Altered Actinobacteria and Firmicutes Phylum Associated Epitopes in Patients With Parkinson’s Disease

[SvetlanaUP]

Altered Actinobacteria and Firmicutes Phylum Associated Epitopes in Patients With Parkinson’s Disease – Zhuo Li – Frontiers in Immunology
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.632482/full#supplementary-material

[KateRasheed]

Good morning @SvetlanaUP . Can I be assigned this paper please?

[KateRasheed]

This paper is ready for review. Thank you so much @SvetlanaUP

[AleruDivine]

Good afternoon @SvetlanaUP P, I'd like to review this paper.

[AleruDivine]

Well done @KateRasheed. This is an excellent curation.👏👏

I'd like for you to consider the statistical test for this study.
The paper states "(1) the linear discriminant analysis (LDA) effect size (LEfSe) algorithm was used to identify taxonomic biomarkers (with LDA > 2.5); (2) The DESeq2 package was used to identify potential functional biomarkers (with P < 0.05, False Discovery Rate (FDR) < 0.05, and |deseq2.logfoldchange| > 0.58);"

I believe the statistical test is LEfSe because a "taxonomic biomarker" identifies an organism based on its taxonomic classification. In contrast, "functional biomarker" means a biological molecule that reflects a specific biological process or activity within an organism.
Table S1 has the caption "Potential bacterial biomarkers with altered abundance" and from the table, we can see the various LDA scores.

Let me know what you think about this. Thank you so much!

[KateRasheed]

Hi @AleruDivine . I used LEfSe at first but its only DESeq2 that used FDR, and from the article, the supplementary table was adjusted for, that's why I used DESeq2. See "A set of robust bacterial biomarkers were selected, which are listed in Table S1 (FDR < 0.05)."

Do you think they should be combined?

[AleruDivine]

@KateRasheed, I believe only LEfSe was used to identify taxonomic (bacterial) biomarkers in this study. Keep in mind that FDR can be applied to LEfSe results separately, so the indication (FDR < 0.05) doesn’t necessarily imply the use of DESeq2. Perhaps we can clarify this during office hours tomorrow.

[KateRasheed]

Good afternoon @AleruDivine . I've changed the statistical test in this study. I would also keep in mind that FDR can be applied to LEfSe results separately.

Thank you.

[KateRasheed]

Good morning @AleruDivine . Please can this issue be closed?

[AleruDivine]

Yes please. I left a comment last night but it didn’t go through because of network.

@SvetlanaUP, this review is complete.