Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis

[Omabekee]

Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis -- Guo M et al. -- mBio

https://journals.asm.org/doi/10.1128/mbio.03519-22

[zheeburg]

Isaac Hi @SvetlanaUP, I'd love to curate this article.

[zheeburg]

Thank you very much

[zheeburg]

Hi @SvetlanaUP I am done curating this study for review. Here is the link to the curation. https://bugsigdb.org/Study_885

[cmirzayi]

Hi @zheeburg I think something was wrong here in the curation and I'm not quite sure where things went off track. It looks like you curated the same signatures for every experiment. Is that correct?

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	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	0
10	Identified correct statistical test	1	0
11	Identified MHT correction	1	0
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	1
16	All signature sources correctly identified (-1 for each error)	2	0
17	Abundance direction correctly selected	1	1
18	Members of Signatures identified correctly	2	0
19	Correct use of NCBI taxonomy	2	1
	TOTAL	23	11

• Giving you credit since large intestine is close, but the body site should really be feces
• Sequencing was WGS done with Illumina
• Statistical test used in Fig. 2A was KW followed by Dunn's test. No PERMANOVA.
• Dunn's test controls for multiple comparisons
• Figs. 4A, 5B, 6B, 7B entered as signature sources but are incorrect
• Fig. 2A is incorrectly curated. There should be three signatures from the pairwise comparison
• Every signature is just a duplicate of the signature's in experiment 1 it looks like
• No confounders weer controlled for
• Age and sex was matching for the healthy control group

[AleruDivine]

Hi @SvetlanaUP, I would like to help out with the correction of this study. Thank you so much!

[SvetlanaUP]

@AleruDivine go ahead!

[fiddyhamma]

Hello @zheeburg @SvetlanaUP Can we work together on correcting this study?

Oh @AleruDivine is already working on it 👍

[AleruDivine]

Yeah I’m currently working on the corrections @fiddyhamma 😊

[AleruDivine]

Good morning @SvetlanaUP, I have finished correcting this study. I opted not to include the matched-on factors since they only pertained to healthy controls. Additionally, I omitted the comparison between COVID-19 and healthy controls due to the absence of alpha diversity measures and differential abundance results.

The comparisons between Mild and Moderate, Mild and Severe, as well as Moderate and Severe, lacked any reference to matched-on factors.

[SvetlanaUP]

https://bugsigdb.org/Study_885 reviewed.

[AleruDivine]

Good afternoon @SvetlanaUP I've noticed that this study is marked as incomplete. I'd like to review it to correct any mistakes and will report the changes I make, if that's okay with you.

Thank you so much!

[AleruDivine]

Thank you @SvetlanaUP 🙏

[AleruDivine]

Good day @SvetlanaUP

After reviewing this study, I noticed that Figure 2A presents signatures for the three severity groups, with a one-to-all comparison approach applied. As the excerpt from the paper states:

"We then focused on the 17 mild group-enriched HQMAGs and 16 severe/critical group-enriched HQMAGs because they were all identified by RDA analysis and were significantly different between the three severity groups."

They focused on HQMAGs that were enriched in the mild group compared to both the moderate and severe/critical groups, and in the severe/critical group compared to both the mild and moderate groups.

I have made adjustments accordingly and would like to submit this for a second review.

In addition to that, I’d like to delete the following:

• Signature 2 in experiments 1 and 2
• Experiment 2

Thank you so much!

[SvetlanaUP]

@AleruDivine Did you mean Experiment 3 as the second point to delete?

[AleruDivine]

Yes, experiment 3. Oh my days! My apologies @SvetlanaUP .

Thank you so much!