Longitudinal analysis of the rectal microbiome in dogs with diabetes mellitus after initiation of insulin therapy

Nicole L. Laia; Patrick C. Barko; Drew R. Sullivan; Maureen A. McMichael; David A. Williams; Jennifer M. Reinhart

doi:10.1371/journal.pone.0273792

Peer Review History

Original SubmissionMarch 29, 2022
12 Jul 2022 Decision Letter - Jasbir Singh Bedi, Editor PONE-D-22-09246Longitudinal analysis of the rectal microbiome in dogs with diabetes mellitus after initiation of insulin therapyPLOS ONE Dear Dr. Reinhart, 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. Please submit your revised manuscript by 31.07.2022. 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. 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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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 [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? 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Reviewer #1: 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: Line 91 Enterobacteriaceae should be italicized Line 216 As should be added before per Line 264 “was a large and significant” should be reframed Line 267 “from” to be removed Line 282 Please add full stop Line 320 Instead of Diabetic it should be Insulin Line 353 Check spelling of Enterobacteriaceae Line 359 Please see “in” Line 381 Replace Methods with method Line 398 Studies. There are few questions: 1. The authors said “The objective of this pilot study was to characterize the gastrointestinal microbiome of dogs with diabetes mellitus at the time of diagnosis and over the first 12 weeks of insulin therapy and identify associations with glycemic control” However they are also suggesting that “This pilot study was not designed to make inferences about cause and effect between the intestinal microbial composition and host health; however, it does demonstrate shifts within the intestinal microbiome of dogs with diabetes during initial insulin therapy”. So, if, the objective was not to make any inference of cause and effect between the intestinal microbial composition and host health then what is the purpose of this study? 2. In this study statistically significant changes in microbial diversity were not observed thus it means that the microbiome did not change significantly before and after the initiation of the insulin therapy. Does it mean that there is no significant role of microbial diversity in DM in dogs. ****** 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 ******** [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. Attachments Attachment Submitted filename: Review.docx https://doi.org/10.1371/journal.pone.0273792.r001
Revision 1
18 Jul 2022 Author Response Many thanks to the reviewer for their comments and questions. We have done our best to address all concerns, both in the manuscript and below. Line 91 Enterobacteriaceae should be italicized – corrected Line 216 As should be added before per – added Line 264 “was a large and significant” should be reframed – “large and” removed Line 267 “from” to be removed – removed Line 282 Please add full stop – period removed Line 320 Instead of Diabetic it should be Insulin – corrected Line 353 Check spelling of Enterobacteriaceae – corrected and italicized Line 359 Please see “in” – I’m sorry I don’t understand this correction Line 381 Replace Methods with method – corrected Line 398 Studies. – I don’t understand this correction either Thank you for the above corrections. There were a couple (lines 359 and 398) that I didn’t understand. For some reason, the line numbers provided don’t match up with my version of the proof. If you could provide further context and more specific recommendations, I would be happy to address them. There are few questions: 1. The authors said “The objective of this pilot study was to characterize the gastrointestinal microbiome of dogs with diabetes mellitus at the time of diagnosis and over the first 12 weeks of insulin therapy and identify associations with glycemic control” However they are also suggesting that “This pilot study was not designed to make inferences about cause and effect between the intestinal microbial composition and host health; however, it does demonstrate shifts within the intestinal microbiome of dogs with diabetes during initial insulin therapy”. So, if, the objective was not to make any inference of cause and effect between the intestinal microbial composition and host health then what is the purpose of this study? Thank you, this is a point that deserves clarification. In our study, we characterized the GI microbial changes in our population during initial treatment for DM. However, because our study design was single-arm longitudinal (it would be unethical to include an untreated control group), we cannot say definitively that the changes we observed were due to treatment. However, the changes in relative abundance that we found are consistent with what would be expected as glycemic control improves, based on studies in people and mice. Therefore, some relationship between microbial composition and diabetic status seems likely but cannot be definitively stated based on our results and warrants future study. I have clarified this point in the discussion (lines 414-417). 2. In this study statistically significant changes in microbial diversity were not observed thus it means that the microbiome did not change significantly before and after the initiation of the insulin therapy. Does it mean that there is no significant role of microbial diversity in DM in dogs. Another point that deserves clarification, thank you. It is an incorrect, albeit common, assumption that if there are no changes in measures of microbial diversity, then there are no changes in microbial composition. Measures of alpha and beta diversity broadly assess intra- and inter-individual diversity, respectively. They are an attempt to identify and explain large shifts in microbial populations due to investigated factors. However, measures of diversity are insensitive to changes in individual bacterial taxa, which often have important effects on the host. This is why we also assessed the relative abundance of bacterial taxa (analogous to ASVs) and found several genera/species that demonstrated significant changes over time and correlations with fructosamine (see Tables 2 and 3). So, in short, lack of significant changes in measures of diversity does not mean there are no changes within the microbiome. I have added language to the discussion to clarify this point for readers (lines 365-375). Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0273792.r002
16 Aug 2022 Decision Letter - Jasbir Singh Bedi, Editor Longitudinal analysis of the rectal microbiome in dogs with diabetes mellitus after initiation of insulin therapy PONE-D-22-09246R1 Dear Dr. Jennifer 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, Jasbir Singh Bedi Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0273792.r003
Formally Accepted
26 Aug 2022 Acceptance Letter - Jasbir Singh Bedi, Editor PONE-D-22-09246R1 Longitudinal analysis of the rectal microbiome in dogs with diabetes mellitus after initiation of insulin therapy Dear Dr. Reinhart: 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. Jasbir Singh Bedi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0273792.r004

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