PONE-D-20-06300

Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones

PLOS ONE

Dear Dr. Kailun,

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.

The revisions suggested by reviewers pertain mostly to the quality of writing and presentation of the information, including making sure the authors properly define all acronyms and making sure their figures are numbered and labelled correctly.  There are also a number of comments asking for more detail on the methods, and for the authors to reflect on certain aspects.  While minor, I do recommend that the authors take their time to consider all reviewer comments fully.  Thank you for your patience during this unexpectedly long review process.

Please submit your revised manuscript by Jan 09 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:

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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

We look forward to receiving your revised manuscript.

Kind regards,

Suzanne L. Ishaq, PhD

Academic Editor

PLOS ONE

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4. In your Ethics Statement, please confirm that this animal study is approved by IACUC in Xinjiang Agricultural University.

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"This work was supported by the Ministry of Science and Technology of Xinjiang Uygur

Autonomous Region, Autonomous Region Key Laboratory Project (grant number 2016D03012)."

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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

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

Reviewer #1: Yes

Reviewer #2: 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

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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: Yes

Reviewer #2: No

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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: The authors investigate the effect of isoflavone-transforming bacteria HXBM408 isolated from fresh feces of pregnant horses on rat intestinal bacterial diversity and the metabolism of soybean isoflavones. The authors culture the soybean isoflavone transformant HXBM408 in vitro and orally administrate to SD rats to investigate the transformation of soybean isoflavones in vivo, and find that the contents of DAI, DHD and Eq is significantly different between the test group and the control group in the first 14 day post gavage of HXBM408, but the differences are not observed in plasma; in addition, they also find that the administration of HXBM408 can also have an effect on the relative abundance of bacteria in rat feces and intestines, which are quite intriguing. I would support accepting this paper to PLOS ONE after suitable revisions are made.

1. There are several abbreviations in the manuscript that have no full name annotation, like “OTU” in page 9 and “LEfSe” in page 12, the authors should check the manuscript and make sure that there is no obscure abbreviation.

2. There is no figure 1 in this manuscript and the text jumps into figure 2? (the first mentioned figure throughout this manuscript is in page 9, but the figure number is figure 2-1)

3. Several “LAD SCORE” in page 12 should be “LDA SCORE”.

4. Figure 2-2 A, B and C, page 12 of the text, the authors show the LDA SCORE of test group on 7th day, LDA SCORE of control group on 21th day and 35th. How about the LDA SCORE of control group on 7th day? And LDA SCORE of test group on 21th day and 35th?

5. Figure 2-2, there are annotation like “Control group” and “Trial group” in the figure, will it be better to remove the corresponding Chinese annotation?

Reviewer #2: The submission reported the effect of HXBM408 on the bioconversion of DAI and so as the microflora in the rat GI. Following concerns should be addressed before further consideration.

1. Why did the authors choose female Sprague-Dawley rats instead of males? You were only evaluating microflora but not female related cancers?

2. What's the age of your rats?

3. Please mentioned Pediococcus acidilactici instead of HXBM408 in you content which was misleading.

4. what's 3500 r/min? Its not the standard expression.

5. Why not the authors preform the test in a dose-depentdant manner? How did you confirm the dosage at 1 g/kg?

6. 1.5.1:

7. What's the difference b/w administration of DAI for bioconversion and direct feeding of Eq?

8. From 3.1: The results seemed not really successful, what's the comment from the authors?

9. Figure 2: Please remove the Chinese words from the content.

10. It seems that there was no long-trem effect from the feedding of HXBM408. What's the comment from the authors?

11. The English style should be revised.

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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.

PONE-D-20-06300R1

Effect of the Pediococcus acidilactici bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones

PLOS ONE

Dear Dr. Kailun,

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.

The authors have done well to address the comments from the first review, but some additional detail in the methods has been requested.

Please submit your revised manuscript by Jun 03 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,

Suzanne L. Ishaq, PhD

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.

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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: All comments have been addressed

Reviewer #2: All comments have been addressed

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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: Yes

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: No

**********

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: The authors have adequately addressed my comments raised in the previous round of review. And the manuscript is technically sound, and the data support the conclusions, and the statistical analysis is performed appropriately and rigorously. So I feel that this manuscript is now acceptable for publication.

Reviewer #2: 1. Please clarify the term "plasma" in your ms. Especially the title 1.5.2.2.

2. Detail of microflora analysis should be revealed.

3. Other methods for isoflavone conversion should be touched at least.

(a) Chen, KI, Yao, Y, Chen, HJ, Lo, YC, Yu, RC and Cheng, KC. Hydrolysis of isoflavone in black soy milk using cellulose bead as enzyme immobilizer. 2016. Journal of Food and Drug Analysis 24(4):788-795.

(b) Chen, KI, Lo, YC, Liu, CW, Yu, RC, Chou, CC and Cheng, KC. Enrichment of two isoflavone aglycones in black soymilk by using coffee grounds as an immobilizer for b-glucosidase. 2013. Food Chemistry. 139:79-85.

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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: 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.

Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones

PONE-D-20-06300R2

Dear Dr. Kailun,

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,

Suzanne L. Ishaq, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: