Pangenome Analysis Reveals a High Degree of Genetic Diversity in Gardnerella vaginalis: An In Silico Approach

Round 1

Reviewer 1 Report

The title of the manuscript is all-encompassing.

English language has good quality.

Once the pathogenic microorganism is mentioned, use the shortened name, all of them should be formatted in italics.

Thanks for providing details about genome formats which were downloaded from databases.

Please provide more details about Prokka, Gegenees, PGAdb-builder, MegaX, GIPSy, BRIG, Mauve, Orthofinder  softwares (versions, developers, countries, year, etc).

The figures meet the required standards.

Provide definitions for the abbreviations when using them in the titles of figures.

Explain the role of Alloscardovia omnicolens in your analysis.

The references cited in the article are predominantly from more than 5 years ago, comprising 80% of the total.

Are there any limitations in the study?

There is an unnecessary coma in the line 64.

How could your study enhance the diagnosis and treatment of bacterial vaginosis?

Could you please consider in the "Discussion" section any relevant studies that report on Gardnerella resistance? This would provide additional support for your conclusion about the genes more closely associated with virulence and resistance.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

1. The current work found distinct clusters in the analysis of Genbank Gardnerella vaginalis genomes. Other studies found the heterogeneity as well, and used their own designations for it. The topic would benefit from bringing various ways to describe the genetic diversity of Gardnerella together. The authors (lines 343–351) show the agreement among their findings and those of Tarracchini et al., 2021. The names of the newly defined species as in Vaneechoutte et al., 2019 can also be used where applicable, e.g. GV37 strain is known as G. swidsinskii. This naming is already used in databases as cpnDB https://www.cpndb.ca/search.php . Bohr et al., 2020 [1] used similar approach on Gardnerella genomes, however their work is not referenced in the current study. 

[1] Bohr LL, Mortimer TD, Pepperell CS. Lateral Gene Transfer Shapes Diversity of Gardnerella spp. Front Cell Infect Microbiol. 2020 Jun 23;10:293. doi: 10.3389/fcimb.2020.00293. PMID: 32656099; PMCID: PMC7324480. 

2. Four of the analysed G. vaginalis genomes were identical at 100%. However, strain depositories already show that several codes are being used for the same strain. NCBI Taxonomy browser lists G. vaginalis type strain synonymously as ATCC:14018, DSM:4944, JCM:11026, NCTC:10287  https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2702&lvl=3&lin=f&keep=1&srchmode=1&unlock  This could be addressed in the Discussion.

The sentence structure should be improved throughout. The Conclusions (lines 394–398) do not carry the message that was intended. The descriptions of the genomic islands in the legend of Figure 3 need to be translated. Figures 7 and 8 show data category '-' that is not defined in the legend. The References need editing, e.g. Vaneechoutte et al., 2019 is referenced twice.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

I think this version can be acceptable and I do not have any more comments.