Title: Genetically Predicted Gut Microbiota Mediate the Association Between Plasma
Lipidomics and Primary Sclerosing Cholangitis
Version: 0 Date: 15 Apr 2024
Reviewer's report:
The authors talk about microbial species throughout the results section. However, the 400+
microbiome features that they used in Table S2 include higher taxa levels, genes and pathways.
Among the 3 associated microbial features, just one (E. rectale) is actually a bacteria species.
Could the authors justify why features other than species were kept in the analysis? Microbiome
taxonomy analyses are done stratifying by taxa level (species, genus, family, etc.) and analysing
gene functions and taxonomy separately.
In methods, could the authors comment on any data pre-processing and normalisation done on
the microbiome dataset?
For microbiome field readers, less familiar with MR, it might be good to introduce the basics of
MR and why it would be useful to use it. As well as outlining the main aspects of the datasets
that were used in the study and why they were chosen.
Minor comments;
- Line 93: please revise the definition of the microbiome in introduction. "flora" needs to be
replaced by "microbiota", and gut microbiota is also composed of Archaea and Eukaryotes, not
only Bacteria.
Title: Genetically Predicted Gut Microbiota Mediate the Association Between Plasma
Lipidomics and Primary Sclerosing Cholangitis
Version: 0 Date: 15 Apr 2024
Reviewer's report:
The authors talk about microbial species throughout the results section. However, the 400+
microbiome features that they used in Table S2 include higher taxa levels, genes and pathways.
Among the 3 associated microbial features, just one (E. rectale) is actually a bacteria species.
Could the authors justify why features other than species were kept in the analysis? Microbiome
taxonomy analyses are done stratifying by taxa level (species, genus, family, etc.) and analysing
gene functions and taxonomy separately.
In methods, could the authors comment on any data pre-processing and normalisation done on
the microbiome dataset?
For microbiome field readers, less familiar with MR, it might be good to introduce the basics of
MR and why it would be useful to use it. As well as outlining the main aspects of the datasets
that were used in the study and why they were chosen.
Minor comments;
- Line 93: please revise the definition of the microbiome in introduction. "flora" needs to be
replaced by "microbiota", and gut microbiota is also composed of Archaea and Eukaryotes, not
only Bacteria.
Please review this paper.
user
Title: Genetically Predicted Gut Microbiota Mediate the Association Between Plasma
Lipidomics and Primary Sclerosing Cholangitis
Version: 0 Date: 15 Apr 2024
Reviewer's report:
The authors talk about microbial species throughout the results section. However, the 400+
microbiome features that they used in Table S2 include higher taxa levels, genes and pathways.
Among the 3 associated microbial features, just one (E. rectale) is actually a bacteria species.
Could the authors justify why features other than species were kept in the analysis? Microbiome
taxonomy analyses are done stratifying by taxa level (species, genus, family, etc.) and analysing
gene functions and taxonomy separately.
In methods, could the authors comment on any data pre-processing and normalisation done on
the microbiome dataset?
For microbiome field readers, less familiar with MR, it might be good to introduce the basics of
MR and why it would be useful to use it. As well as outlining the main aspects of the datasets
that were used in the study and why they were chosen.
Minor comments;
- Line 93: please revise the definition of the microbiome in introduction. "flora" needs to be
replaced by "microbiota", and gut microbiota is also composed of Archaea and Eukaryotes, not
only Bacteria.
assistant