Poseidonibacter ostreae sp. nov., Isolated from the Gut of Ostrea from the Seomjin River
Round 1
Reviewer 1 Report
Comments for author File: 
Comments.pdf
Author Response
- ‘Three Gram’ should not be in italics (Line 25).
- Can the author remove all the commas from Line 26 to 27? ‘It should be: These strains are oxidase- and catalase-positive coccoids that thrive aerobically. Phylogenetic analysis based on the 16S rRNA gene revealed that all three isolates belong to’.
- Check Line 80. It should be 2.2 16S, not ‘2.2.16.S’
→ Response: We changed it based on the reviewer's feedback.
- In 2.2, no PCR conditions and reagents used were mentioned. At least if the author can cite the article used for the PCR. Also, the author mentioned that Sanger sequencing was performed; it would be good for the author to cite the article used.
→ Response: We changed it based on the reviewer's feedback. We wrote the PCR conditions and reagents used in the experiment in the text (In 2.2).
- Line 120 needs clarity. ‘The morphology of colonies and cells’; is the author referring to the morphology of colonies and cells of the three strains (SJOD-M-6T, SJOD-M-5 and SJOD-M-33)? There should be clarity.
→ Thank you for your nice comments. We observed the cell shape of the three strains (SJOD-M-6T, SJOD-M-5 and SJOD-M-33). We'll delete the word "colonies" for clarity.
- Line 157 to 159 needs a reference.
We added a reference.
→ Response: We changed it based on the reviewer's feedback. We added a reference.
- The author mentioned that ‘the nearly complete 16S rRNA gene sequences’ were obtained (Line 181). Many readers would love to know the exact gene fragment sizes (e.g., 1,500, 1,300 or 1,400 base pairs). Specifying the length of the gene fragments will satisfy readers’ curiosity and give the paper more chance to be cited.
→ Response: We obtained 1,517 bp 16S rRNA sequence genes for all three strains. Also, we uploaded the 16S rRNA genes of the three strains to NCBI to obtain accession numbers. We have amended the following sentence based on the reviewer's comments.
“The nearly complete 16S rRNA gene sequences (1,517 bp) ~”
- In Section 2.3, whole-genome sequencing was done. The author mentioned that microbial DNA was prepared. Can the author specify that the genomic DNA was extracted from the three isolates? In Section 3.3, the author only reported SJOD-M-6T result. Any justification for this?
→ Response: As a result of 16S rRNA gene comparison analysis, the three strains were 100% identical. So, we extracted genomic DNA from all three strains and proceeded with whole genome sequencing. As a result of ANI and dDDH analysis, the three strains were identified as the same species. Among the three strains, we designated strain SJOD-M-6T as the representative strain. The results of the genome analysis of 3 strains are summarized in Table S1 and Figure S1 among supplementary data.
- According to Section 2.4 (Lines 129 and 135), the morphological, physiological, and biochemical characterization was also performed on the strains but only SJOD-M-6T (Section 3.4) result was discussed. Why?
→ Response: All three strains were isolated together from the same source. Through analysis of 16S rRNA base sequences and genome comparison, it was determined that the three strains belong to the same species. Additionally, the morphological and physiological characteristics were found to be identical. To further characterize the strains biochemically, strain SJOD-M-6T was selected as the representative strain. Nevertheless, we will incorporate the reviewer's suggestions and make appropriate revisions to the text.
- It would be so good if all the analyses conducted for strain SJOD-M-6T were also conducted for strains SJOD-M-5 and SJOD-M-33.
→ Response: I will amend the title according to the reviewer's opinion.
- The author failed to report on the genome features, morphological, physiological, biochemical and chemotaxonomic characteristics of SJOD-M-5 and SJOD-M-33 (only SJOD-M-6T was reported) in Section 3. Any reason for this?
