Dear Dr. Capone,

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 Feb 27 2026 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.

• A 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 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,

Marcello Otake Sato, Ph.D., D.V.M.

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 note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 1 in your text; if accepted, production will need this reference to link the reader to the Table.

3. Thank you for stating the following financial disclosure:

“This work was supported by the National Science Foundation (Award # 2412444 to DC). This research was also funded by the Indiana University Advanced Summer Research Scholarship (2024 award to AH).”

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

If this statement is not correct you must amend it as needed.

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

4. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

5. 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.

Additional Editor Comments:

The manuscript by Heintzman, Keenum, and Capone addresses an interesting and underexplored area of zoonotic research, particularly within developed countries. The reviewers and the editor raised several minor points that should be addressed in a revised version.

First, concerns were noted regarding the title and the use of the term “pathogen.” As multiple species are examined, organisms identified as pathogens in one host species may act as commensals or symbionts in another. Therefore, the terminology should be clarified or adjusted as appropriate throughout the manuscript.

In addition, the explanation of the sample size calculation requires further clarification and methodological detail.

Finally, several issues related to the presentation of tables and figures were identified and should be carefully addressed by the authors in the revised manuscript.

[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?

Reviewer #1: Yes

Reviewer #2: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

**********

Reviewer #1: The manuscript is well-structured and clearly written. The Methodology section (Materials and Methods) is consistent with the presented Results. All perceived contradictions (e.g., the diagnosis of Ascaris lumbricoides in swine) were appropriately addressed and clarified within the Discussion section.

General Recommendations for Figures and Tables

My primary suggestion is to implement minor revisions to the titles and captions of all main figures and tables to ensure they are self-explanatory and can be fully understood without referencing the main text.

As a general guideline, all figure and table titles/captions should be concise, descriptive, and contain the following essential components:

What is it? (The variables/data being presented).

Context/Subject of the Data. (The sample source/population).

Origin of the Data. (Location/Setting of the study).

Period in which the samples or data were obtained.

Additionally, the Notes section of each table/figure should briefly define all symbols, abbreviations, or statistical tests used.

For instance, the current title "Table 1. Prevalence of molecular targets" is excessively brief and requires expansion to meet these criteria.

Specific Observations on Supporting Information

Supporting Information / Supplementary Materials.docx

Table S2 & Table S3: Please revise the titles and notes according to the general recommendation above. Ensure the titles explicitly state the 'What,' 'Context,' 'Origin,' and 'Period.' The notes must clearly explain all symbols, abbreviations (e.g., TAC), and statistical analyses.

Table S4: The table number appears to be repeated in the manuscript draft, and the title remains extremely brief. Please correct the numbering and specify the exact object or assay system that was used for these tests.

Table S6: The same observations apply; please implement the general recommendations regarding the comprehensive title and notes.

Figure S2: I recommend omitting this figure. Its resolution is insufficient, and microscopic images of Ascaris sp. eggs are considered common knowledge within the field, being readily available in high quality in classic parasitology textbooks.

Table S7: Please complete the title information by including the location where the samples were obtained.

The term "Ascaris suum" should be replaced with "Ascaris type" or a similar designation. This is necessary because the manuscript acknowledges that "Eggs of A. suum and A. lumbricoides are morphologically indistinguishable" (Lines 298-299), thus preventing an unsupported species-level diagnosis based solely on morphology.

These constitute my only observations on the manuscript.

Reviewer #2: Please consider the following points:

1. The study objective should be clearly stated.

2. Regarding the research methodology, aspects such as sample size require explanation. Please specify the method used to determine the number of subjects.

**********

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.]

To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures

You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation.

NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.

Attachments

Attachment

Submitted filename: 3-ReviewerComment-PLOS 6Jan25.docx

Diverse enteric bacterial, viral, and parasitic pathogen genes are shed in animal feces in Indiana

PONE-D-25-54640R1

Dear Dr. Capone,

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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager®  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support .

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,

Marcello Otake Sato, Ph.D., D.V.M.

Academic Editor

PLOS One

Additional Editor Comments (optional):

I suggest to rephrase the sample calculation as: "No formal sample size calculation was performed, as the study was designed to provide a broad exploratory assessment of enteric pathogens and associated genes in animal fecal samples." in the subsequent stages of proofreading.