PONE-D-21-02685

Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus

PLOS ONE

Dear Dr. Reveles,

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.

As presented, it is difficult to assess the soundness of the data, because of the confusing presentation. Please follow the Reviewer's advice to improve the data presentation.

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Academic Editor

PLOS ONE

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Additional Editor Comments:

The data needs to be presented in a more common fashion. I believe the authors are wrongly using the Wilcoxon as their data from two cohorts can't be paired. As suggested by Rewiewer 1, Table 2 need to be represented graphically with actual relative abundances. It is absolutely fine that there were no remarkable difference between groups. But the granular differences need to be shown with even more rigor. I would guess that some taxa (Haemophilus, Pyramidobacter) were extremely low abundant, and therefore may be irrelevant to present.

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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: Partly

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

Reviewer #1: 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: No

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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

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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: Kitten and colleagues present a valuably and timely study of the gut microbiome of Mexican Americans with T2D. Indeed, T2D is a significant problem in this population and although we know from other populations that the microbiome plays an important role in T2D, there are almost no studies examining the microbiome Mexican Americans specifically. Though the sample size is quite small, this is nonetheless an important contribution to the literature. The manuscript is clear and well written, however there are some concerns that need to be addressed.

The microbiome data should be reported as relative abundance, not raw counts.

Table 2 is difficult to read, but this would probably be addressed by reporting values as relative abundance instead of counts. Also consider reporting the distributions graphically (as in Fig1) rather than as a table.

Table 2 mentions "normalized counts" but there is no discription of how this normalization was performed in the Methods section.

Will the authors make the microbiome data publicly available upon publication? It is common practice to upload all raw sequencing data the the NCBI SRA upon publication and cite the SRA Study Accession number in the mansucript.

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Reviewer #1: No

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Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus

PONE-D-21-02685R1

Dear Dr. Reveles,

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.

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Kind regards,

Franck Carbonero, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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

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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

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

Reviewer #1: Yes

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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: Yes

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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: Yes

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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: All of my concerns have been addressed in this revision.

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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: Aleksandar David Kostic