Limobrevibacterium gyesilva gen. nov., sp. nov., Isolated from Forest Soil
Round 1
Reviewer 1 Report
Dear Authors,
Thank you for your manuscript submission “Limobrevibacterium gyesilva gen. nov., sp. nov., isolated from forest soil.” The manuscript represented a new species of the family Acetobacteraceae by characterizing the phylogenetic analysis of strain RN2-1T isolated from forest soil sample. Here are my specific comments:
- Introduction is short. More background regarding metagenomic studies, such as current status or their role in phytogenetic analysis of strain RN2-1 T isolated from soil, should be provided
- Line 113, what is S RNA phylogeny? Do you mean 16S rRNA? Similar issue in section 3.3 title (line 206)
- What kits did you use for extraction of genomic DNA of strain RN2-1 T?
- Line 94, what is the purpose of adding Tween 80? Can we add other agents or surfactants instead?
- Are there any assumptions during your sample preparation, extraction, and data analysis?
- Figure 1 is too small to read content and see scale bar. Replacing a new figure should be considered
- Line 225-227, how did you get the numbers for complete genome of strain RN2-1T? Can you provide a graphical genome map of strain RN2-1T?
- Are there any limitations for the method in this study?
- Future research is missing
Some typos are still present in the main context. Please double check them
Author Response
Introduction is short. More background regarding metagenomic studies, such as current status or their role in phytogenetic analysis of strain RN2-1 T isolated from soil, should be provided
Answer: more background was added in introduction as suggested (L40-57)
Line 113, what is S RNA phylogeny? Do you mean 16S rRNA? Similar issue in section 3.3 title (line 206)
Answer: revised as suggested (L126, 225)
What kits did you use for extraction of genomic DNA of strain RN2-1 T?
Answer: added as suggested (L139-142) as well as
Line 94, what is the purpose of adding Tween 80? Can we add other agents or surfactants instead?
Answer: We used Tween 80 to detect the ability of bacteria to hydrolyze the lipid. This also tested in API ZYM.
Are there any assumptions during your sample preparation, extraction, and data analysis?
Answer: We tried to isolate uncultured soil bacteria by using our modified culture method including further characterization and classification.
Figure 1 is too small to read content and see scale bar. Replacing a new figure should be considered
Answer: replaced as suggested
Line 225-227, how did you get the numbers for complete genome of strain RN2-1T? Can you provide a graphical genome map of strain RN2-1T?
Answer: We obtained that information from Macrogen, a sequencing company (see L139-142); a graphical genome map was provided as suggested (Fig. 5)
Are there any limitations for the method in this study?
Answer: RN2-1 can grow on different media than the reference strains, and so fatty acid composition could not be compared by the standard way.
Future research is missing
Answer: added in conclusion as indicated (L299-300)
Reviewer 2 Report
The topic of the manuscript falls into the scope of the Journal - it is interesting attempt to identify and classify selected microorganism considered as new specie.
Introduction focuses on main characteristics of Acetobacteraceae to which studied strain was found to belong. This is very short chapter ending with the aim. This section is ok, but could be extended a little.
The section 2.1 should be re-written as it looks like combination exact protocol (do this, do that) and a standard description what has been done by the researchers.
I noticed that Authors write species names without italics (e.g in line 31, 60-63) and taxons in italics. It should be rather in the other way.
The stain name is once written as RN2-1T (upper index for T) and sometimes as RN2-1T (no index). Please unify.
Line 102: There is R2A with smaller font size for '2'. For other places R2A is used. Please unify.
When writing chemical formulas please used proper indices (lower-index for numbers)
Line 40: The sentence starting from "And" could be connected with the previous to form a single sentence.
The methods are very well described and properly selected being supported by bioinformatics allowing good description of the studied microorganisms.
Did you place the sequence of the microorganism into GenBank? Is there any accession number available?
Results are clearly presented showing all studied traits.
The explanation of "Summed features" should be placed below Table 2.
Authors nicely captured differences of several characteristics of their strain to the closest neighbor what is a good premise to think about this strain as new specie. Probably more studies need to be done for confirmation. Maybe this microbe is present in other environments. In addition, its technological potential could be next goal of future studies.
The language is good with no key issues.
Author Response
Introduction focuses on main characteristics of Acetobacteraceae to which studied strain was found to belong. This is very short chapter ending with the aim. This section is ok, but could be extended a little.
Answer: extended as suggested (L40-57)
The section 2.1 should be re-written as it looks like combination exact protocol (do this, do that) and a standard description what has been done by the researchers.
Answer: rewritten as suggested (L63-66)
I noticed that Authors write species names without italics (e.g in line 31, 60-63) and taxons in italics. It should be rather in the other way.
Answer: revised for all the species names and higher taxa with italics as suggested as well as recommendation from ICNP.
The stain name is once written as RN2-1T (upper index for T) and sometimes as RN2-1T (no index). Please unify.
Answer: unified as suggested through the entire manuscript with RN2-1T
Line 102: There is R2A with smaller font size for '2'. For other places R2A is used. Please unify.
Answer: unified with R2A as suggested (L115)
When writing chemical formulas please used proper indices (lower-index for numbers)
Answer: revised as suggested through the entire manuscript
Line 40: The sentence starting from "And" could be connected with the previous to form a single sentence.
Answer: revised as suggested (L38-40)
The methods are very well described and properly selected being supported by bioinformatics allowing good description of the studied microorganisms.
Answer: Thank you.
Did you place the sequence of the microorganism into GenBank? Is there any accession number available?
Answer: yes, mentioned in the end of the Description (L331-333)
Results are clearly presented showing all studied traits.
Answer: Thank you.
The explanation of "Summed features" should be placed below Table 2.
Answer: placed as suggested (L222-224)
Authors nicely captured differences of several characteristics of their strain to the closest neighbor what is a good premise to think about this strain as new specie. Probably more studies need to be done for confirmation. Maybe this microbe is present in other environments. In addition, its technological potential could be next goal of future studies.
Answer: Thank you.
Round 2
Reviewer 1 Report
Dear Authors,
Thank you for your manuscript submission. All of my concerns have been carefully considered. In my opinion, the revised manuscript meets the criteria to publish in Diversity journal. Therefore, I recommend to accept this manuscript.
