Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome

Round 1

Reviewer 1 Report

Khan et al. nicely revised the current status of IBD studies in the context of microbiota and therapeutic approaches. The context is well designed and subsections of manuscript describe each context adequately. One important thing that is missing is the studies from 2019. There are at least two critical studies that are summarizing most of the microbiota profile that they mentioned in this review. Therefore, I'd like to ask author kindly to check the further literature from 2019 and add at least these two critical manuscripts into their review. These manuscripts provides intellectual inputs for their review.

1 -https://www.nature.com/articles/s41591-018-0308-z

2 - https://www.nature.com/articles/s41586-019-1237-9

Besides that, there are numerous typos in the manuscript. It is important that authors go through the text carefully and revise the manuscript.

Some of those typos and sentences that need to be corrected are as the following:

- There are some bold sentences or group of words should be converted non-bold state.

- Figures' quality are relatively bad and authors should provide a better resolution.

Line 34 - "modles" should be "models"

Line 35 - 37 - Sentence needs to be revised. Grammatically wrong.

Line 38 - Less and conflicting results? Not clear!

Line 48 - Chron’s disease need to be corrected into Crohn’s disease

Line  113 - (SCFAs) is already introduced in Line 86. No need to repeat the meaning of abbreviation.

Line 120 - 124 - The authors show the microbial differences in IBD patients compared to control but they should also mentioned differences between CD vs Control or UC vs Control.

Line 186-202 - species is missing "s" at the end.

Line 192 - enterobacteriacae should be Enterobacteriacae

Line 231 - 234 - The sentence needs to be revised. It is repetative of the same statement.

Line 234 - "Needs" to be

Line  271 - in to should be "into"

Line 285 - sub sets should be subsets 

First letter of Enterobacteriacae and Bifidobacteria should be capitalized. It was observed in couple of places that this is not the case.

Author Response

Please, find a point-by-point response to the reviewer-1 report , as an attachment named Response to reviewer-1.

Author Response File: Author Response.docx

Reviewer 2 Report

This review article is scientifically designed, and the presentation is also overall and elaborated form data collection to literature review, making the conclusion very convincing.The topic of the paper is very relevant. However, some minor revisions are needed.

Manuscript revision

Line 25. Replace Crohon’s with Crohn’s

Line 26. Review the grammatical in “Although the etiology of IBD is unknown, however the gut microbiota alteration 26 (dysibiosis) considered as a novel factor to be involved in IBD pathogenesis”.

Line 38

Replace Less with less

Line 66

Replace [18, 19]  with [18,19] 

Lines 117 and 204

Replace etio-pathology with etiopathology

Line 127

Replace [28,84, 85] with [28,84,85]

Line 129

Relocate [88, 89]

Line 136

Replace entero-pathy with enteropathy

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Replace pre-biotics with prebiotics

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Replace etio-pathogenesis with etiopathogenesis

Line 511

In the Conclusion section, the wording should be improved

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Replace colleague with colleagues.

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Replace “Nature reviews Gastroenterology & hepatology” with “Nature Reviews Gastroenterology & Hepatology”

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Replace “The American journal of gastroenterology” with “The American Journal of Gastroenterology”. There are similar problems in other references.

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Replace “A human gut microbial gene catalogue established by metagenomic sequencing. nature, 464(7285), 59” with “A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59-65”

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Matsuoka, K., & Kanai, T. (2015, January). The gut microbiota and inflammatory bowel disease. In Seminars in immunopathology (Vol. 37, No. 1, pp. 47-55). Springer Berlin Heidelberg

with

Matsuoka, K., Kanai, T. (2015). The gut microbiota and inflammatory bowel disease. In Seminars in Immunopathology, 37(1), 47-55

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Ward, J. M., Anver, M. R., Haines, D. C., Melhorn, J. M., Gorelick, P., Yan, L., & Fox, J. G. (1996). Imflammatory large bowel disease in immunodeficient mice naturally infected with. Helicobacter hepaticus. Lab. Anim. Sci, 46, 15.

With

Ward, J. M., Anver, M. R., Haines, D. C., Melhorn, J. M., Gorelick, P., Yan, L., & Fox, J. G. (1996). Imflammatory large bowel disease in immunodeficient mice naturally infected with Helicobacter hepaticus. Lab. Anim. Sci, 46(1), 15-20.

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Author Response

Please, find a point-by-point response to the reviewer-2 report , as an attachment named Response to reviewer-2.

Author Response File: Author Response.docx