Genome resource of chitin-degrading bacterium Brevibacillus formosus YSY-2.2

  1. Dinh Minh TRAN
  2. To Uyen Huynh
  3. Dinh Sy Nguyen
  4. Iuliia Pentekhina

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Abstract

This work announced the whole genome resource of Brevibacillus formosus YSY-2.2, a chitin-degrading bacterium possessing antifungal activity and producing phytohormones previously isolated from Yok Don National Park, Vietnam. The genome contained 6,191,946 bp with 47.3% GC content, 5,791 CDSs, 116 RNAs, 101 CAZymes, and 13 BGCs. It showed the highest values of both ANI (95.07%) and dDDH (72.6%) to those of B. formosus NF2 (CP018145). The genome sequence will provide useful information for further studies on the functional gene and application of B. formosus YSY-2.2.

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  1. Access Microbiology

    Thank you very much for submitting your revised manuscript to Access Microbiology and applying some of the corrections suggested. However, the amendments proposed by the reviewer have not been addressed yet. The methods do not show all the clarifications requested and the requirement of providing the commands and code lines used on the different genome assembly and and annotation tools has not been fulfilled. Additionally, an explanation on the calculation of the completeness percentage is missing, and the link https://dfast.nig.ac.jp/ cited in the Methods section is not accessible online. Please deposit the command lines used for each tool in protocols.io and refer to them in the relevant sections, or alternatively provide them as supplementary material, and address the rest of the proposed corrections in a revised version of the manuscript. Otherwise, I am afraid that the manuscript would no longer be considered for publication in Access Microbiology. Please provide your revised manuscript (including a tracked changes document) along with a new point-by-point response to the reviewer comments within one month.

  2. Version published to 10.1099/acmi.0.000934.v4 on Access Microbiology
  3. Access Microbiology

    Thank you very much for submitting a revised version of your manuscript to Access Microbiology. It has now been reviewed by one of the reviewers that provided recommendations to you previously. Although they acknowledge that the manuscript has improved in this new version, there are still issues that need to be addressed. Please find their comments below. Please provide a revised version of the manuscript (including a tracked changes document), along with a point-by-point response to the reviewer's comments within one month.

  4. Access Microbiology

    Comments to Author

    Thank you for sharing the updated manuscript. This is certainly improved; however, there are still some issues outstanding that need to be addressed. (1) Missing details required for repeatability According to this journal's instructions to authors, "the Methods section should be comprehensive and provide sufficient detail to allow your work to be replicated". Although the authors provide the names and version numbers for the software used, the Methods section still falls short of being comprehensive and providing sufficient detail for the work to be replicated. In my view, the authors should provide the actual command lines used for each step in the computer analysis workflow. There are several ways of doing this. One easy way is to follow the journal's recommendation to deposit the steps as a protocol in protocols.io. Ultimately, it is an editorial decision whether or not to require the full details of the command lines used in this work and I defer to the editor's final decision. However, I don't believe that simply writing the software name and version and "with default parameters" is sufficient. What was the command line used to run Fastp 0.23.1 ? After filtering and trimming, how much of the data was removed, leaving how many reads and with what mean read length? At line 51, what is meant by "qualify"? What does it mean to "qualify ... raw reads"? What was the Unicycler 0.4.8 command line? Unicycler is basically a wrapper for SPAdes. Which version of SPAdes was used? What was the Trimmomatic 0.36 command line? Why was Trimmomatic used (line 52) if the Fastp had already been used to filter for adapters, repeated reads, and low-quality sequences (line 51)? Annotation was performed using DFAST 1.2.0. What was the exact command line? Or was this done by a webserver? Either way, what were the options and parameter values? Did the authors submit the DFAST annotation to NCBI and/or DDBJ? Which version of ANI calculator was used? If the authors used a webserver rather than a local installation of the software then please provide the URL of the website used and the date that it was accessed (if a version number is not available). Same applies for dbCAN3 and antiSMASH. (2) Citation of references for third-party data According to the instructions at https://www.microbiologyresearch.org/prepare-an-article: "where any data has been used that was not generated by the authors, those who generated the data should be cited and a link provided to the database in which the information can be accessed." Therefore, please provide literature citations (where possible) and database links for each item in Table 2. (3) Genome assembly completeness Lines 60 - 61. The authors claim 99.73% completeness, though they do not explain what this means and they do not mention this in Table 1. According to https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_045298735.1/, CheckM calculated a completeness of 98.22% (55th percentile for assemblies of this species). Please address this apparent contradiction. (4) G+C content At lines 65 to 67, the authors mention that some genomes of B. formosus show atypically high G+C content and in Table 2 the G+C content varies as high as 52%. The authors are right to be surprised by such variation of G+C content within a species and within a genus. However, according to https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=54913 (viewed on 26th December 2024), all the genomes from this genus have a G+C content that falls within a narrow range (around 47.5%). The results at https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=54913 are much more plausible that those presented in the text here and in Table 2. How can the authors explain the discrepancy? (5) Very minor point Line 34. Instead of writing the imprecise "at least 10", why not simply write the actual number? On 26th December 2024 the number is 12 (excluding YSY-2.2). Line 35. Please insert a full stop or a semicolon before "however". Line 43. The phrase "functional gene and application" does not really make sense. Perhaps it should be something like "functions of genes and their applications"? Table 1. Please be consistent in the use of capital or lowercase for first letter of each row (e.g. "*c*arbohydrate esterase" versus "*G*lycosyl hydrolase" . Also, avoid unnecessary italics. Line 60. It is incorrect to say "the assembly generated a draft chromosome". Rather, it is correct to say "the draft assembly generated 60 contigs". In Table 1, the property "Genome size" is misleading. Rather, this should be "Genome assembly size". The size of the assembly is not necessarily the same as the size of the actual genome. Same applies to line 62.

