The Complex and Changing Genus Bacillus: A Diverse Bacterial Powerhouse for Many Applications

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The article attempts to conduct a literature review in order to explain the classification of a microorganism and its placement in relation to others. It begins with an overview of what was initially done, followed by a historical review based on a timeline. Next, it presents some characteristics of the microorganism and its applications, concluding with a paragraph that highlights some characteristics and applications. All stages are validated with bibliography, which includes 88 titles, although most are a few years old (from 2023, if I am not mistaken, there is only one reference). While this situation may be justified from the perspective of some historical statements, the article should include more recent bibliography.

The authors are invited to include something new, something that could increase interest in the article and justify its publication, whether from an epidemiological perspective or another. As it stands, the article does not have a contribution that justifies its publication.

Comments on the Quality of English Language

Some sentences and expressions could be simplified.

Author Response

• Thank you for your valuable observations. We have incorporated new information that includes more recent data from 2023 and 2024, which we believe will provide significant contributions to the topic.

Reviewer 2 Report

Comments and Suggestions for Authors

The review is dedicated to the Bacillus genus. It covers the phylogeny of Bacillus group and its possible biotechnological application. The review is well written and provide a lot of useful information dispersed across many artciles. Some comments:

1. The main idea of the review should be stressed. One half is dedicated to the phylogeny, the other is dedicated to the biotechnology. Which one is more important.

2. The conclusion should be improved. It is well known that some of Bacillus could be used as probiotics.

3. The current status of the phylogeny is not well described. It is know in the process of revising with the new methods of genomic.

Author Response

• Thank you for your comments. We have revised the wording of the objective in our review to clearly convey the main idea. We believe this adjustment enhances the clarity and focus of our work.
• The conclusion has been improved
• We have enhanced the description of the current status of phylogeny and have added updated references on new genomic methods. We believe these changes significantly strengthen our work.

Reviewer 3 Report

Comments and Suggestions for Authors

This study by Blanco-Crivelli et al. describes several loosely connected properties of the genus Bacillus. This genus has been and still is a model genus for endospore forming Gram-positive bacteria with a characteristic (predominantly) aerobic life-style (as are several species members of it such as B. subtilis or B. cereus). This genus has undergone several major changes in the last decades (and this is still ongoing) with several species (groups) excluded from Bacillus sensu stricto now forming new clades.

 

General comments:

1)   In my opinion, this review is a relatively broad yet shallow description of the Bacillus sensu lato group of organisms. It reads more like a textbook chapter than a sensu stricto review. Nevertheless, it provides topics with occasionally fairly recent references, so the interested senior reader or interested student can use this resource as a starting point for further, deeper readings.

2)   Because of the very broad scope of this review, I do not think the title is meaningful. I suggest something to the effect of “The complex and changing ‘genus’ Bacillus, a diverse bacterial powerhouse for many applications” instead.

3)   While broad in scope, I think the authors could seize the opportunity to check and update detail information. For example, the utility of species-typing (“does a new isolate belong to “Bacillus”?) using single “Bacillus” genes could be revisited. I guess the gyrA (topoisomerase gene) could be quite useful for this feat.

4)   It is a pity the authors have not included any figure or table to make their text a bit more visually appealing.

 

 

 

Specific comments:

5)   I will use the abstract as an example of more thorough editing, which is required throughout: “…group of individual species whose major common trait…sporulation in the presence of oxygen. …several species into new genera and to a…”. In the abstract the authors should mention that the genus Bacillus (sensu stricto) also comprises a number of notorious pathogens (B. anthracis, B. cereus, B. thuringiensis). Not to forget Bacillus sensu lato, e.g., Paenibacilli spp.

6)   Lines 60-64: this sentence is too long. Please split into two.

7)   L 72-77: as written, it seems gyrA is not a good PCR marker for Bacillus typing. This is not true in my experience. Is gyrA-typing valid for all new Bacillus sensu lato group isolates? Where are the limits? This should be explored using the plethora of Bacillus spp. genomes available now.

8)   L 201: better: “… for producing recombinant proteins…”.

Comments on the Quality of English Language

While not a major issue at this stage of the manuscript, the text should be edited for proper English language. See also formatting issues in line 315.

Author Response

• Thank you for your comments. We have added updated references. We believe these changes significantly strengthen our work.
• We agree that your proposed title better aligns with the content of our work. As a result, we have revised the title to reflect your recommendation.
• We have reviewed and updated the detailed information according to your suggestions. Specifically, we have re-evaluated the utility of species-typing using individual "Bacillus" genes. As you suggested we included a table.
• We believe that a table would further enrich our work, but we are unsure which item it should address within the review. We would like to consult with you to see if you think the section on identification would be the most appropriate, or if you have any other suggestions in this regard.
• We have thoroughly reviewed and edited the text.
• We splited the sentence in two according to your suggestion. Lies 98-100
• We have revised and expanded the information regarding gyrA to clarify any potential confusion. The updated details are now more comprehensive and aim to provide a clearer understanding of the role and applications of gyrA in our study.
• We have made the changes according to your suggestion. Line: 299
• We edited for proper english as you suggested

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

It is clear that the authors made a clear attempt to improve the work, which is to be appreciated. There are better and more up-to-date bibliographical references. I propose that the work be read again, especially in the last parts (with special emphasis on the conclusion) and that an attempt be made to add something to it that will "awaken" the interest of readers. They could also highlight any limitations and the added value that the work can add to science.

Comments on the Quality of English Language

Minor fixes, nothing special or significant

Author Response

We sincerely appreciate your comments on our manuscript. based on their suggestions, we carefully reviewed the work and made significant modifications, particularly in the conclusion section, as well as minor editorial modifications. We hope these changes improve the clarity and impact of our study.