Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer's Disease

[ftzohra22]

Condition: Alzheimer's Disease URL: https://pubmed.ncbi.nlm.nih.gov/33614635/

[sopeadeniji]

Hi, Please, assign me to this article.

[ftzohra22]

Assigned to you @sopeadeniji

[sopeadeniji]

@ftzohra22 @cmirzayi Please review this recent curation https://bugsigdb.org/Study_736

[mcarlsn]

@sopeadeniji Great curation, please see below for my review and additional comments. Let me know if you have any questions.

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): 1
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 (Not removing points for this but please update group labels. To match the same language used in the article, Group 1 can be updated and labelled as “Alzheimer’s disease patients”)
7. Groups correctly labelled as 1 and 0 (1=cases, 0=controls) (1 point): 1
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): 2
10. Identified correct statistical test (1 point): 0 (Should only list the method(s) used to detect features & Figure 2 is LEfSe output so this should just be LEfSe)
11. Identified MHT correction (1 point): 0 (I cannot find evidence of MHT correction in this study. However, if you find that I’m incorrect, please post your response in the chat below).
12. Correctly recorded matched on factors (1 point): 1
13. Entered correct number of statistical tests per experiment (1 point): 0 (Should only list the method(s) used to detect features & Figure 2 is LEfSe output so this should just be LEfSe)
14. All diversity measures identified (1 point): 1
15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): 1
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 (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): 0 (Check out the results section for the full lists. Should be 13 that significantly increased in AD patients and 3 that drastically decreased).
19. Correct use of NCBI taxonomy (don't deduct if can't easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): 2

Total (maximum 23 points): 18

[sopeadeniji]

@ mcarlsn https://bugsigdb.org/Study_736 has been updated with suggested corrections. Please, review.

[mcarlsn]

Thank you for updating the curation, @sopeadeniji!

[atrayees]

Study 736 Corrected the MHT correction, the rest of the curation seems fine.

[lwaldron]

Thanks @atrayees ! Please go ahead and mark everything as "reviewed" then close this issue.