Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition

[SvetlanaUP]

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition – Emily M. Mercer et al. – Microbiome https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01735-3

[tayyabak26]

@SvetlanaUP Kindly assign me this paper to curate. Thank You

[tayyabak26]

Hi @SvetlanaUP I am done curating this study and it is ready for review.

Thank you. Link to study : https://bugsigdb.org/Study_993

[tayyabak26]

@SvetlanaUP

[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	0.5
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	1
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	2
17	Abundance direction correctly selected	1	1
18	Members of signatures identified correctly	2	1
19	Correct use of NCBI taxonomy	2	1
	TOTAL	23	19

• metabolomics is done in urine samples, whereas microbiome analysis in fecal samples: body site is only feces (corrected)
• DESeq2 uses a negative binomial model which requires counts or else it will not converge. (corrected)
• for fungal squencing, ITS2 rRNA gene sequencing is used (corrected)
• experiment2/signature2: Meyerozyma guilliermondii missed (corrected)
• some signatures have irrelevant taxa recorded (deleted)
• experiment1/signature2: Bacteroides caccae increased (corrected)