Title: Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated
Blautia species and bile acid metabolic pathways
Version: 2 Date: 23 May 2025
Reviewer's report:
Review comments:
1. In the abstract, line 30, sentences are repeated. They give a similar meaning of line 24
2. Lines 45 & 46 remove unnecessary hyphens
3.  Line 50 & 116Check reference format and size.
4. Sample size is relatively small, and a regionally homogenous cohort may limit
generalizability.
5. Give justification for the sample collection time.
6. How DNA concentration and purity was checked, give clear methodology for that.
7. Check the all references format and size
8. Check the sentence in line 166, you mentioned 51 CCA patients, but in the methodology you
pointed out 29 healthy individual  and 23 CCA sample. Clarify that.
9. Line 263, the KEGG abbreviations are repeated
10. The methods mention using ROC and DCA for model evaluation, but these are not included
in the figures or results section.
11. OTU terminology is outdated for WGS data. Replace with MAG, species bin, or
metagenomic contigs.
12. The term “Blautia streptococcus spp.” is not taxonomically valid. Revise taxonomy
references. Ensure species-level assignments are based on accepted thresholds.
13.  The connection between reduced Blautia and decreased bile acid metabolism is plausible
but hypothetical. Acknowledge the limitation and propose validation (e.g., qPCR of metabolic
genes, butyrate measurement, or animal studies).
Title: Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated
Blautia species and bile acid metabolic pathways
Version: 2 Date: 23 May 2025
Reviewer's report:
Review comments:
1. In the abstract, line 30, sentences are repeated. They give a similar meaning of line 24
2. Lines 45 & 46 remove unnecessary hyphens
3.  Line 50 & 116Check reference format and size.
4. Sample size is relatively small, and a regionally homogenous cohort may limit
generalizability.
5. Give justification for the sample collection time.
6. How DNA concentration and purity was checked, give clear methodology for that.
7. Check the all references format and size
8. Check the sentence in line 166, you mentioned 51 CCA patients, but in the methodology you
pointed out 29 healthy individual  and 23 CCA sample. Clarify that.
9. Line 263, the KEGG abbreviations are repeated
10. The methods mention using ROC and DCA for model evaluation, but these are not included
in the figures or results section.
11. OTU terminology is outdated for WGS data. Replace with MAG, species bin, or
metagenomic contigs.
12. The term “Blautia streptococcus spp.” is not taxonomically valid. Revise taxonomy
references. Ensure species-level assignments are based on accepted thresholds.
13.  The connection between reduced Blautia and decreased bile acid metabolism is plausible
but hypothetical. Acknowledge the limitation and propose validation (e.g., qPCR of metabolic
genes, butyrate measurement, or animal studies).
Please review this paper.
user
Title: Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated
Blautia species and bile acid metabolic pathways
Version: 2 Date: 23 May 2025
Reviewer's report:
Review comments:
1. In the abstract, line 30, sentences are repeated. They give a similar meaning of line 24
2. Lines 45 & 46 remove unnecessary hyphens
3.  Line 50 & 116Check reference format and size.
4. Sample size is relatively small, and a regionally homogenous cohort may limit
generalizability.
5. Give justification for the sample collection time.
6. How DNA concentration and purity was checked, give clear methodology for that.
7. Check the all references format and size
8. Check the sentence in line 166, you mentioned 51 CCA patients, but in the methodology you
pointed out 29 healthy individual  and 23 CCA sample. Clarify that.
9. Line 263, the KEGG abbreviations are repeated
10. The methods mention using ROC and DCA for model evaluation, but these are not included
in the figures or results section.
11. OTU terminology is outdated for WGS data. Replace with MAG, species bin, or
metagenomic contigs.
12. The term “Blautia streptococcus spp.” is not taxonomically valid. Revise taxonomy
references. Ensure species-level assignments are based on accepted thresholds.
13.  The connection between reduced Blautia and decreased bile acid metabolism is plausible
but hypothetical. Acknowledge the limitation and propose validation (e.g., qPCR of metabolic
genes, butyrate measurement, or animal studies).
assistant