Dysbiosis of gut microbiota in a selected population of Parkinson's patients

[Omabekee]

Dysbiosis of gut microbiota in a selected population of Parkinson's patients - Pietrucci et al. - Parkinsonism & Related Disorders https://pubmed.ncbi.nlm.nih.gov/31174953/

[Tiwalade0002]

Hello @SvetlanaUP, please assign this to me.

[Marhiposa]

Hello, @Omabekee @SvetlanaUP My name is Mariam, and I just finished my first task. Please, can I be assigned to this?

[SvetlanaUP]

Assigned to Tiwalade0002

[Tiwalade0002]

@SvetlanaUP @Omabekee @Marhiposa I just completed my contribution. I would appreciate your review of my curation. (https://bugsigdb.org/Study_924)

[cmirzayi]

Item	Description	max	points
1	All elements marked "Needs review" (none "Incomplete")	1	1
2	Correct study design	1	1
3	Entered all relevant experiments and no irrelevant experiments	1	0
4	Body site correctly identified (i.e. does not include multiple sites)	1	1
5	Condition entered according to contrast (correct EFO ontology)	1	1
6	Contrast groups correctly identified	1	0
7	Groups correctly labeled as 1 and 0 (1=cases, 0=controls)	1	1
8	Antibiotic exclusion correctly identified	1	1
9	Correctly identified sequencing details	2	1
10	Identified correct statistical test	1	0
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	0
13	Entered correct number of statistical tests per experiment	1	0
14	All diversity measures identified	1	1
15	Diversity results correctly entered as increased/decreased/unchanged	1	0
16	All signature sources correctly identified (-1 for each error)	2	1
17	Abundance direction correctly selected	1	0
18	Members of Signatures identified correctly	2	1
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	13

• There are two experiments present in this study: PD vs. HC and PD vs. HC with patients on COMT inhibitors excluded.
• V3-V4 region was sequenced but missing from experiment 1
• Statistical test was a linear model
• No matching was done. They controlled for confounders in their GLMs
• No sig. differences in diversity were found.
• Missing decreased signature for signature 1
• Lachnospiraceae incorrectly curated as increased when it is decreased

[fiddyhamma]

Hello @cmirzayi @SvetlanaUP It seems the corrections made have not yet been effected on the study, can I go ahead and make these corrections?

[SvetlanaUP]

@fiddyhamma yes please :) also make notes here what and how you correct it. Thank you!

[fiddyhamma]

Noted, thank you @SvetlanaUP

[fiddyhamma]

Hello @SvetlanaUP I'm unable to access the full article online, can you help me please?

[SvetlanaUP]

1-s2.0-S1353802019302640-main.pdf 1-s2.0-S1353802019302640-mmc1.docx

[fiddyhamma]

Thank you

[fiddyhamma]

Hello @SvetlanaUP I made these changes to this study;

1. Added concise definitions to group 1
2. Curated Suppl table S7 which showed differentially abundant genera
3. I curated Lachnospiraceae as decreased in both experiments (1&2)
4. I removed matched on, lda score of 3 as I didn't find this in the study
5. I changed the statistical test to linear regression and Wilcoxon and set the alpha diversity as unchanged
6. Completed experiment 2 with both increased and decreased taxas

[Scholarpat]

Hi @SvetlanaUP,

Here are the changes I made to this curation:

• Corrected a misspelling in Group 1 name for both experiments.
• Changed Group 1 definition in experiment 2.
• Changed the signature source from 'Table 1A, Figure 1, Suppl table S7A, and text' to just 'Supplementary Table S7A and S7B' for experiments 1 and 2 respectively. This is because the supplementary table is easier to interpret and has all the signatures reported together, unlike the other sources.

This curation is complete. Thank you.

[SvetlanaUP]

https://bugsigdb.org/Study_924 reviewed.