Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study

[SvetlanaUP]

Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study – Deborah Traversi – Scientific Reports https://www.nature.com/articles/s41598-020-74678-6

[IfeanyiSam]

Samuel Nnanna I would like to claim this article @SvetlanaUP

[IfeanyiSam]

I'll get started

[IfeanyiSam]

https://bugsigdb.org/Study_1109 @SvetlanaUP ready for review

[SvetlanaUP]

Hi @IfeanyiSam, thank you for your contribution. This is a good curation.

There are some details to recheck and correct:

• Signature source: you reported Table 3, maybe I am missing it but I see only in the text significant taxa reported?
• Significance threshold of 0.05 is not correct: please see "DeSeq2 showed 48 significantly abundant OTUs (p < 0.001)"
• Data transformation: DESeq2 uses a negative binomial model which requires raw counts
• How did you identify confounding factors for this study?: If they didn't state any clearly (usually using words like "adjusted for" or "controlled for") they probably didn't control for any confounders. Maybe I missed it, please do let me know.

Looking forward to your answers and corrections.

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	0.5
11	Identified MHT correction	1	1
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	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	2
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	20.5

[IfeanyiSam]

Thank you for the review, I'll make the corrections and report back ASAP.

[IfeanyiSam]

I've made the necessary corrections, thank you for pointing them out.

For the Confounding Factors, please review the text below and then table 4; "The multivariable analysis produced a ­ R2=0.6259 (p < 0.001). After adjusting for confounding factors, the likelihood of having diabetes is significantly higher in those with higher amount of Firmicutes, lower amount of Bifidobacterium spp and a higher amount of total carbohydrate intake (Table 4)."

what do you think?

@SvetlanaUP

[SvetlanaUP]

@IfeanyiSam Signature source: "From Text" is too vague. Corrected to "Results: T1D risk factors"

As for the "Confounding factors that have been accounted for by stratification or model adjustment", in the table 4 they are not reported for statistical analysis for differential abundances.

https://bugsigdb.org/Study_1109 reviewed and corrected.

[IfeanyiSam]

Okay, thank you for the corrections and clarifications. @SvetlanaUP