PONE-D-23-38263Microbiota in different compartments of the digestive tract of paddlefish (Polyodon spathula) are related to their functionsPLOS ONE

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Reviewers' comments:

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Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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5. Review Comments to the Author

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Reviewer #1: This study used high-throughput sequencing to analyze the microbial communities in different digestive tract compartments (mouth, stomach, and intestine) of paddlefish (Polyodon spathula). The aim is to reveal their characteristics and differences, exploring their associations with host functions. The research, focusing on the economically and ecologically valuable freshwater fish, paddlefish, holds significance for the sustainable development of aquaculture.

Reviewer's Comments:

1. Provide more detailed descriptions of the high-throughput sequencing technology and bioinformatics analysis methods in the article, including steps involved in data analysis and specifics about the software used, ensuring the study's replicability.

2. Offer a more specific explanation of the steps involved in denoising and deduplication of sequencing data to ensure the accuracy and reliability of research results.

3. Provide a more thorough explanation, elucidating the ecological significance of diversity and abundance indices such as Chao1, Ace, Shannon, and Simpson. This will help readers better understand how these indices reflect the characteristics of microbial communities.

4. Provide detailed explanations of the statistical analysis methods used to characterize the microbial communities in different parts, including which statistical tests were employed and whether multiple comparison corrections were applied.

5. Include graphical representations of the results from Mothur software for diversity analysis to better illustrate the outcomes of diversity analysis.

6. The article mentions changes in microbial diversity and community structure without delving into the relationship between these changes and the physiological functions and health status of paddlefish. Further exploration through functional analysis is recommended to investigate the correlation between microbial composition and physiological functions such as nutrient absorption and the immune system in paddlefish.

7. The ariticle does not address whether the study considered temporal variations. Microbial communities may undergo changes over time. Conducting a time-series study would provide better insights into the dynamic changes of microbial communities and their relationship with seasonal or other time-related factors.

8. Analyze the metabolic functions of the microbial community to gain a deeper understanding of their roles in different parts of paddlefish. This includes studying functions such as enzyme production and acid production, which can help explain the microbial involvement in the digestive process of paddlefish.

9. Consider the microbial differences among individual paddlefish, taking into account factors such as age and gender. This in-depth analysis can provide insights into the individual variations in microbial communities among paddlefish.

Reviewer #2: The authors conducted a preliminary exploration of the microbiome in different segments of the digestive tract of paddlefish (Polyodon spathula). It is noteworthy that the experimental structure and design closely resemble the approach outlined by Yang G. et al., as published in 2020 (https://doi.org/10.1016/j.aqrep.2020.100402). While the study offers some insights, the novelty is somewhat lacking, and the microbiome analysis appears restricted to composition and abundance. Moreover, the content presented in tables and figures seems repetitive.

To enhance the manuscript, the authors should consider providing a more in-depth discussion of the findings, emphasizing unique aspects that distinguish their work from Yang G. et al. Additionally, addressing the following points will contribute to the overall clarity and rigor of the study:

Materials and Methods:

Line 100: Clarify the rationale for using fish within the weight range of 1967.2-2471.4g for the study.

Lines 112-115: Specify which part of the organ (e.g., saliva, mouth tissue, digesta, or intestine tissue) was utilized for microbiome analysis.

Line 148: Reconsider the use of T-test for comparing three groups of data. A more suitable approach, such as Kruskal-Wallis, followed by post hoc tests like Dunn’s test, should be employed.

Reviewer #3: This study investigated the microbial diversity and community structure in intestine, stomach, and mouth of paddlefish using high-throughput sequencing, which provide a microbiological basis for the development of aquaculture. However, there are still some problems worth further discussion and revision. Please refer to the attachment for details.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Attachments

Attachment

Submitted filename: Comments.doc

Microbiota in different digestive tract of paddlefish (Polyodon spathula) are related to their functions.

PONE-D-23-38263R1

Dear Dr. Long Chengxing,

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.

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Kind regards,

Nafiu Bala Sanda, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The manuscript can be accepted for publication in PLOS ONE journal. Congratulation!

Reviewers' comments: