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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery #518

Closed SvetlanaUP closed 2 weeks ago

SvetlanaUP commented 3 weeks ago

Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery – Celia Boukadida – Microbiome https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01925-7

IfeanyiSam commented 3 weeks ago

Hello @SvetlanaUP, I'd like to work on this paper

IfeanyiSam commented 2 weeks ago

@SvetlanaUP Hi, i've studied the paper and i'm a bit confused about how to report the differential abundance. Under "Bacterial dysbiosis is associated with advanced stages of HIV infection" section, they mentioned this (we explored differences in bacterial communities by differential abundance analysis (DAA) using Microbiome Multivariate Association with Linear Models (MaAsLin2). First, the top 3 phyla were Bacteroidota, Bacillota, and Pseudomonadota (formally Bacteroidetes, Firmicutes, and Proteobacteria, respectively), accounting for more than 97% of all phyla. At the genus level, Prevotella, Bacteroides, Faecalibacterium, Alloprevotella, and UCG-002 accounted for more than 50% of all genera. For DAA, we ran two models: the first one included CD4 T cell counts and HIV status, while the second one considered the five-study group stratification, in addition to age, sexual preference, BMI, antibiotic use, and hospitalization. Both models demonstrated that hospitalization was positively associated with Enterococcus and Streptococcus, and negatively with alpha diversity (Shannon index), while HIV status was positively associated with Coprococcus (Excel S7).) but looking at the supplementary data &, i can't tell what they're comparing.

what do you think?

SvetlanaUP commented 2 weeks ago

Hi @IfeanyiSam, this question is for Slack.

SvetlanaUP commented 2 weeks ago

@Rahila-me https://github.com/Rahila-me you could help in here.

Rahila-me commented 2 weeks ago

@SvetlanaUP got it. @IfeanyiSam pls what's your name on slack so we can collaborate on this curation. I am Liza. waiting for your kind reply

SvetlanaUP commented 2 weeks ago

Yes, please contact @IfeanyiSam and enjoy your team work!

IfeanyiSam commented 2 weeks ago

@SvetlanaUP Thanks for the clarification. I'll work with @Rahila-me on this.

SvetlanaUP commented 2 weeks ago

@Rahila-me @IfeanyiSam this study is not curatable. Please see https://community-bioc.slack.com/archives/C04RATV9VCY/p1731066637591289?thread_ts=1730988400.486679&cid=C04RATV9VCY