_Ascaris suum_ infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome

[lwaldron]

Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome

https://www.sciencedirect.com/science/article/pii/S0020751919300074?casa_token=zTI42d_k7gAAAAAA:CdhNW8hJpkMRhKHhamjBx-PNHhZm1IcX4Idbrze4ab7QpJTcxcE6wvzDz85SIeR6ZZ_wHrdRyjb-

[TharaEhizogie]

Thara Ehizogie

I would like to be assigned this project Thank you

[cmirzayi]

Hi @TharaEhizogie. I'm not able to find your first curation. Have you submitted that yet? If so did you perhaps give a different github username? Thanks.

[TharaEhizogie]

Hello, Yes i gave a wrong name. i contributed as TharaaOmo not TharaEhizogie. Do i need to do it again?

[cmirzayi]

No that's fine. I just wanted to make sure you've done the first contribution before proceeding to the second contribution. Assigning you this article.

[BearGrabs]

Hello, Roderick Momin here. I would like to tackle this for my Second Contribution.

[BearGrabs]

@Omabekee Hello, re-comment as per request.

[SvetlanaUP]

https://bugsigdb.org/Study_886 Ready for review.

[Omabekee]

This was a good attempt @BearGrabs. Here are some errors you made and their corrections. Please work with Scholastica to effect the corrections.

• Figure 1A and table 2 should not be combined because they’re different stat tests and diff experiments; one of them is from LEfSe the other is from Kruskal Wallis. 1A compared CC vs INC, Table 2 compared WBH vs WBL

• There should be only 5 alpha diversity measures. I’m not sure where you saw Richness.

• Experiment 2 group descriptions should be stated clearly for proper comprehension without reading the whole paper.

• All source descriptions should be re-written for proper comprehension.

• I wouldn’t curate Figures 2 and 3 because they’re relative abundance results and they did not indicate the significance (p value).

CURATION RESULTS

1.All elements marked "Needs review" (none "Incomplete") (1 point): 1

2. Correct study design (1 point): 1
3. Entered all relevant experiments and no irrelevant experiments (1 point): 0.5
4. Body site correctly identified (i.e. does not include multiple sites) (1 point): 1
5. Condition entered according to contrast (correct EFO ontology) (1 point): 1
6. Contrast groups correctly identified (1 point): 0.5
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 1
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (2 points): 2
10. Identified correct statistical test (1 point): 1
11. Identified MHT correction (1 point): 1
12. Correctly recorded matched on factors (1 point): 1
13. Entered correct number of statistical tests per experiment (1 point): 0
14. All diversity measures identified (1 point): 0.5
15. Diversity results correctly entered as increased/decreased/unchanged (1 point): 1
16. All signature sources correctly identified (-1 for each error) (2 points): 1
17. Abundance direction correctly selected (1 point): 1
18. Members of Signatures identified correctly (2 points): 0
19. Correct use of NCBI taxonomy (2 points): 2 Total = 17.5 @SvetlanaUP, grading of Study 886 complete. ✅ Review still in progress

[Omabekee]

@Scholarpat please I need your assistance here, can you work with @BearGrabs to complete this curation?

[Scholarpat]

I'll love to @Omabekee . Thank you 😊

[Scholarpat]

Hello @Omabekee , please can you help with the supplementary file as I'm unable to access it. 🙏

Thank you.

[SvetlanaUP]

@Scholarpat @Omabekee we could not get the supplementary material. Roderick @BearGrabs even tried to email them (https://community-bioc.slack.com/archives/C04RATV9VCY/p1711029904115979) but no luck.

[Scholarpat]

Okay @SvetlanaUP , thank you. I'll see what I can deduce from the main article.

[BearGrabs]

@Omabekee Changes made based on feedback (more to come), however I have some questions that I would like cleared up.

• MHT correction: My understanding is there is no MHT correction for this case study which I've inputted as, yet I received 0 marks on it. I would like to know where I went wrong and which part I overlooked in the study.
• I agree with Figure 3 not being curated as it is using Normalized Counts however I am confused as to why Figure 2 should not be? (I've removed data from it regardless) My understanding is that Figure 1A and Figure 1B are also using relative abundances for Statistical Analysis with a p-value of < 0.05, LDA>2 using LEfSe and my understanding is that Figure 2 is implying to have done the same for its statistical analysis using LEfSe.

[Scholarpat]

Hello @Omabekee,

We have implemented some of the corrections you recommended. However, we require clarification on how to proceed with Table 2. I have tagged you in a post on the Slack channel regarding this matter. I posted on Slack so others can contribute and learn alongside us. We eagerly await your response.

Link to Slack post: https://community-bioc.slack.com/archives/C04RATV9VCY/p1712751340538189

Thank you.

[Omabekee]

@BearGrabs Figures 2 and 3 can't be curated because they’re relative abundance results and they did not indicate the significance (p value). There's a difference but we can't really tell from the image if the difference is significant.

I've added the mark for MHT, I apologize for the oversight.

[BearGrabs]

@Omabekee Final changes made which is the addition of data from Table 2.

Table 2 is comparing Uninfected Piglets to WBL and WBH in line with the title of the study/table. (In contrast to what you have stated as WBL vs WBH above).

However, I have added the information as Experiment 3 (Uninfected vs WBL) and Experiment 4 (Uninfected vs WBH) after the thread in Slack.

Signatures of both Experiment 3 and 4 that has been added are identical. Should you wish to condense the information to one Experiment of either Uninfected vs Infected (in line with results/title of the paper) or Uninfected vs WBL+WBH combined (condensed version of the Slack thread) then delete Experiment 4 kindly and I will make changes to the relevant descriptions to reflect so.

[Scholarpat]

Hello @Omabekee, the source description for the signatures has also been updated to be more descriptive. Thank you for your time and patience.

[Omabekee]

Thank you both! @SvetlanaUP Review of 886 complete. ✅