401-402: sentence should be revised We have revised the sentence for better clarity. Materials and methods - Please add a title “Antifungal assays” before the paragraph in line 448 We have made the suggested change. Additionally, the authors should check their English writing. It should be improved. We appreciate the reviewer’s comment. We have read through our manuscript and corrected any grammar or language issues. Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0266470.r002
22 Mar 2022 Decision Letter - Filippo Giarratana, Editor Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey PONE-D-22-02605R1 Dear Dr. Zirui Ray Xiong, 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, Filippo Giarratana Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0266470.r003
Formally Accepted
28 Mar 2022 Acceptance Letter - Filippo Giarratana, Editor PONE-D-22-02605R1 Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey Dear Dr. Xiong: 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. Filippo Giarratana Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0266470.r004

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