PONE-D-22-12448Antibacterial activity of medicinal plants in Indonesia on Streptococcus pneumoniaePLOS ONE

Dear Dr. Tafroji,

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. I would suggest you have your manuscript undergo language editing, as pointed out by reviewers. Considering the conflicting reviews, the authors are advised to provide a stronger justification of their study, by formulating a clearer hypothesis.

Please submit your revised manuscript by Aug 07 2022 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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We look forward to receiving your revised manuscript.

Kind regards,

Olivier Habimana

Academic Editor

PLOS ONE

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2. Thank you for stating the following in the Acknowledgments Section of your manuscript: 

"This study was funded by National Geographic Society through Young Explorer Program Grant number: HJ-081ER-17, Indonesia Toray Science Foundation (ITSF) through Science and Technology Research Grant 2018, and National Research and Innovation Agency Republic of Indonesia. We thank Rohayati, Smitha Mirsyad Warsadiharja, and Pak Azhar for laboratory assistance in plant extraction and laboratory testing. We also gratefully thank to Ade Irwan Rifai, Sodri, Muhammad Dailami, and Diyan for helping this study in specimen collection."

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: 

"WT received funding from National Geographic Society through The Young Explorer Grants; Grant no. HJ-081ER-17 (https://www.nationalgeographic.org/) and Indonesia Toray Science Foundation (ITSF) through Science and Technology Research Grant 2018 (https://itsf.or.id/winners).

DS received funding from National Research and Innovation Agency Republic of Indonesia (https://international.brin.go.id/) 

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

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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: Partly

Reviewer #3: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: I Don't Know

Reviewer #2: I Don't Know

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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: No

Reviewer #2: Yes

Reviewer #3: Yes

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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: There is a lack of novelty in the manuscript. Why authors did this study with plant extract? what are the photochemical compounds in these extracts? many articles published regarding this topic and what is important in this study?

I recommend the rejection of this article.

Reviewer #2: In the manuscript entitled " Antibacterial activity of medicinal p 1 lants in Indonesia on Streptococcus pneumoniae", the authors prepared extracts from many different types of medical plants using different solvents and tested the antibacterial activity of these extracts against Streptococcus pneumoniae. Most conclusions are supported by appropriate results. I recommend that the manuscript can be considered to accept for publication after the following issues have been addressed:

1. There are many grammar errors in the manuscript.

2. Using commas as the decimal point is not an international way. For example, MIC 0,16 mg/mL is suggested to be modified as “0.16 mg/mL”. Also, the number in line 65, 400.000 is suggested to be modified as “400,000” or “400000”.

3. In line 66, the authors wrote “Drug resistant Streptococcus pneumoniae was reported in Indonesia”, and in line 67, the authors wrote “many drug resistant Streptococcus pneumoniae was reported in Indonesia”. This sentence is repeated.

4. In line 72, such as what bacteria?

5. In line 79, the word “were” should be deleted.

6. In the method section, line 110, the extraction was done using hexane, and followed by acetate, ethanol…, or the extraction was done in hexane, acetate, ethanol…., respectively to get different extractions?

7. In the method section, line 132, why did the authors choose “30 µg” vancomycin as a positive control for the disc diffusion? The authors should explain this. Otherwise, it is hard to judge if 30 µg vancomycin is a suitable control. Also, in the later tests, the authors adopted 4 µg/mL vancomycin as control. Similarly, the authors should explain why they choose “4 µg” vancomycin as a control? Why do you think it is a suitable control?

8. This work used DMSO as the solvent to dissolve plant extracts and used them to do antibacterial tests. The application of these solutions might be a problem DMSO is toxic to cells. It is suggested to use safer solvents if possible.

9. In Fig. 1A, which plant extracts were used to get these data? It needs to be clarified.

10. In Fig. 3, where are the curves of 1 X MIC and 2X MIC? If these curves are overlapped with that of 10 X MIC, please describe it in the main text. If 1 X MIC and 2X are different to that of 10 X MIC, please add the data.

11. In the Mechanism of Actions section, Bacterial lysis, the authors used the growth curves of bacteria by measuring absorbance at 595 nm, and saying bacterial lysis happened because of the decrease of the absorbance at 595 nm. Why? I do not agree with this, because it is a normal growth curves measurement. The decrease of the absorbance only shows the inhibitive effects of the drug you use, but the mechanism behind is unknown. This part needs serious revision.

12. In Fig.5, the description of a to e should be added in the figure caption.

Reviewer #3: The finding is interesting, however, there are some minor mistakes have been observed (like grammar, spellings, commas, pronunciations etc.). The authors are requested to kindly correct all those errors. Also, there is a need to update the references. over-all the manuscript looks good. Tables and graphs are fine and beautifully presented. I recommend that this manuscript can be accepted for publication after minor revisions. Congratulations to authors for this wonderful work.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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[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.]

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PONE-D-22-12448R1Antibacterial activity of medicinal plants in Indonesia on Streptococcus pneumoniaePLOS ONE

Dear Dr. Tafroji,

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.

It should be pointed out that it is expected that the authors address all comments made by all reviewers on a point-by-point basis. To the author's benefit, it would be to address the comments raised by reviewer 1 concerning the justification of the study's experimental design and purpose. I highly recommend that the authors present a complete rebuttal addressing all remarks before a decision can be made.

Please submit your revised manuscript by Oct 02 2022 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: https://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,

Olivier Habimana

Academic Editor

PLOS ONE

[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 #3: (No Response)

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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: (No Response)

Reviewer #3: (No Response)

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

Reviewer #3: (No Response)

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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: (No Response)

Reviewer #3: (No Response)

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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: (No Response)

Reviewer #3: (No Response)

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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: There is a lack of novelty in the manuscript. Why authors did this study with plant extract? what are the photochemical compounds in these extracts? many articles published regarding this topic and what is important in this study?

I recommend the rejection of this article.

Reviewer #3: This manuscript can be accepted in its present form. The authors have carefully revised the manuscript and responded all the queries

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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: #########

Reviewer #3: No

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[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.

Antibacterial activity of medicinal plants in Indonesia on Streptococcus pneumoniae

PONE-D-22-12448R2

Dear Dr. Tafroji,

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,

Olivier Habimana

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The response to all reviewers, as well as the revisions to original manuscript satisfactory.