Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species

[SvetlanaUP]

Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species – Lize Delanghe – Scientific Reports

https://www.nature.com/articles/s41598-024-74513-2

[Joiejoie1]

This study provides valuable insights into the microbiome shifts associated with mild atopic dermatitis, particularly the increase in non-staphylococcus pathobionts and the loss of specific beneficial species. Understanding these microbial changes can inform targeted therapies and improve disease management. I want to curate this!

[Rahila-me]

Good morning @Joiejoie1 @SvetlanaUP , joy please I am open for collaboration i just wanted to know if you need help to finish up this paper. Waiting for your reply.. Thank you

[Joiejoie1]

Good morning @Joiejoie1 @SvetlanaUP , joy please I am open for collaboration i just wanted to know if you need help to finish up this paper. Waiting for your reply.. Thank you

Hi @Rahila-me . Thanks for reaching out. I am done with the paper. It needs review. Is there anyway you can help with the review?

[Joiejoie1]

Hi @SvetlanaUP. I am done with curation and the paper is ready for review. This is the link for review: https://bugsigdb.org/Study_1084

[SvetlanaUP]

https://bugsigdb.org/Study_108 ready for review.

[Scholarpat]

Hi @SvetlanaUP, can I review this?

[Scholarpat]

Hi @Joiejoie1,

This curation requires some improvements. Although there were a few correct entries, some areas need further attention. Kindly review the points listed below and make the necessary corrections:

CURATION RESULTS:

S/N	Criteria	Total Points	Points Earned
1	All elements marked "Needs review" (none "Incomplete")	1	0.5
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	0.5
6	Contrast groups correctly identified	1	0.5
7	Groups correctly labeled as 1 and 0 (1=cases, 0=controls)	1	0.5
8	Antibiotic exclusion correctly identified	1	0.5
9	Correctly identified sequencing details	2	1
10	Identified correct statistical test	1	0
11	Identified MHT correction	1	0.5
12	Correctly recorded matched on factors	1	0
13	Entered correct number of statistical tests per experiment	1	0
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	0

Total = 5/23

Notes for correction:

• There are 3 distinct experiments to curate:
  • mildAD vs Healthy
  • mildAD vs Healthy under 12 years old
  • mildAD vs Healthy above 12 years old
• Signatures can be found in Figure 3a. Be sure to curate only significant taxa.
• For healthy participants, skin swabs were taken from the elbow bend. For AD patients, swabs were taken from a selected lesion site (which included different skin surface for each participant). Skin is a more correct term since they refer to different skin surfaces and not just the elbow.
• There was no antibiotic exclusion for the cases, but healthy participants were excluded for antibiotic use. Note this on the discussion page.
• Maaslin2 was used for differential abundance analysis.
• Leave the LDA field blank if it doesn't apply—no need to enter a value of zero.
• For alpha diversity, only two measures were used: observed diversity (richness) and Inverse Simpson index.

Please make the necessary corrections and ask for a second review.

[Joiejoie1]

Hi @Joiejoie1,

This curation requires some improvements. Although there were a few correct entries, some areas need further attention. Kindly review the points listed below and make the necessary corrections:

CURATION RESULTS:

S/N Criteria Total Points Points Earned 1 All elements marked "Needs review" (none "Incomplete") 1 0.5 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 0.5 6 Contrast groups correctly identified 1 0.5 7 Groups correctly labeled as 1 and 0 (1=cases, 0=controls) 1 0.5 8 Antibiotic exclusion correctly identified 1 0.5 9 Correctly identified sequencing details 2 1 10 Identified correct statistical test 1 0 11 Identified MHT correction 1 0.5 12 Correctly recorded matched on factors 1 0 13 Entered correct number of statistical tests per experiment 1 0 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 0 Total = 5/23

Notes for correction:

• There are 3 distinct experiments to curate:

  • mildAD vs Healthy
  • mildAD vs Healthy under 12 years old
  • mildAD vs Healthy above 12 years old
• Signatures can be found in Figure 3a. Be sure to curate only significant taxa.
• For healthy participants, skin swabs were taken from the elbow bend. For AD patients, swabs were taken from a selected lesion site (which included different skin surface for each participant). Skin is a more correct term since they refer to different skin surfaces and not just the elbow.
• There was no antibiotic exclusion for the cases, but healthy participants were excluded for antibiotic use. Note this on the discussion page.
• Maaslin2 was used for differential abundance analysis.
• Leave the LDA field blank if it doesn't apply—no need to enter a value of zero.
• For alpha diversity, only two measures were used: observed diversity (richness) and Inverse Simpson index.

Please make the necessary corrections and ask for a second review.

Thanks @SvetlanaUP I'll make the necessary corrections.

[AleruDivine]

Hi @Joiejoie1, I'll be very happy to collaborate on reviewing and making the necessary corrections in this study if that's okay with you.

Thank you so much!

[Joiejoie1]

Hi @Joiejoie1, I'll be very happy to collaborate on reviewing and making the necessary corrections in this study if that's okay with you.

Thank you so much!

Yes please @AleruDivine , Let's collaborate. Thank you

[AleruDivine]

Okay @Joiejoie1 I'll send a message on Slack Thank you!

[Joiejoie1]

Okay @Joiejoie1 I'll send a message on Slack Thank you!

Greetings @SvetlanaUP , I trust you are doing great, @AleruDivine would like to collaborate with me on this can she also be assigned to it. Thanks

[Joiejoie1]

Hi @SvetlanaUP, @Scholarpat, @AleruDivine and I are done with curating the paper: https://bugsigdb.org/Study_1084. It is ready to be graded. Thanks

[SvetlanaUP]

@Scholarpat please see corrections here, thanks!

[Scholarpat]

Hi @SvetlanaUP, in experiment 3, signature 2, I corrected the signature source from Fig 3b to 3a. The curation is now complete. Thank you, and well done @Joiejoie1 and @AleruDivine!

[AleruDivine]

Thank you so much for the review 😊 @Scholarpat

[Joiejoie1]

Thank you @Scholarpat and @SvetlanaUP for the review. 😊