Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity

[Omabekee]

Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity -- Zhang et al. -- Frontiers in Immunology https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9127079/

[Shulamite54]

Good day @SvetlanaUP, My name is Precious, please I will love to work on this paper curation, can it be assigned to me.

[Shulamite54]

Thanks @SvetlanaUP

[Shulamite54]

Good day @SvetlanaUP @Omabekee Please can you help review my work, here is the link: https://bugsigdb.org/Study_970/Experiment_1 Thank you.

[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	0
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	1
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	0
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	0
17	Abundance direction correctly selected	1	0
18	Members of signatures identified correctly	2	0
19	Correct use of NCBI taxonomy	2	1
	TOTAL	23	12

• incorrect body site: this is gut microbiome study where fecal samples are used for microbiome analysis
• missing sequencing details: in the supplementary material (section: 16S rDNA sequencing) there is information on universal primers used – 341F-805R primers – for V3-V4.
• incorrect statistical tests and details
• Source: Figure 5SC is incorrect; Figure 4C should be curated
• more details to check and fix

[SvetlanaUP]

RotimiDesire you could help out here in correcting this curation.

[RotimiDesire]

@SvetlanaUP Thank you.

[RotimiDesire]

Hi @SvetlanaUP

I've made the corrections like you asked now and you can review it again. Two things though; I couldn't find the sample sizes for the contrast groups. So, I left their input fields blank. Also, I couldn't find any sequencing regions in the paper or its supplementary but you already mentioned it to be V3 - V4 and so, I inputted those.

[SvetlanaUP]

@RotimiDesire Great! They did not write "V3-V4" but from "using universal 341F-805R primers" we know that the primers are for V3-V4 regions amplification. See here Illumina amplicon primers.

[RotimiDesire]

Thank You.

[Shulamite54]

Thanks, @SvetlanaUP for the feedback, thanks @RotimiDesire for helping in the correction. I appreciate. Is there any other things I can work on @SvetlanaUP, I will be very glad and happy to continue contributing. Thank you.

[Scholarpat]

Hi @SvetlanaUP,

Here are the changes I made:

• I adjusted the group names to include definitions of the acronyms.
• I updated the source description to make it more descriptive.
• The phylum Bacteroidetes was not initially curated in signature 2. I've curated its homotypic synonym Bacteroidota.

Thank you very much. This curation is complete.

[SvetlanaUP]

https://bugsigdb.org/Study_970 reviewed.