A Pilot Microbiota Study in Parkinson's Disease Patients versus Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in Parkinsonian and Multiple System Atrophy Mouse Models

[Omabekee]

A Pilot Microbiota Study in Parkinson's Disease Patients versus Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in Parkinsonian and Multiple System Atrophy Mouse Models - Vidal-Martinez et al. - Journal of Parkinson's disease https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7029363/

[FlourishRalph]

Hi @Omabekee I'd like to work on this, please assign it to me.

[FlourishRalph]

@SvetlanaUP please assign this to me

[FlourishRalph]

@buraah @rotimidesire @alerudivine @lonercode @scholarpat thank you for reviewing!

[FlourishRalph]

Hi @SvetlanaUP
I’m done with curating this paper and it’s ready for review

Here is the link:

https://bugsigdb.org/Study_922 
Thank you.

[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	1
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	1
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	2
10	Identified correct statistical test	1	0
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	1
13	Entered correct number of statistical tests per experiment	1	1
14	All diversity measures identified	1	1
15	Diversity results correctly entered as increased/decreased/unchanged	1	1
16	All signature sources correctly identified (-1 for each error)	2	2
17	Abundance direction correctly selected	1	0
18	Members of Signatures identified correctly	2	0
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	19

Figure 1B just repeats what is present on the genus level in Table 1 Column A. Based on Table 1, there were only 3 significant taxa in 2 experiments:

Mouse 10 month (A53T) Firmicutes

Human Verrucomicrobiarceae Akkermansia

I am not sure where the significant results for 17 months A53T and 10-11 months CNPaSyn are coming from because they are not present in the identified source.

[FlourishRalph]

Hi @cmirzayi, thank you for your review.

The antibiotic exclusion is on page 186 and states that 'use of antibiotics within 2 weeks prior to initiation of the study' was part of the exclusion criteria. This was included in my curation so I'm unsure why I got zero points in number 8 (Antibiotic exclusion correctly identified).

[cmirzayi]

Apologies. I've added the point back.

[FlourishRalph]

Thank you!

[Scholarpat]

Hello @SvetlanaUP , I'll love to help out in correcting this.

[SvetlanaUP]

@Scholarpat go ahead!

[Scholarpat]

Hello @cmirzayi @SvetlanaUP ,

Here are the changes and observations I made to this curation (https://bugsigdb.org/Study_922):

1. Humans were not matched on any factor; only mice were matched on age. Therefore, I removed "matched-on" from Experiment 1 and included it in Experiment 2.

2. The statistical test used in the human experiment (Experiment 1) is Mann-Whitney (Wilcoxon), while that of the mice group (Experiment 2) is not specified. The initial curator stated Spearman Correlation as the statistical test for Experiment 2, but I edited that part out and left it blank.

3. Two taxa are significant in the human experiment:

   • Verrucomicrobiarceae
   • Akkermansia Both are increased in the PD group, hence eliminating the need for 'Signature 2' in Experiment 1.

4. One significant taxon (Firmicutes) is increased in 10-month-old transgenic (Tg) mice, and none are significantly decreased, eliminating the need for 'Signature 2' in Experiment 2.

5. There are no significant results for 17-month A53T and 10-11-month CNPaSyn, as you also stated above, and there's also no alpha diversity for these experiments. Therefore, I'm wondering if there's any need to curate these experiments (Experiment 3 and 4). Can they can be deleted?

Please I’d like to delete;

• Signature 2 in exp. 1
• Signature 2 in exp. 2
• Experiments 3 & 4 and their signatures

[cmirzayi]

@SvetlanaUP Deleted the signatures and experiments as requested, made one small change to a missing statistical method in experiment 2, and marked as reviewed.