Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor

[SvetlanaUP]

Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor – Chen et al. – Microbiology Spectrum https://journals.asm.org/doi/10.1128/spectrum.02805-22

[eve10111]

Hi @SvetlanaUP , can you assign this paper to me to curate? Thank you.

[SvetlanaUP]

@eve10111 is this paper ready for review https://github.com/waldronlab/BugSigDBcuration/issues/232 ?

[PreciousMike]

Hello @SvetlanaUP please kindly assign this paper to me.

[PreciousMike]

Hello @SvetlanaUP I'm done curating this study and I'll appreciate your review on it. Here's the link to the study: https://bugsigdb.org/Study_985

Also, my study sampled four groups but the bugsigdb form only allows for comparison of two groups, is there a way to incorporate the other two groups or can they be ignored? Thank you

[SvetlanaUP]

Hi @PreciousMike, from your question and a quick look at your curation, we can conclude that https://bugsigdb.org/Study_985 is not ready for review.

Please ask support in the Slack #bugsigdb, especially if you have this kind of doubts. @Scholarpat and/or @MyleeeA, could you help out here?

[MyleeeA]

Yes I can help @SvetlanaUP

@PreciousMike I’m willing to help on this 😊

[Scholarpat]

Yes, I'll be happy to help @SvetlanaUP. @PreciousMike and @MyleeeA let's work together on this.

[PreciousMike]

Thank you for taking a look at it @SvetlanaUP .

@MyleeeA and @Scholarpat, I'll be super happy to work with you two on this. What's the way forward?

[Scholarpat]

@PreciousMike I already chatted @MyleeeA on slack. What's your username on slack so we can collaborate there.

[PreciousMike]

@Scholarpat That's awesome. My username is Mkpouto Shedrack (MK).

[PreciousMike]

Hello @SvetlanaUP , This study https://bugsigdb.org/Study_985 is now ready for review.

[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	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	1
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	0
13	Entered correct number of statistical tests per experiment	1	1
14	All diversity measures identified	1	0.5
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	1
18	Members of signatures identified correctly	2	2
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	21.5

Well done @PreciousMike @Scholarpat @MyleeeA

• a proper matching was not done in this study (corrected)
• Figure 1 does show alpha diversity between healthy and 3 disease subgroups (Experiment 2-4), but for the Experiment 1 does not. (corrected)

[Scholarpat]

Thank you @SvetlanaUP for the review and corrections. I have taken note of the corrections for future curations.

[PreciousMike]

Thank you so much @SvetlanaUP for the review, I appreciate and have taken note of all the corrections.