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The authors have addressed all of the reviewers' comments
[# PeerJ Staff Note - this decision was reviewed and approved by Konstantinos Kormas, a PeerJ Section Editor covering this Section #]
Dear Authors, could you address the concerns of the two reviewers?
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
• The manuscript is written in clear and professional English. Minor edits could improve clarity, particularly in lines such as 23, 45, and 63.
• The literature review is comprehensive and current, including recent studies (2024–2025). Comparative studies on ecological/geographic distribution of Apis cerana japonica could further strengthen the context.
• Figures and tables are of high quality and appropriately labeled. Figures 1 and 2 are especially effective.
• Raw data have been shared via DRA and FigShare, with sufficient metadata provided.
• The research question is clearly defined and relevant, focusing on microbiota changes in overwintering Apis cerana japonica.
• Sample collection from four colonies across three time points (BO, OW, AO) ensures systematic representation.
• High-throughput sequencing using MiSeq and analysis via DADA2, SILVA DB, and GLMM are robust and properly described.
• The study design is methodologically sound and ethically appropriate.
• The dataset is strong in sample size (n=360) and depth (coverage >99%).
• Statistical analyses (NMDS, PERMANOVA, GLMM) are well-executed and support conclusions.
• Functional implications of bacterial shifts are plausible but speculative, as no SCFA or gene expression data are presented.
• Conclusions are generally supported by data, with proper limitations discussed.
Strengths:
• Novel investigation on Apis cerana japonica with ecological and phylogenetic relevance.
• Identification of potential novel species is a significant contribution.
Areas for Improvement:
1. Add functional validation or explicitly state as a limitation.
2. Discuss inter-colony variability more thoroughly.
3. Deepen discussion on ecological factors (e.g., pollen/honey quality) with caution regarding speculative claims.
Some scientific and linguistic corrections have been made, and the file is attached.
No comment
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Corrections are attached.
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