Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove

  1. Anwesha Ghosh
  2. Simran Kaur Bhambra
  3. Raghu Chandrasekaran
  4. Punyasloke Bhadury

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Abstract

A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in Indian Sundarbans mangrove. The isolate was cultured from sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against GTDB database showed closest identity with S. terrae SKN60 and belong to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is about 7.2 Mb and has a G+C % of 73%. The average amino acid identity (AAI) was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and has 19 biosynthetic gene clusters predicted.

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  1. Version published to 10.1099/acmi.0.000892.v4 on Access Microbiology
  3. Version published to 10.1099/acmi.0.000892.v3 on Access Microbiology
  4. Access Microbiology

    Abstract - I still do not understand the final sentence in your abstract. What are you trying to say? Secondary metabolite clusters are not essential genes and they differ from species to species, so how can you use these to judge completeness of your assembly? Please rephrase this. I suggest something along these lines: The assembly reflected the presence of all essential genes and has 19 biosynthetic gene clusters predicted. ll 53 the phylum has a new name, please check this reference and correct it https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005056#tab2

  5. Version published to 10.1099/acmi.0.000892.v2 on Access Microbiology
  6. Access Microbiology

    Comments to Author

    Reviewer Comments to Author box. Please include specific and constructive comments on each of the following criteria: Here, Ghosh et al describe the genome of Streptomyces sp. SBR177 they have isolated from the Indian Sundarbans mangrove. I note, however, that they have not yet made the genome publicly available. Their work is methodologically sound, however the presentation of their results needs improved to clarify a few points. Please see below for comments which I believe would help improve/round out the manuscript, and that I would recommend be addressed before acceptance. 1. Methodological rigour, reproducibility and availability of underlying data The authors sequencing and bioinformatic analysis is mostly sound, however can they expand on the settings they used for their bioinformatic tools (e.g. antiSMASH strictness settings). I would like to see the genome made publicly available as well. 2. Presentation of results Could the authors please include images of their Gram stain results and of colony morphology? I think this important to aid future researchers to reisolate this organism. For both phylogenetic trees (Fig. 1 and Fig. S1) could the authors please: 1. Provide high-resolution images of the trees they feature. TYGS provides the option to download the trees it generates as SVG files. 2. Amend the figure legends to provide detail of the node labels - I assume these are bootstrap values but I'm not sure 3. Remove the bars at the sides of the trees and instead provide them as a separate bar chart - without an axis to measure them against these bars aren't informative. Also, for Figure 2, could the authors please clarify whether or not the genome of their isolate is circular? As Streptomyces generally have linear chromosomes, this would be super interesting. 3. How the style and organization of the paper communicates and represents key findings The bulk of the manuscript is organized as a 3 page paragraph, could the authors please tidy this up for readability. The content of the paper flows logically and communicates what it needs to, however formatting needs improvement. 4. Literature analysis or discussion Can the authors please more thoroughly cite throughout their manuscript? Although the methods section is referenced appropriately lines 50-54 lack citation. Likewise for lines 115-157. 5. Any other relevant comments Apart from the above, can the authors do a final read-through for stylistic consistency throughout (For example, in the abstract, GC content is referred to as (G+C%) in the abstract and G-C at line 112. Gene names should be italicized in their entirety.

    Please rate the manuscript for methodological rigour

    Very good

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

    Satisfactory

    To what extent are the conclusions supported by the data?

    Strongly support

    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: No animal work performed

  7. Access Microbiology

    In line with Access Open Data Policy the genome data (raw reads and assembly) will need to be publicly available (https://www.microbiologyresearch.org/open-data). Please make sure you add all the details about versions for the computational analysis.

