Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The authors have undertaken a multi-omics investigation of functional variations in the gut microbiomes in mice obtained from two separate vendors. However, to strengthen this manuscript, several points must be considered:

1. The authors should state that the very small assignment of samples (a mere 3 per group) might compromise the generalizability of the findings.

2. The authors can provide more specific examples of how findings could translate into advancing precision health and medicine.

3. The authors may want to consider tracking the changes in microbiome other by some additional factors, namely, diet, bedding, and environment variations due to the differences in vendors.

4. The authors should be encouraged to broaden their consideration of longitudinal studies tracking microbiome changes with time, as a means to inform the dynamics of gut microbiome and its relation to host phenotypes.

5. A more thorough discussion of the limitations of this study would be welcome.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

applmicrobiol-3310722-peer-review-v1

 

The current work is interesting, and authors have constructed well planned and presented manuscript. In my opinion paper can be recommended for publication, however, some adjustments needs to be made.

Authors need to provide more inflammation regrading obtained results in the abstract section.

L104: 2.2. Maybe provide a bit more details?

Please, for all suppliers of material and equipment, provide address (headquarter, and not local distributors), including name of the company, address, state (in case of federal countries) in abbreviated way, and country. In next occasion, only name of the company will be sufficient.

Please, the former Lactobacillus genus representatives needs to be presented with new names and abbreviated according to suggestions. https://doi.org/10.1099/ijsem.0.004107.32293557 and https://doi.org/10.1163/18762891-20230114

Maybe well separated and dedicated conclusion section will be appropriate at the end of the manuscript.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors adequately addressed my concerns, so I recommend this article for publication.