Review for 10.1186/s12876-024-03169-z (2024)

Title: Association between colorectal cancer, the frequency of Bacteroides fragilis, and the
levels of mismatch repair genes expression in the biopsy samples of Iranian patients
Version: 2 Date: 01 Nov 2023
Reviewer's report:
Dear Sir
The manuscript entitled: "Association between colorectal cancer, the frequency of Bacteroides
fragilis, and the level of mismatch repair genes expression in the biopsy samples of Iranian
patients" is submitted to the esteemed BMC Gastro for publication. The manuscript tries to
find out the association between the presence of B. fragilis and several genes expression with
colorectal cancer. I believe that the manuscript has several major and many minor defects.
Major considerations:
1- In the body it is pointed many times that the association between the bacterium and also MMR
genes with CRC has been proved many times. What is the main advantage of the research? We
know that the sample size is not higher than other publications, the geographical distribution is
not important in this field.
2- It seems that two different aims are  (prevalence of the bacterium and MMR genes expression)
are incompatible match. The rationality for this assessment is not obvious and is not mentioned
Because of the mentioned major considerations I believe that the manuscript is not suitable for
publication
Minor considerations:
1- The importance of this topic is not mentioned in the abstract or the introduction. We know
about the importance and the prevalence and the mortality rate of CRC, but why assessment of
MMR genes or bacterial prevalence in CRE
2- The sentence of " Bacteroides fragilis (B.fragilis) is one of the essential bacteria in the
incidence and expansion of CRC" shows that the main question has been elucidated before.
3- The abstract has too many non-essential statements.
4- There is no need to write DNA or RNA extraction methods in the abstract
5- This sentence:". One of the mechanisms that may help in early diagnosis in the clinic is the
role of microorganisms, especially bacteria, in certain human cancers" and similar sentences are
totally irrelevant  to the topic research.
6- What do we mean by this sentence:" and the establishment of balance in energy and nutrition
"??
7- Again, the sentence "CRC patients have been shown to be significantly affected by abnormal
expression of genes within this system" shows that this research is not relevant. The question
has answered before.
8- "Abundance",  "prevalence" and "Frequency" are technical idioms that have been used vice
versa so many times
9- There are many comparisons that mentioned in the manuscript and interestingly the statistical
results are also mentioned.  Unfortunately these comparisons had not definite aims,  the ample
size for them had not been defined and the used statistical tests are not mentioned, and also there
are no explanations about them.
In the discussion:
10- In many parts of the discussion the results are repeated again
11- The discussion is too long and contains many unnecessary items. The discussion can be
abstracted to 1/3rd of recent writings
The conclusion:
12- The conclusion of the abstract is not related to this research. It could be deduced without
this research
13- The conclusion at the end of the manuscript is not related to this manuscript. Assessment of
the genes as diagnostic tool or a biomarker need other research plans
Statistics:
14- The comparison are not correct. In order to assess the statistical relationship between
bacterial prevalence and CRC the applied test is not mentioned. I believe that  logic regression
and T student test are useful tests
15- The P value must be written as "<" value and not "="