  8. Access Microbiology

    Comments to Author

    # ACMI-D-24-00154 This manuscript describes the genome of a Streptomyces isolate obtained from sediment in the Sunderban Delta, India. The work is clearly of interest but the manuscript is currently lacking precision and methodological information required to understand the genome resource. Some elements of the text could be reorganised to improve the narrative flow. Please see detailed comments below. - ll.33-34: The genome clearly has all essential genes if the isolate could be grown. This appears to refer to the assembly. Please be precise about this distinction throughout. - ll.55-56: The capability to encode natural products is not a consequence of their large genome size. Please reword. - l.56: "The Streptomyces" seems to mean the isolate, not the genus - please reword - l.57: Please define Stn177 on first use - l.60: Noting sterile collection bottles is less important than knowing the depth of the sediment sample (below the water, and also the depth within the sediment), and the size of the sample - volume or weight - and from where in the sample the 10mg was taken (surface, middle?). - ll.62-63: Please provide a catalogue number for the agar - l.62: "grinded" -> "ground" and please state how (mortar and pestle? to a desired particle size?) - l.66: Please state conditions (aerobic/anaerobic, temperature) for the mother plate - ll.67-68: How many restreaks were required to obtain purity? - l.67: What does "pre-selected" mean? Why not "selected"? - l.69: "ensure pure culture" or "ensure pure culture conditions"? How was purity determined, precisely? - l.69: Are these microscope observations different to the previous statement? Please combine if it's the same thing. - ll.82-84: Please state software used for identification, the database that was queried, and the accession number and taxonomic identity of the matching record. - ll.85-86: Was the gDNA sheared and/or size-selected in library prep? If so, how? If not, please make this explicit. - l.87: Please state the number of raw reads obtained, and a measure of their length (e.g. N50). Please describe the filtering (software used with version/citation, and parameters) - l.87: Please state the basecaller used, and the model also (e.g. sup, hac, etc.) - l.88: Please state the length of the assembled genome, the number of contigs (and scaffolds, if scaffolding performed). If the genome is believed to be complete, please state whether replicons are circular or linear and explain how this was determined (e.g. presence of telomeres, overlapping ends, etc.) - l.91: Please provide TYGS version number (it's on the landing page) - l.94: "balance" -> "balanced" - l.96: Please provide MiGA version number. - l.98: Please provide EZBioCloud version number (it's on the website) - l.99: Please state the genome accession number for S. roseicoloratus and explain why comparison was only performed against this genome. I would have expected that the most similar genome would be identified for this. - ll.100-103: Descriptions of physical appearance would be better placed in the text describing practical isolation. - l.100: Please state antiSMASH version number and parameters. - l.104: How was closest identity to S. roseicoloratus determined? This is not clear in the text. - ll.104-105: Is this comparison with the 16S sequence amplified earlier, or with 16S sequence as determined from the assembled genome? If from the amplified sequence, please move this text to that location for clarity. If from the genome sequence, as Streptomyces genomes may contain multiple distinct 16S sequences, please be explicit about the sequence region used. In any case, whole genome-based taxonomic placement is expected to be more accurate and precise and should be preferred, and the software (with version number/citation), parameters used, and database should be stated. - l.106: This closest identity contradicts l.104 - which is correct? - ll.108-109: This isolate may belong to a species that is not represented in GTDB, but as GTDB is a subset of all sequenced bacteria that is not sufficient to claim this is a novel species. More evidence is required for this claim. The title may need to be changed to reflect this. - l.111: G-C or G+C? - ll.112-113: Please state the accessions for these comparisons. - ll.114-end: Genome annotations are predictions, so please modify the text to reflect this rather than implying that they are confirmed functions. The genome is "predicted to contain" and all of these functions, unless confirmed by experiment, are predicted functions. - ll.150-152: Are these percentages from anitSMASH? If so, then please adjust the text to reflect the meaning of this percentage as defined in the antiSMASH documentation. - ll.159-160: Bioprojects may be augmented with additional read and/or sequence data, so this BoiProject accession is ambiguous when describing the assembly and reads reported in this manuscript. Please provide accessions specific for both the publicly available assembly and the sequencing reads. - This paper contains numerous English language usage errors and typos. Please have this manuscript properly edited before resubmission. - For all software, the parameters used (even if they are default) must be listed. If default parameters are routinely used, a blanket statement could be made, e.g. "Unless otherwise noted, default parameters were used for all software."

    Please rate the manuscript for methodological rigour

    Poor

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

    Good

    To what extent are the conclusions supported by the data?

    Partially support

    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

  9. Version published to 10.1099/acmi.0.000892.v1 on Access Microbiology