Title: The gut microbiota composition in patients with right- and left-sided colorectal cancer
and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing
Version: 3 Date: 14 Apr 2022
Reviewer's report:
The manuscript by Suga et al explored microbial composition in 31 patients with colon cancer
with and without curative colectomy compared with 10 healthy controls. This is an interesting
topic in part because the regional microenvironment of the colon especially in relation to cancer
is not well understood. The author is found changes an alpha diversity specific to the region of
cancer and resection. Changes in genus level abundance and clostridial clusters were associated
with patient groups. A variety of computational techniques were included, including Standard
diversity assessment and enrichment tools, as well as predictive meta-genomics.
The significance in age between some of the patient groups mentioned in the results and
displayed in the table should be included in the discussion as a limitation. Another important
limitation is the lack of dietary intake across patients that could potentially skew results given
the relatively modest sample sizes.
The methods and/or results lack details on how many reads were obtained across samples or
on average within samples. Also what rarefaction depth was used in analysis, including alpha
diversity etc. They should be reported.
In LEfSe the LDA used as significant should be reported, I assume 2.0, but please state in the
methods.
The legend for figure 1 should include the statistical symbols currently shown in the figure. The
same figure legend states that Shannon and Simpson diversity indexes were used in the study
but are not displayed.
In the legend for figure 2 A and B, please address whether PERMANOVA or a comparable beta
diversity statistics were included to determine significance in beta diversity between groups.
This should be mentioned with the Legend.
The manuscript requires light grammatical editing
Title: The gut microbiota composition in patients with right- and left-sided colorectal cancer
and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing
Version: 3 Date: 14 Apr 2022
Reviewer's report:
The manuscript by Suga et al explored microbial composition in 31 patients with colon cancer
with and without curative colectomy compared with 10 healthy controls. This is an interesting
topic in part because the regional microenvironment of the colon especially in relation to cancer
is not well understood. The author is found changes an alpha diversity specific to the region of
cancer and resection. Changes in genus level abundance and clostridial clusters were associated
with patient groups. A variety of computational techniques were included, including Standard
diversity assessment and enrichment tools, as well as predictive meta-genomics.
The significance in age between some of the patient groups mentioned in the results and
displayed in the table should be included in the discussion as a limitation. Another important
limitation is the lack of dietary intake across patients that could potentially skew results given
the relatively modest sample sizes.
The methods and/or results lack details on how many reads were obtained across samples or
on average within samples. Also what rarefaction depth was used in analysis, including alpha
diversity etc. They should be reported.
In LEfSe the LDA used as significant should be reported, I assume 2.0, but please state in the
methods.
The legend for figure 1 should include the statistical symbols currently shown in the figure. The
same figure legend states that Shannon and Simpson diversity indexes were used in the study
but are not displayed.
In the legend for figure 2 A and B, please address whether PERMANOVA or a comparable beta
diversity statistics were included to determine significance in beta diversity between groups.
This should be mentioned with the Legend.
The manuscript requires light grammatical editing
Please review this paper.
user
Title: The gut microbiota composition in patients with right- and left-sided colorectal cancer
and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing
Version: 3 Date: 14 Apr 2022
Reviewer's report:
The manuscript by Suga et al explored microbial composition in 31 patients with colon cancer
with and without curative colectomy compared with 10 healthy controls. This is an interesting
topic in part because the regional microenvironment of the colon especially in relation to cancer
is not well understood. The author is found changes an alpha diversity specific to the region of
cancer and resection. Changes in genus level abundance and clostridial clusters were associated
with patient groups. A variety of computational techniques were included, including Standard
diversity assessment and enrichment tools, as well as predictive meta-genomics.
The significance in age between some of the patient groups mentioned in the results and
displayed in the table should be included in the discussion as a limitation. Another important
limitation is the lack of dietary intake across patients that could potentially skew results given
the relatively modest sample sizes.
The methods and/or results lack details on how many reads were obtained across samples or
on average within samples. Also what rarefaction depth was used in analysis, including alpha
diversity etc. They should be reported.
In LEfSe the LDA used as significant should be reported, I assume 2.0, but please state in the
methods.
The legend for figure 1 should include the statistical symbols currently shown in the figure. The
same figure legend states that Shannon and Simpson diversity indexes were used in the study
but are not displayed.
In the legend for figure 2 A and B, please address whether PERMANOVA or a comparable beta
diversity statistics were included to determine significance in beta diversity between groups.
This should be mentioned with the Legend.
The manuscript requires light grammatical editing
assistant