→ We performed genomic, morphological, physiological, biochemical, and chemotaxonomic experiments on all three strains (SJOD-M-6T, SJOD-M-5, and SJOD-M-33) belonging to Poseidonibacter ostreae. All three strains were found to be the same strain as a result of genetic, physiological activity, and chemotaxonomic data analysis. Morphological, physiological, biochemical, and chemotaxonomic data are summarized in Table 1, and genomic data are summarized in Table S1. In this manuscript, only the SJOD-M-6T type strain, which is the representative strain among the three strains, is described in detail.
- The author should change H2S to H2S (Line 328)
→ Response: We changed it based on the reviewer's feedback.
Reviewer 2 Report
In this work, the authors described a novel species Poseudonibacter ostrea, obtained from the gut of Ostrea denselamellosa in the Seomjin River (Republic of Korea). In general, this paper is clearly laid out, well planned and easy to read.
Some specific suggestions or questions are listed below:
1) Introduction part should be more detailed. The authors should briefly place the study in a broad context and highlight why it is important. It should define the purpose of the work and its significance. The current state of the research field should be reviewed, and key publications cited.
2) In Results and Discussion section, please, add more discussion. For example in “3.3. Genome features” the authors write about new knowledge about ecology and physiology that can be gained through genomic analysis. Nevertheless, no further assumptions are made. Also, provide a comparison of the genomic properties of the novel isolate and its closest neighbors.
3) At the beginning of the article one author is listed (Ahyoung Choi), but in the Author Contributions section there are already several authors. Please correct this inconsistency.
4) The exact ANI values should be given in the text (not just the threshold of 95%). I think that the Figure S1 would fit nicely in the main text.
5) Phylogenomic tree is missing, only 16S rRNA-based tree is present.
6) Page 3: The sentence “The resulting contigs were annotated using the Rapid Annotation using the Subsystem Technology (RAST)” one extra “using”
7) Page 2 Section 2.2. 16S rRNA check the spelling
Author Response
-
Overall comment
In this work, the authors described a novel species Poseudonibacter ostrea, obtained from the gut of Ostrea denselamellosa in the Seomjin River (Republic of Korea). In general, this paper is clearly laid out, well planned and easy to read.
Some specific suggestions or questions are listed below:
1) Introduction part should be more detailed. The authors should briefly place the study in a broad context and highlight why it is important. It should define the purpose of the work and its significance. The current state of the research field should be reviewed, and key publications cited.
→ Response: We have added content to the text to reflect your comments.
2) In Results and Discussion section, please, add more discussion. For example in “3.3. Genome features” the authors write about new knowledge about ecology and physiology that can be gained through genomic analysis. Nevertheless, no further assumptions are made. Also, provide a comparison of the genomic properties of the novel isolate and its closest neighbors.
→ Response: Thank you for your feedback. We conducted a genome comparative analysis, incorporated the text, and included the results of pan-genome orthologous groups (POGs) along with related species in a supplementary figure (Figure S4).
3) At the beginning of the article one author is listed (Ahyoung Choi), but in the Author Contributions section there are already several authors. Please correct this inconsistency.
→ Response: We have corrected the authors in the text and supplementary data file.
4) The exact ANI values should be given in the text (not just the threshold of 95%). I think that the Figure S1 would fit nicely in the main text.
→ Response: We changed it based on the reviewer's feedback.
5) Phylogenomic tree is missing, only 16S rRNA-based tree is present.
→ Response: Thank you for your critical point. We added a phylogenomic tree (Figure S5).
6) Page 3: The sentence “The resulting contigs were annotated using the Rapid Annotation using the Subsystem Technology (RAST)” one extra “using”
→ Response: We changed it based on the reviewer's feedback.
7) Page 2 Section 2.2. 16S rRNA check the spelling
→ Response: We changed it based on the reviewer's feedback.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
All comments have been taken into account. The only thing left, please, move the Figure with the phylogenomic tree to the main text.
Author Response
All comments have been taken into account. The only thing left, please, move the Figure with the phylogenomic tree to the main text.
→ Response: We changed it based on the reviewer's feedback.
