Analysis on the change of gut microbiota and metabolome in lung transplant patients

[SvetlanaUP]

Analysis on the change of gut microbiota and metabolome in lung transplant patients – Hou et al. – Microbiology Spectrum https://journals.asm.org/doi/10.1128/spectrum.03142-23

[Gloshe]

hello @SvetlanaUP I would like to curate this paper

[Abiola-Salako]

@SvetlanaUP I would like to curate this paper.Thank you

[Gloshe]

Hi @SvetlanaUP I am done curating this study, your review on it will be appreciated

[SvetlanaUP]

https://bugsigdb.org/Study_958 ready for review

[SvetlanaUP]

Item	Description	max	points
1	All elements marked "Needs review" (none "Incomplete")	1	1
2	Correct study design	1	0
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	0.5
7	Groups correctly labeled as 1 and 0 (1=cases, 0=controls)	1	0.5
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	0
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	0
16	All signature sources correctly identified (-1 for each error)	2	1
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	14

• Study design is not cross-sectional observational (corrected)
• Diversity results incorrectly entered (corrected)
• LDA score missed (corrected)
• MHT correction with LEfSe is rare and I see no evidence to suggest that was done (corrected)
• Fig3C can be curated and 1 experiment (with unchanged alpha diversity) is missing (should be corrected)
• not all the members recorded in the signatures (should be corrected)

[Gloshe]

Thank you @SvetlanaUP for the review, let me go through to see where I went wrong. However i request for another chance to curate more papers as I learn more and gaining knowledge. Thank you.

[SvetlanaUP]

@Gloshe first 4 points in my feedback notes are corrected, but the last two points can be corrected by you.

[fiddyhamma]

Hi @Gloshe do you mind making the last two corrections together?

[SvetlanaUP]

@Gloshe @fiddyhamma go ahead with correction. Please make notes about your corrections. Thank you.

[fiddyhamma]

Okay, will do that. Thank you @SvetlanaUP

[fiddyhamma]

Hello @SvetlanaUP I've made corrections to this study I added complete signatures 1&2 to both experiments 1,2 And also added experiment 3, with unchanged alpha diversity and a significant taxa

[Gloshe]

Good morning @SvetlanaUP, I had an issue with internet service provider, which was supposed to be worked on yesterday but since it was a public holiday and its been worked on today. I realized the points to be corrected by me were corrected by others. I am sorry for delay to correct the points raised in my paper.

[SvetlanaUP]

@Gloshe no worries!

[Folakunmi21]

@SvetlanaUP Study 958 reviewed