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Thank you for the thorough response to all of the reviewers' comments.
[# PeerJ Staff Note - this decision was reviewed and approved by Valeria Souza, a PeerJ Section Editor covering this Section #]
The authors have dealt with the comments I made in an appropriate manner.
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The authors have dealt with the comments I made in an appropriate manner.
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The manuscript is well written and shows great information.
I have just found a minor correction:
Line 321 Add “)” after 19 in (14-17, 19
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L154, My previous comment meant I wonder this part should be "observed ASV", rather than "observed OTU".
Please provide a point-by-point response to all of the reviewers' comments.
This is a very interesting paper. I have flagged up a couple of anomalies in terms of what has been reported within it from existing literature, but these should be relatively easy to address.
Generally a good and solid approach. As I have mentioned, I am rather surprised that the authors did not take the opportunity to analyse the caecal contents in this work, but nevertheless the data from faecal samples is novel and interesting.
One question about figure 5 but otherwise no issues.
A few typos which could dramatically change the course of the content. Otherwise nothing to add.
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I only suggest to improve discussion in following lines:
In lines (407-408), authors should improve the evidence to support the idea that Nanopore platform is the technology of choice for metagenomics studies, because I think before that, they should correct nanopore reads before the taxonomic assignation, to make that statement.
In lines 385-386. I suggest that authors should add the geographic difference and the kind of plants that they have in the area to to support the idea of "absence Spirochetes in hares is a reflection of geographical differences".
Manuscript is well writing and it has a novel informations, but I suggest to improve discussion in following lines:
In lines (407-408), authors should improve the evidence to support the idea that Nanopore platform is the technology of choice for metagenomics studies, because I think before that, they should correct nanopore reads before the taxonomic assignation, to make that statement.
In lines 385-386. I suggest that authors should add the geographic difference and the kind of plants that they have in the area to to support the idea of "absence Spirochetes in hares is a reflection of geographical differences".
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The manuscript submitted by Shanmuganandam et al studied microbial community structure of European hares and rabbits in Australia. The authors found significant difference in microbial composition between hare and rabbit in terms of beta diversity and taxonomic structure. Also, authors compared microbiome in hares in Australia and those in Europe and found some differences in taxonomy, especially absence and presence of the phylum Spirochaetes. They also stated the similarity of community structure of hares/rabbits fecal microbiome analyzed by difference sequencing platforms, Illumina and Nanopore.
Generally, this experiment was precisely conducted and clearly documented. I would recommend it for acceptance after a few minor concerns listed below are addressed.
L152, In this study, the raw sequence reads were converted to ASVs. Authors should clarify the cut-off similarity for "OTU" in this manuscript.
L277-279, There was DNA contamination in ROCs, and 40-90% of ROCs were assigned as Firmicutes or Bacteroidetes. Authors should document how to exclude the effect of contaminated DNA in Hare and Rabbit samples.
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