Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn’s Disease Patients and Healthy Individuals

Round 1

Reviewer 1 Report

In this study, Maria N Siniagina, et al. typed 63 cultivated E. coli from Crohn Disease (CD) patients and healthy volunteers revealing a high genetic and phenotypic heterogeneity of the strains. They showed that different E. coli strains coexisting in the human gut of CD patients and healthy individuals exhibit similarity in the distribution of virulence determinants, antibiotic resistance genes, and bacteriocin-producing systems.

Strengths of this study:

Study question is valid.

Adequate literature review was performed.

Major findings were clearly presented. They adequately address the stated research objectives.

The research results validate the authors' conclusions.

I have a few suggestions to consider:

• Consider including participants characteristics. Authors may want to use Montreal classification for CD.
• How was the diagnosis of CD made?
• Did participants have any recent antibiotic exposure?
• Consider adding statical analysis details.

Comments for author File: Comments.docx

Author Response

Dear reviewer, thank you for your critical reading of our manuscript and important remarks.

Point 1: Authors may want to use Montreal classification for CD.

Dear reviewer, thank you for your critical reading of our manuscript and important remarks. We added information about the patients and controls into the manuscript (Table 1).

Point 2: How was the diagnosis of CD made?

To make the diagnose we performed clinical examination and endoscopy with further histological analysis. We provided the list of inclusion/exclusion criteria for patients and healthy individuals in our previous reports (Lo Sasso et al., 2020, doi: 10.1093/ibd/izaa188). We added this information to the manuscript.

Point 3: Did participants have any recent antibiotic exposure?

We excluded individuals taking antibiotics six months before sample collection from the study.

Point 4: Consider adding statical analysis details.

We made the necessary changes to the manuscript

Reviewer 2 Report

In the paper "Diversity and adaptations of Escherichia coli strains: exploring the intestinal community in Crohn's disease patients and healthy individuals," the authors developed a genetic profile of E.coli bacteria in Crohn's disease patients and healthy individuals.  For this purpose the genomes of sixty-three E. coli strains from the gut of patients 16 with CD and healthy subjects were sequenced. In the introduction, the authors briefly discussed the topic of the involvement of the gut microbiota in the pathogenesis of Crohn's disease. In scientific experiments they used adequate to the purpose, modern analytical methods. The results of the study are presented in descriptive form and in 3 figures. It should be emphasized that the authors presented the results of their research in a clear and transparent way. In the discussion chapter the authors of the paper showed a very good knowledge of the discussed topic.

Both the subject of the study and the obtained results are undoubtedly valuable.

In their paper authors quoted 89 publications. It should be added that the publications were selected properly.

In my opinion, the paper qualifies for approval for printing in its current form.

Author Response

Dear reviewer, we are grateful for your careful reading of our manuscript.

Reviewer 3 Report

In the current study, the authors investigated the genetic and metabolic similarities and differences of the E. coli strains isolated from the CD patients and healthy controls. The authors claimed that these stains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems.  However, the results need more details, and results need more analysis and description. I do not think it is suitable or sufficient to be published in Microorganism journal.

1. Lines 137-138: The total number of 27 isolates from CD patients, 37 isolates from controls, and one from contaminated isolate, is not 64. Please check the number.
2. Lines 139-140: As the patients with isolates were separated to three subgroups, how about the control group?
3. Line 141: Were all the 18 high quality E. coli-like MAGs from the CD patients? Or from both patients and healthy controls? If the later, how many from patients and controls?

Were these MAGs chosen randomly, or just the total can be constructed?

4. Figure 1: The high-quality graphic of panel (a) should be provided, it is blurry when zoom in to see the details.

    Panel (b): Is there some difference of the isolates from control and patients? It may be easy to read if the sample from control and patients were separated with different symbol shape.

5. Lines 193-220: The authors may summarize these data with a bar chart or other type of figure to show the differences in which will be much easy to follow, such as the type of the virulence factors.
6. Line 242: The similar story for the antibiotic resistance data which may be shown with figure and keep the original data as the supplemental table.
7. Why the supplemental table 6 cited prior the supplemental table 4 and 5? Please check the order.
8. Is the location, colonic, ileal, and ileocolonic, impact the characters of the E. coli isolates performed in this study? Why didn’t the authors show anything about this?

Author Response

Dear reviewer, thank you for your critical reading of our manuscript and important remarks, which have been very helpful in improving the article. We present our responses to comments in the attached file.  Please see the attachment. 

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

The manuscript has been improved a lot now, and easer to follow. Just two more minor comments:

1. The second paragraph of the discussion is super long, the authors may consider separating the metabolites-related discussion to another paragraph.
2. The authors should not be afraid to identify any potential weaknesses in their approach - this would serve to highlight the strengths in my opinion.

Author Response

Dear reviewer, we greatly appreciate your comments that helped improve the manuscript. 

Point 1: The second paragraph of the discussion is super long, the authors may consider separating the metabolites-related discussion to another paragraph.

We made the necessary changes.

Point 2: The authors should not be afraid to identify any potential weaknesses in their approach - this would serve to highlight the strengths in my opinion.

We slightly modified the discussion to highlight the limitations of the study.