Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites

[SvetlanaUP]

Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites – Zhang et al. – Microbiology Spectrum https://journals.asm.org/doi/10.1128/spectrum.01437-23

[Iam-Iman]

Hi, @SvetlanaUP may I please be assigned this paper ? Name: Iman Ngwepe-Ntshibida

[eve10111]

@SvetlanaUP , I can see this article has not been assigned yet. Would you kindly assign it to me. Thank you very much

[Juliana-Oluwatobi]

I am interested in contributing to this paper kindly assign it to me @SvetlanaUP

[Iam-Iman]

Thank you @SvetlanaUP https://bugsigdb.org/Study_895

[SvetlanaUP]

Ready for review https://bugsigdb.org/Study_895

[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	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
7	Groups correctly labeled as 1 and 0 (1=cases, 0=controls)	1	0
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	0
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	12

• Richness is reported as the Chao1 index; not both richness and Chao1.
• significant differences in alpha diversity is reported in the experiment: samples collected at baseline (BSL) versus 7 days post-SD (7d-SD)
• Figure 3D is source of the signatures in several experiments that are missed in this curation: "LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples collected at baseline (BSL), 7 days post-SD (7d-SD), and 14 days of saline (21d-SA) or mixed probiotics (21d-MP) after SD."

[AleruDivine]

@SvetlanaUP this still has "needs review" highlighted and the feedback note does not say it has been corrected. I would love to help out with the correction of this study from the feedback given.

[SvetlanaUP]

@SvetlanaUP sure!

[AleruDivine]

Good morning @SvetlanaUP, I somehow missed this email. I will get started with the corrections right away. Thank you so much!

[AleruDivine]

Hi @SvetlanaUP, I have completed the corrections to the curation based on the feedback you provided. Corrections and changes made include:

1. Remove the matched-on factor because the paper did not state that the rats were matched on any factor. Only that 6 weeks old rats were purchased.
2. Removed Mann-Whitney U test as one of the statistical test, the reason is Mann-Whitney U test was used to compare differences in gut microbiota alpha diversity among the groups. I left LEfSe as the statistical test used because only LEfSe was used to identify differential bacterial species between groups.
3. Changed data transformation to be centered-log ratio and here is an excerpt explaining why "One-way analysis of variance (ANOVA) was used to compare the relative abundances of taxa (transformed into a centered-log ratio) among the four groups.".
4. Corrected alpha diversity measures to only Chao1 index (richness) and Shannon index (diversity).
5. Corrected the contrast groups for experiment 1 and curated an additional 5 experiments resulting in a total of 6. The reason for the additional 3 experiments is because the study stated that the effect of multi-probiotic supplementation was also assessed in alleviating SD-induced anxiety-like behavior.

Contrast groups Baseline (0) vs D7-SD (1) Baseline (0) vs D21-SA (1) Baseline (0) vs D21-MP (1) D7-SD (0) vs D21-SA (1) D7-SD (0) vs D21-MP (1) D21-SA (0) vs D21-MP (1)

6. All signatures have been identified and curated from figure 3d.

[Scholarpat]

Hi @SvetlanaUP, For this curation I changed data transformation from centered-log ratio to relative abundance. I've also updated the signature description for clarity. This curation is complete. Thank you!

Well done @AleruDivine 👏, interpreting the signatures must have been tasking.

[SvetlanaUP]

https://bugsigdb.org/Study_895 reviewed.

[SvetlanaUP]

❤️ for @AleruDivine

[AleruDivine]

Thank you @Scholarpat and @SvetlanaUP