The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model

[cmirzayi]

Mouse study!

Jeong SM, Jin EJ, Wei S, Bae JH, Ji Y, Jo Y, Jeong JH, Im SJ, Ryu D. The impact of cancer cachexia on gut microbiota composition and short-chain fatty acid metabolism in a murine model. BMB Rep. 2023 Jul;56(7):404-409. doi: 10.5483/BMBRep.2023-0068. PMID: 37220908; PMCID: PMC10390285.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10390285/

[deegrayce]

Grace Ogundaini

[cmirzayi]

Assigned.

[deegrayce]

Hello. In need of review please.

[cmirzayi]

Marked for review.

[cmirzayi]

@deegrayce Can you link me to the curation?

[deegrayce]

@cmirzayi sure, here's the link https://bugsigdb.org/Study_802

[cmirzayi]

Hi @deegracye. Great curation.

I noticed a few small errors

• The direction of all the alpha diversity measures are reversed from what they should be.
• Clostridium sensu stricto 1 is curated as Clostridia. These are not equivalent. You may have to enter this one as clostridium sensu stricto 1 without finding the accompanying taxonomy in the browser. We've had issues identifying clostridium genera before.
• Candidatus Arthromitus is curated as Candidatus Arthromitus sp. SFB-mouse. Though this is a study of mice, these are not equivalent.

Please make these changes. Thank you!

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	1
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	0
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	2
	TOTAL	23	21

[deegrayce]

Hello @cmirzayi thank you for the corrections. I have made the changes accordingly. https://bugsigdb.org/Study_802

[Peacesandy]

Reviewed