    Please rate the manuscript for methodological rigour

    Satisfactory

    Please rate the quality of the presentation and structure of the manuscript

    Satisfactory

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  5. Version published to 10.1099/acmi.0.000934.v3 on Access Microbiology
  6. Access Microbiology

    Thank you for submitting a revised version of your manuscript to Access Microbiology. We appreciate the efforts in amending this manuscript, however many of the reviewer and editorial requests were not addressed or only partially addressed, therefore this version cannot be accepted for publication. Specifically Reviewer 2 requested to explain the methods followed for the genome analysis in a more comprehensive manner, including code lines and version/date of use of the online tools used for the analysis. This has not been fulfilled. Reviewer 2 also warned the authors that the genome announced in this manuscript is not included in the NCBI genome list for this species, and it is still not included as of today. The authors must address this with NCBI before submitting a corrected version of the manuscript. Reviewer 2 also suggested to the authors that the bioinformatics pipeline and protocols used for the genome analysis can be comprehensively explained and cited with a DOI on the protocols.io repository, or alternatively on Github. This has to be addressed. From the editorial perspective, we requested to combine this submission with a similar submission by the authors ("Genome description of the chitinase-producer Brevibacillus brevis YSY-3.4 isolated from the dipterocarp forest ecosystem") describing a strain with similar features and isolated from the same source location, in agreement with our editorial guidelines. This is not addressed at all in this version of the manuscript. Please provide a revised version of the manuscript addressing all the editorial and reviewer requests (including a tracked-changes document) along with a point-by-point response to the requests indicating the changes proposed and the manuscript lines where they can be found within 2 months.

  7. Version published to 10.1099/acmi.0.000934.v2 on Access Microbiology
  8. Access Microbiology

    Thank you very much for submitting your manuscript to Access Microbiology. It has now been reviewed by two peers whose comments are attached at the bottom of this email. They have important concerns on the lack of structure and missing essential information in the manuscript as it would be required for a genome announcement. Please address these amendments carefully. Additionally, we have identified another submission ("Genome description of the chitinase-producer Brevibacillus brevis YSY-3.4 isolated from the dipterocarp forest ecosystem"), with a high similarity to this manuscript, submitted by the authors announcing the genome of another strain with similar properties as the one described in this work and sourced from the same isolation site (a National Park in Vietnam). As per our editorial guidelines, we strongly recommend that authors group genome announcements of strains with similar properties and/or from same isolation source in a single manuscript. Following these recommendations and the reviewers' suggestions, please submit a revised version of the manuscript (including a tracked-changes version) combining both submissions, along with a point-by-point response to the reviewers' comments within two months.

