Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore

[cmirzayi]

Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore – Seok Hwee Koo – Singapore Medical Journal

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6875812/

[RotimiDesire]

Hi @SvetlanaUP

I'd love to curate this article.

Desire Oluwarotimi.

[RotimiDesire]

Thank You.

[RotimiDesire]

Hi @SvetlanaUP

My curation is ready for review.

https://bugsigdb.org/Study_896

[RotimiDesire]

@AleruDivine @MyleeeA @Scholarpat

[Omabekee]

Overall this was a good second curation! @RotimiDesire , some points to take note:

1. Matched-on should only be entered if it's stated in the paper. You can do that easily by Ctrl + F "matched on". In cases where you're not sure, please don't assume, please ask questions.
2. We're only interested in antibiotics exclusion in bugsigdb.
3. It's good for source descriptions (for signatures) to be descriptive enough so that anyone who comes across the study in the future can immediately tell what's going on without reading the whole paper.
4. The paper claimed to carry out alpha diversity for chao, richess, PD, shannon and simpson, however, only shannon and simpson showed statistical results (with _p_values) for all experiments (Figure 1). Although, they made mention of the mean SD of other alpha diversity indices, there was no mention of their respective p values in the table. This made it harder to tell if they were significant or not, so I wouldn't curate this. I only curated richness for Day 1 vs Day 7 which was mentioned within the text. Again, it is good to ask questions especially when you're not sure.
5. Some experiments were deleted because they were redundant (repeated when they didn't need to be). I re-curated edited experiments based on the LEfSe results and the alpha diversity results observed. E.g. Chinese Vs Indian and Indian vs Malay, because the alpha diversity results of these comparisons were shown and the LEfSe results were displayed as well. This way, we avoid unnecessary duplication of signatures. The same goes for the timepoints experiments.

CURATION RESULTS

1. All elements marked "Needs review" (none "Incomplete") (1 point): 1
2. Correct study design (1 point): 1
3. Entered all relevant experiments and no irrelevant experiments (1 point): 0.5
4. Body site correctly identified (i.e. does not include multiple sites) (1 point): 1
5. Condition entered according to contrast (correct EFO ontology) (1 point): 1
6. Contrast groups correctly identified (1 point): 1
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 1
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (2 points): 2
10. Identified correct statistical test (1 point): 1
11. Identified MHT correction (1 point): 1
12. Correctly recorded matched on factors (1 point): 0
13. Entered correct number of statistical tests per experiment (1 point): 1
14. All diversity measures identified (1 point): 0.5
15. Diversity results correctly entered as increased/decreased/unchanged (1 point): 0.5
16. All signature sources correctly identified (-1 for each error) (2 points): 2
17. Abundance direction correctly selected (1 point): 1
18. Members of Signatures identified correctly (2 points): 1
19. Correct use of NCBI taxonomy (2 points): 2 Total = 19.5

@SvetlanaUP , review of Study 896 complete. ✅

[RotimiDesire]

Thank You.