The Value of a Prophage-Borne Defense System in Phage–Phage Competition

PLOS Computational Biology

Dear Dr. Wingreen,

Thank you for submitting your manuscript to PLOS Computational Biology. After careful consideration, we feel that it has merit but does not fully meet PLOS Computational Biology'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.

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We look forward to receiving your revised manuscript.

Kind regards,

Boyang Ji, Ph.D.

Academic Editor

PLOS Computational Biology

Amber Smith

Section Editor

PLOS Computational Biology

Journal Requirements:

1) Please ensure that the CRediT author contributions listed for every co-author are completed accurately and in full.

At this stage, the following Authors/Authors require contributions: Yigal Meir, and Ned S. Wingreen. Please ensure that the full contributions of each author are acknowledged in the "Add/Edit/Remove Authors" section of our submission form.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: See, the attached PDF.

Reviewer #2: The authors model competition between two temperate phage variants that differ by the carriage of a costly defense system, identifying three cost-dependent regimes: dominance of the defense-carrying prophage, coexistence, and loss of the defense-carrying variant. They further extend the model by allowing mutational loss of the defense system, which eliminates the takeover regime. The manuscript also briefly considers a three-phage system, showing that non-transitive relationships can emerge.

The modeling framework is clear and, to my assessment, the results appear scientifically sound. However, I find that the main conclusions follow rather directly from general ecological and evolutionary principles governing competition between a costly trait and a trait-free variant. In particular, the three-regime, cost-dependent outcome is an expected consequence of fitness trade-offs and does not seem specific to temperate phage biology. Similarly, the additional results, including defense loss by mutation and the possibility of non-transitive interactions in a three-phage system, are largely consistent with straightforward expectations from the model structure.

While the study provides a useful formalization and adds incremental knowledge to the field, I do not see a sufficiently strong conceptual advance or unexpected biological insight to justify publication in this journal. In my view, the manuscript would be better suited for a more specialized journal.

Reviewer #3: Meir et al. propose a simplified mathematical framework that identifies regimes under which phage-encoded defense systems can be evolutionarily stable. The conclusions derived from the model are interesting, and the study has the potential to make a meaningful contribution to the field. I have some minor comments that should be addressed to improve the manuscript’s readability, organization, and thoroughness.

L20f: The Introduction section would benefit from a more thorough literature review of mathematical models developed to address similar questions. It can help position this study against prior modeling efforts.

L38f: There is no dedicated “Methods and Materials” section, and key descriptions of the models (e.g., the two-phage system, system with mutation, and the governing equations) currently appear within the Results section. I suggest moving model formulation and equation descriptions into a Methods and Materials section, which would help separate model setup from interpretation of results.

The Results section would also benefit from clearer subsections organized around the main questions being addressed or the main takeaways of each figure.

L44f: Assumptions (1) and (2): Do other mathematical models developed in a similar context also adopt these assumptions?

Figure 1A-B: It took me some time to understand what diagrams mean and how they connect to the equations. In the current design, blue and red circles inside the orange blobs represent lysogens’ identity while blue and red circles outside the orange blobs represent released phage virions with and without a defense system. The labels next to blue and red circles at the bottom of Panel(A) are somewhat confusing. It would also help to label the reaction/process rates directly on the schematic.

L50f: In Eq. (3), the absence of an invasion loss term analogous to that in Eq. (2) (the third term in Eq.(2)) appears to encode the protection conferred by the defense system. It may help to state this explicitly when introducing the equations. On a similar note, the authors should explain the biological meaning of each term in the equations, rather than only introducing the reaction-rate parameters.

L55: It’s assumed that non-defense prophage carriage has no cost. This assumption is important for interpreting the competition between L1 and L2, but it is not fully justified. The authors should explain why this assumption is reasonable, or discuss whether the results are sensitive to allowing a small fitness cost for L1.

L63-65: what is the rationale for selecting the three alpha_L2 levels? How do you determine that alpha_L2 = 0.8 is relatively high for the growth rate?

L70-71: I understand authors are trying to say a successful defense may remove the very threat that made the defense beneficial. But it sounds more like evolutionary intuition than a direct result emerging from the model. Because it immediately follows “Fig. 1F suggests…,” readers may interpret this as a continuation of the interpretation of Fig. 1, rather than a conceptual motivation for introducing defense loss caused by mutation in Fig. 2.

