Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease

[Omabekee]

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease - Sampson et al. - Cell https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718049/

[Toyosiolann]

kindly assign me

[Toyosiolann]

@SvetlanaUP

[Toyosiolann]

Hello @SvetlanaUP I am done curating this paper and it's ready for review.

Link: https://bugsigdb.org/Study_910

[SvetlanaUP]

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	0
8	Antibiotic exclusion correctly identified	1	0
9	Correctly identified sequencing details	2	2
10	Identified correct statistical test	1	1
11	Identified MHT correction	1	0
12	Correctly recorded matched on factors	1	1
13	Entered correct number of statistical tests per experiment	1	0.5
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	1
17	Abundance direction correctly selected	1	0
18	Members of signatures identified correctly	2	0
19	Correct use of NCBI taxonomy	2	0.5
	TOTAL	23	12

Unfortunately, this curation has 3 main errors:

• This is a laboratory study done in mice models, thus the host species is not Homo sapiens (although human feces was used for fecal transfer).

• There are two experiments:

  1. germ-free, wild-type (WT) mice colonized with fecal microbes from healthy controls (HC) versus germ-free, wild-type (WT) mice colonized with fecal microbes from Parkinson’s disease patients (PD); and

2. germ-free, Thy1-α-synuclein genotype (ASO) mice colonized with fecal microbes from healthy controls (HC) versus germ-free mice, Thy1-α-synuclein genotype (ASO) colonized with fecal microbes from Parkinson’s disease patients (PD).

• The signature source is correctly identified – Figure 6E – a figure fairly difficult to curate. However, it's wrongly interpreted by the curator.

✅ https://bugsigdb.org/Study_910 reviewed and corrected

[Toyosiolann]

Thank you for the review, all corrections duly noted. @SvetlanaUP