Isolation, Description and Genome Analysis of a Putative Novel Methylobacter Species (‘Ca. Methylobacter coli’) Isolated from the Faeces of a Blackbuck (Indian Antelope)
, Jyoti Mohite 1,2, Pranitha Pandit 1,2, Rahul A. Bahulikar 3 and Monali C. Rahalkar 1,2,*Round 1
Reviewer 1 Report
In this manuscript the authors describe the isolation and characterization of a novel methanotroph strain derived from the faeces of black buck. They further determine the genome sequence of the strain through whole genome sequencing and perform comparative analysis with available gene sequences from similar species. I believe this work is both novel and of high interest to readers in the field. I have minor comments:
- Add more details about the steps taken to ensure high quality WGS data.
- A separate method section can be devoted for WGS. You could include details about the library preparation and how the data was processed. Include details about the tools used to compare genes and for phylogenetic analysis.
- Lines 219-224 can be moved to methods or data access section
- Format the text and figures consistently.
Author Response
Answers to the reviewer comments/suggestions
Reviewer 1
In this manuscript the authors describe the isolation and characterization of a novel methanotroph strain derived from the faeces of black buck. They further determine the genome sequence of the strain through whole genome sequencing and perform comparative analysis with available gene sequences from similar species. I believe this work is both novel and of high interest to readers in the field. I have minor comments:
- Add more details about the steps taken to ensure high quality WGS data.
- A separate method section can be devoted for WGS. You could include details about the library preparation and how the data was processed. Include details about the tools used to compare genes and for phylogenetic analysis.
Answers:
- and 2.
We have now added the details about the whole genome sequencing as supplementary material.
To ensure high quality data before giving for whole genome sequencing, we checked the purity of the material by sequencing the 16S rRNA gene and we obtained a clean sequence of BlB1.
HiSeq Illumina was used for sequencing. A large amount of filtered data (~4.2 Gb) was obtained giving us ~900x coverage. A single copy of 5S, 16S, and 23S rRNA, also confirms that there was no contamination.
- Lines 219-224 can be moved to methods or data access section
Answer: Removed.
- Format the text and figures consistently.
Answer: We have formatted all the text and figures.
Reviewer 2 Report
The manuscript ID microbiolres-1180007 entitled "Isolation, description and genome analysis of a putative novel Methylobacter species ('Ca. Methylobacter coli') isolated from the feces of a blackbuck (Indian antelope)" by Khatri et al. characterizes a new isolate of a methanotroph bacterium from the ruminant feces. The genome sequencing of this new isolate suggests a new Methylobacter species, named Methylobacter coli strain BlB1. The new strain was demonstrated to consume methane and growing conditions were optimized. The genome sequence revealed the proposed enzymes responsible for its methanotroph characteristic and despite cryopreservation still not being possible, the authors were able to propagate the isolated bacterium on solid medium. The work is well described and the manuscript is well written. It is a good starting point for future studies of its methane mitigation capablities in vivo. I will recommend it for publication after minor edits. Below I listed a few points that can be improved by the authors.
Abstract: I suggest replacing the term "similarity" with "identity" since you are referring to DNA sequences. This will make your statement more precise.
Abstract line 20: Define DDH and ANIb in the first mention.
Line 34: Do the authors mean "global methane emissions" or "global methane content in the atmosphere"? Please clarify.
Line 74: Define NMS medium.
Lines 137-138: Review the sentence for clarity.
Line 277: consider replacing "C" with "carbon".
Author Response
Reviewer 2
The manuscript ID microbiolres-1180007 entitled "Isolation, description and genome analysis of a putative novel Methylobacter species ('Ca. Methylobacter coli') isolated from the feces of a blackbuck (Indian antelope)" by Khatri et al. characterizes a new isolate of a methanotroph bacterium from the ruminant feces. The genome sequencing of this new isolate suggests a new Methylobacter species, named Methylobacter coli strain BlB1. The new strain was demonstrated to consume methane and growing conditions were optimized. The genome sequence revealed the proposed enzymes responsible for its methanotroph characteristic and despite cryopreservation still not being possible, the authors were able to propagate the isolated bacterium on solid medium. The work is well described and the manuscript is well written. It is a good starting point for future studies of its methane mitigation capablities in vivo. I will recommend it for publication after minor edits. Below I listed a few points that can be improved by the authors.
Abstract: I suggest replacing the term "similarity" with "identity" since you are referring to DNA sequences. This will make your statement more precise.
Answer: Corrected (Lines 16, 17 and 24).
Abstract line 20: Define DDH and ANIb in the first mention.
Answer: Defined (Lines 22 and 23).
Line 34: Do the authors mean "global methane emissions" or "global methane content in the atmosphere"? Please clarify.
Answer: We meant: global methane emissions. Corrected. (Line 35).
Line 74: Define NMS medium.
Answer: Nitrate mineral salt medium (corrected Line 76).
Lines 137-138: Review the sentence for clarity.
Answer: Corrected. Lines 141-142.
Line 277: consider replacing "C" with "carbon".
Answer: Replaced. Line 283.