  9. Access Microbiology

    Comments to Author

    I checked the accession numbers provided in the Data Summary section by searching NCBI on 2nd November 2024. The sequence reads are found under PRJNA1167226 , as stated in the text. A search for BAAFVL000000000.1 found the genome assembly at https://www.ncbi.nlm.nih.gov/nuccore/BAAFVL000000000.1/. However, the genome assembly is under a different BioPRoject and BioSample than the reads. That is potentially confusing. So, please also mention BioSample SAMD00823265 and BioPoject PRJDB18885. I also noticed that on 2nd November, the assembly was not listed here: https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=54913. The authors might consider contacting the NCBI to resolve this. Line 31. "The species Brevibacillus formosus was clarified and described for the first time by Shida et al.". Please cite a reference here. Line 34. " To date, only one genome sequence of this species has been published". That is not true. See https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=54913. at least 10 genome assemblies have been published in GenBank. Line 35. " B. formosus YSY-2.2 was previously isolated from soils collected from Yok Don National Park, Vietnam." Please cite a reference to support this sentence. Line 47. In the Methods section, the authors write "Fastp 0.23.1 [7] was employed to qualify and filter raw read sequences, and Unicycler 0.4.8 [8] and Trimmomatic 0.36 [9] were applied to assemble the genome." This is a good start but it is not sufficient. The description of the methods needs to be complete enough that a competent reader could exactly repeat the analysis. Please provide the exact command lines, including parameter values and selected options, for each step in the process. If the authors prefer not to include this level of detail in the main text then there are several alternatives. For example, they could create a protocol at protocols.io and cite its DOI in this manuscript. They could depsosit their command-line code in a repository such as GitHub, which then allows creation of a snapshot with a DOI via Zenodo. For further advice on best practice in this respect, please see: Ziemann M, Poulain P, Bora A. The five pillars of computational reproducibility: bioinformatics and beyond. Brief Bioinform. 2023;24(6):bbad375. doi:10.1093/bib/bbad375. Line 49. "Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated as described previously [11-12]". Again, as in the previous comment, please provide the exact command lines. Also, please provide the software version number(s) and cite any relevant papers for software used. Line 51. "Carbohydrate-active enzymes (CAZymes) and secondary metabolite biosynthesis gene clusters (BGCs) were identified using the dbCAN3 metaserver [13] and antiSMASH 7.0 [14], respectively". In this case, there are no command lines, but please provide full details of search terms and options selected. Also, since these servers and/or their underlying data are probably updated periodically, please provide version numbers and/or dates on which the analyses were performed. Line 54. "The genome of B. formosus YSY-2.2 included 6,191,946 bp in size generated from 60 contigs". No, the genome is not generated from contigs; the genome assembly may be generated from contigs. The authors are confusing the map with the territory (https://en.wikipedia.org/wiki/Map%E2%80%93territory_relation). The genome assembly may be 6,191,946 bp in size, but the size of the actual genome might be slightly different from this. In fact, using different assembly protocols, you will get slightly different results from the same biological genome. Line 57. "closet bacteria". This was likely intended to be "closest bacteria". However, this could be expressed more precisely. It is not that the bacteria are close. Rather they are closely related (phylogenetically/evolutionarily). Line 57. "The genomic properties of strain YSY-2.2 were distant from those of the close[s]t bacteria ". Which properties, specifically? And does this suggest that there is a problem with the authors' genome assembly (i.e. their model of the genome) rather than a biologically real difference? That might be the more parsimonious explanation? Please elaborate further and present the evidence. Are the authors simply saying that the estimated size of the genome of YSY-2.2 are statistically different from the distribution of genome sizes for the species B. formosus? What is the range of values? Is the value for YSY-2.2 outside of the range? Line 122. "General properties of the Brevibacillus formosus YSY-2.2 genome". these are not properties of the genome. These are properties of the authors' model of the genome, i.e. their genome assembly. Lines 60-68. The reader needs to have some indication of the completeness and reliability of these inferences. Therefore, we need some quality metrics for the genome assembly from which these inferences were made. What is the level of completeness of the genome assembly as judged by CheckM (or BUSCO)? What is the level of contamination as judged by CheckM? Does this compare favourably with the other 10 available genome assemblies for B. formosus?

    Please rate the manuscript for methodological rigour

    Satisfactory

    Please rate the quality of the presentation and structure of the manuscript

    Good

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    No: This work does not involve humans nor animals.

  10. Access Microbiology

    Comments to Author

    Please ONLY put comments for the Author(s) in here 1. Shortening of the title is essential 3. Language proof reading is essential 4. Although it is a genome announcement it is essential to describe bacterial isolation, and source. This will help to compare with the existing reports or resource for comparative study. 5. A brief description of DNA sequencing is lacking 9. Very brief comparison with the reported strain is needed

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Satisfactory

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  11. Version published to 10.1099/acmi.0.000934.v1 on Access Microbiology