Figures 2 C and D: Lines with colors other than green and the mixture of green and red are not labeled.

L80-83: kind of circling back to my previous comment, how were the parameter values associated with “small” versus “high” cost determined? For example, αlpha_L2 =0.90 and 0.95 are only marginally different, and without a clearer baseline it is difficult to interpret what constitutes low or high cost. In addition, what criteria were used to determine “coexistence” and “symmetrical coexistence,” other than visual inspection of the trajectories? Was there a quantitative definition or threshold used to classify these outcomes in the simulations? Relatedly, what is meant precisely by “symmetrical coexistence”?

L86: The conclusion that L2 outcompetes L1, and later that the two coexist as effectively identical competitors, appears to rely on the assumption that carrying a prophage without a defense system imposes negligible fitness cost. Would these conclusions still hold if L1 incurred a non-zero cost?

L90: The authors could consider placing the model formulation of the three-phage system in the Supplementary Information.

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Reviewer #1: None

Reviewer #2: No: It says "code can be made available by request", but it is not publicly available.

Reviewer #3: No:

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Submitted filename: Review.pdf

PCOMPBIOL-D-26-00504R1

The Value of a Prophage-Borne Defense System in Phage–Phage Competition

PLOS Computational Biology

Dear Dr. Wingreen,

Thank you for submitting your manuscript to PLOS Computational Biology. After careful consideration, we feel that it has merit but does not fully meet PLOS Computational Biology'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 Sep 20 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 ploscompbiol@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pcompbiol/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

* A letter that responds to each point raised by the editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. This file does not need to include responses to formatting updates and technical items listed in the 'Journal Requirements' section below.

* 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, competing interests statement, or data availability statement, please make these updates within the submission form at the time of resubmission. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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We look forward to receiving your revised manuscript.

Kind regards,

Boyang Ji, Ph.D.

Academic Editor

PLOS Computational Biology

Amber Smith

Section Editor

PLOS Computational Biology

Additional Editor Comments (if provided):

Most of the comments from the previous round of review have been adequately addressed. Reviewer 2 raised an interesting question regarding the underlying reasons for the observed bistability in this system. It would be valuable for the authors to discuss this issue further, along with the limitations of the current study. In addition, the associated website could be further improved for more details.

Journal Requirements:

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.

1) We noticed that you used the phrase 'not shown' in the manuscript. We do not allow these references, as the PLOS data access policy requires that all data be either published with the manuscript or made available in a publicly accessible database. Please amend the supplementary material to include the referenced data or remove the references.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The Authors addressed all my comments and concerns. A do not have any further comments.

Reviewer #2: I appreciate the authors’ thoughtful response and their effort to extend the manuscript by incorporating the case of abortive infection. This is a welcome addition. In particular, I agree that the inclusion of abortive infection leads to qualitatively different behavior, which goes beyond the standard expectations derived from general ecological trade-off theory.

However, the manuscript still falls short in explaining why such differences arise. The presentation remains largely descriptive. Bistability is typically associated with the presence of positive feedback, yet the authors do not identify where such feedback emerges/being strengthened in their model when abortive infection is introduced. Relatedly, it remains unclear why this feature is absent in the baseline model.

Without a clear mechanistic explanation, the new results remain insufficiently interpreted. As a result, this extension, while intriguing, does not yet provide a fully developed biological insight. I encourage the authors to more explicitly analyze and articulate the underlying mechanism that gives rise to bistability and to contrast it directly with structure of the original model.

Reviewer #3: I thank the authors for their revisions. They have addressed all of my previous comments.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: None

Reviewer #2: No: There is a link to a website, but the content seems to be limited to the model and data for Fig. 1 only. The readme is not properly documented either.

Reviewer #3: Yes

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Dear Prof. Wingreen,

We are pleased to inform you that your manuscript 'The Value of a Prophage-Borne Defense System in Phage–Phage Competition' has been provisionally accepted for publication in PLOS Computational Biology.

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology.

Best regards,

Boyang Ji, Ph.D.

Academic Editor

PLOS Computational Biology

Amber Smith

Section Editor

PLOS Computational Biology

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