Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls

[Omabekee]

Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls - Unger et al. - Parkinsonism & Related Disorders https://www.prd-journal.com/article/S1353-8020(16)30323-6/abstract

[Praiseagbetuyi]

Kindly assign this paper to me for curation, @SvetlanaUP

Thank you.

[SvetlanaUP]

@Praiseagbetuyi you are assigned to https://github.com/waldronlab/BugSigDBcuration/issues/202

[Omabekee]

Download article.pdf

Supplemental. file 1.pdf

Supplemental fig 2.pdf

Supplemental fig 2b.pdf

Supplemental fig 3.pdf

[Ademolawe]

Hello, can I curate this paper for my second curation? Eniola Adebayo

[Ademolawe]

Hello, this curation is ready for review https://bugsigdb.org/Study_944

Eniola Adebayo

[Peacesandy]

Hi @Ademolawe this is a good curation attempt. However here are some few points to note ✍️

• The statistical test used is Kruskal-Wallis test, In the passage it was stated that the Kruskal-Wallis test was applied to analyze global differences between the three groups. Mann-Whitney U test was used for post-hoc comparison. In order to control family-wise error rate caused by multiple comparison Bonferroni correction was carried out.
• The significance threshold is 0.01

N/B This study has been corrected and marked as reviewed. For ease you can go through the reviewed study to see the corrections I made.

CURATION RESULT

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
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): 1
13. Entered correct number of statistical tests per experiment (1 point): 0
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 (2 points): 1
19. Correct use of NCBI taxonomy (2 points): 2

Total (maximum 23 points): 22

@SvetlanaUP https://bugsigdb.org/Study_944 Reviewed and corrected ✅

[Ademolawe]

Good morning, thank you for the review. I have an observation and question. From what we were taught on BugSigDB, the asterisk sign is used to connote significance. For example, from figure 1 there is no asterisk on some taxa when CY and PD group were compared. So is Bifidobacterium sp. significantly different between CY compared to PD group . Same question for Faecalibacterium prausnitzii and Prevotellaceae between CY and PD group, is it significantly different. Thank you. @SvetlanaUP @Peacesandy @Folakunmi21

[Ademolawe]

Hi @Peacesandy @SvetlanaUP I observed that I was scored 1 out of 2 for identified sequencing details. Please, can I get a clarification on it. You only made remark on the statistical details. Thank you.

[Peacesandy]

Hi @Ademolawe please did you check the supplemental material while curating this study? Tho this study is kind of confusing, it is advisable that you also read the text describing the result to get a better understanding of the result interpretation. I just went through the curation with other mentors and the neccessary corrections have been made.

Secondly the grade for sequencing details have been corrected

[Peacesandy]

@SvetlanaUP Reviewed and corrected for the second time

[SvetlanaUP]

https://bugsigdb.org/Study_944 reviewed.