The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children

[SvetlanaUP]

The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children – A. Cristina Paulo et al. – Microbiome 2023 DOI: 10.1186/s40168-023-01640-9 https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01640-9

[Kingecha]

Name: Karen254. Hey @SvetlanaUP I would like to claim this article.

[cmirzayi]

Assigned.

[Kingecha]

Thankyou.

[Kingecha]

Hey @lwaldron @cmirzayi @SvetlanaUP I'm done curating my paper kindly review.

[cmirzayi]

Marked for review.

[cmirzayi]

Unfortunately I think you had a fairly fundamental misunderstanding of the paper and how to curate it. I would focus on the results presented in the supplemental tables S5 through S7 as well as Figure 5E.

The statistical test was a type of linear model, not a chi-squared test.

There were 3 experiments that I could identify: Carriers vs. not Smokers vs. not Child exposure vs. not

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	0
10	Identified correct statistical test	1	0
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	0
17	Abundance direction correctly selected	1	0
18	Members of Signatures identified correctly	2	0
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	11

https://bugsigdb.org/Study_795

[Peacesandy]

https://bugsigdb.org/Study_795

Reviewed