Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. nov. isolated from sea cucumber larvae

Ryota Yamano; Juanwen Yu; Alfabetian Harjuno Condro Haditomo; Chunqi Jiang; Sayaka Mino; Jesús L. Romalde; Kyuhee Kang; Yuichi Sakai; Tomoo Sawabe

doi:10.1371/journal.pone.0286693

Peer Review History

Original SubmissionMarch 13, 2023
18 Apr 2023 Decision Letter - Cristiane Thompson, Editor PONE-D-23-07380Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. nov. isolated from sea cucumber larvaePLOS ONE Dear Dr. Sawabe, 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. ==============================Reviewers have now commented on your paper. You will see that one of the reviewers are advising that you revise your manuscript. 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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, Cristiane Thompson 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 noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://researchers.general.hokudai.ac.jp/profile/en.24b04e78bac629fd520e17560c007669.html?mode=pc https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0271174 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 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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. 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. 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 authors present a sound body of evidence to justify the description of this new species of the genus Thalassotalea. It is a good example of genomic taxonomy. I am convinced that this format is adequate for the description of a new species. Reviewer #2: The study was well conducted, and the results are very interesting. Congratulations.However, I have some points that need to be addressed. First, please check the figure´s quality. "suggesting strain PTE2 may pale an important role in host-microbe interaction during sea cucumber development"Did the authors mean "may play"? The 16S sequence was generated using which technology? How these sequences were processed? Please clarify.It is not clear what genomes were used in OrthoANI and DDH analysis. What were the parameters used in MLSA phylogeny? ML? NJ? Bootstrap?Do you know if the Figure 1 subtitle is correct? Because Idiomarina rambicola is not visible in the figure. How did the MLSA network build? I could not find the section in Methodology.I suggest that the phrase below could be written removing "I was not able"."However, I was not able to identify a pathway to produce some of the major fatty acids such as C15:1 ω8c and iso-C17:1 ω5C." ****** 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. 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Revision 1
11 May 2023 Author Response Dear Professor Thompson, the editor, and reviewers, We appreciate editor and reviewers for constructive suggestions for PONE-D-23-07380. We improved the manuscript according to the editorial office and reviewers’ comments. Responses for specific comments are described as follows. All changes were highlighted in yellow. Editorial office 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates. Response: Thank you so much for careful check. Style was fit to PLOS ONE format. 2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed. Response: Thank you for the suggestion. We used almost same approach, so many parts of body text were overlapped. We did remove redundancy and put the previous paper as reference. Reviewer: 1 1. The authors present a sound body of evidence to justify the description of this new species of the genus Thalassotalea. It is a good example of genomic taxonomy. I am convinced that this format is adequate for the description of a new species. Response: Thank you so much for the positive comments. Reviewer: 2 1. The study was well conducted, and the results are very interesting. Congratulations. However, I have some points that need to be addressed. First, please check the figure´s quality. Response: Thank you for the comments. We tried to increase figs resolution. 2. "suggesting strain PTE2 may pale an important role in host-microbe interaction during sea cucumber development" Did the authors mean "may play"? Response: Thank you so much for the suggestion. We did correct it. 3. The 16S sequence was generated using which technology? How these sequences were processed? Please clarify. Response: Thank you for the comments. We put the methodology. 4. It is not clear what genomes were used in OrthoANI and DDH analysis. Response: Thank you for the comments. We put the option description; calculate OrthoANI with a default setting and DDH by formula 2. 5. Do you know if the Figure 1 subtitle is correct? Because Idiomarina rambicola is not visible in the figure. Response: Idiomarina was used for outgroup, but after figuring rooted subtree shown in Fig 1, Idiomarina position was not visible. We added some explanation in Fig 1 title. 6. What were the parameters used in MLSA phylogeny? ML? NJ? Bootstrap? How did the MLSA network build? I could not find the section in Methodology. Response: Thank you for the comments. We also put some Idiomarina sequences in Fig 3, and options for MLSA. 6. I suggest that the phrase below could be written removing "I was not able". "However, I was not able to identify a pathway to produce some of the major fatty acids such as C15:1 ω8c and iso-C17:1 ω5C." Response: Thank you for the comments. According to the suggestion, we did correct the sentence. Attachments Attachment Submitted filename: Response_letter_30Apr23.docx https://doi.org/10.1371/journal.pone.0286693.r002
22 May 2023 Decision Letter - Cristiane Thompson, Editor Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. nov. isolated from sea cucumber larvae PONE-D-23-07380R1 Dear Dr. Sawabe, 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, Cristiane Thompson Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0286693.r003
Formally Accepted
24 May 2023 Acceptance Letter - Cristiane Thompson, Editor PONE-D-23-07380R1 Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. nov. isolated from sea cucumber larvae Dear Dr. Sawabe: 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 prof. Cristiane Thompson Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0286693.r004

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