Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial

[SvetlanaUP]

Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial – Mary Ni Lochlainn – Nature Communications https://www.nature.com/articles/s41467-024-46116-y

[Rukaya-lab]

@SvetlanaUP Can I be assigned to this one?

[Rukaya-lab]

@SvetlanaUP can you please accept my account creation request on Bugsigdb? Thank you

[Rukaya-lab]

@SvetlanaUP can you kindly review my curated paper. Thank you https://bugsigdb.org/Study_1139

[cmirzayi]

Hi @Rukaya-lab. Thank you for your contribution. This was a good start at a curation. Unfortunately I think you missed a few experiments and made a few common mistakes we see from beginning curations. Please see the details below and revise. Also please ask questions on the Slack channel--this is a challenging curation and collaboration is encouraged!

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	0
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	0
9	Correctly identified sequencing details	2	2
10	Identified correct statistical test	1	0
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	1
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	1
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

• Source for Experiment 1 Signature 1 should be the table or figure the signature data were sourced from. In this case, it appears to be Figure 2 (you were not penalized for this).
• Several experiments are missing: Figure S6, Figure S8, Figure S10.
• Condition should be the prebiotic.
• Antibiotic exclusion criterion should be entered specifically as past 3 months not just as "recent"
• In the supplementary methods, it's stated they used linear models that were CLR-transformed.
• I would change matched on to just twin pairs (you were not penalized for this).
• No changes in alpha diversity for the experiment that was curated as stated in the caption for Figure 2.
• Missing many taxa from Figure 2 and some of those present are coded in the wrong direction (P. massiliensis)

[Rukaya-lab]

@cmirzayi I have made more edit now. Can you kindly review it for me? Also, I don't understand why I can not view all the signatures and experiments on the main page, does it take time to populate after I make changes? I also have a duplicate signature for experiment 2 and I wanted to delete it but it says I do not have the access to do that.

[cmirzayi]

Hi @Rukaya-lab I will take a look next week. Thank you for the edits!

[Rukaya-lab]

Hello @cmirzayi and @SvetlanaUP, I still haven't received feedback on my latest edits. Kindly see to this.

[SvetlanaUP]

@cmirzayi will get back to you asap. Thank you for your patience, @Rukaya-lab!

[cmirzayi]

Hi @Rukaya-lab. Thank you for your patience as I wanted to give your revision the thorough review it deserved. Unfortunately, I think there are still significant problems with the curation. I highly recommend asking questions on Slack and at the office hours for additional help.

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	0
6	Contrast groups correctly identified	1	1
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	0
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	1
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	1
16	All signature sources correctly identified (-1 for each error)	2	2
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	14

• Condition is still incorrect as noted previously. "Gut microbiome measurement" is not a condition. The condition should be something that the experiment contrasted on. This can be really hard to identify in EFO for dietary conditions but I think you were on the right track with fructose in experiments 3 and 4. I might just go with the general "diet" since EFO doesn't have a lot of good options for supplements or prebiotics.
• Experiment 2/Figure S6 is not contrasting prebiotic vs. placebo. It's contrasting on time points. Also it's three separate experiments (both arms, placebo, prebiotic)
• Statistical test infromation is still incorrect. As noted previously, they used CLR-transformed data and the statistical test was linear models.
• Diversity information for experiments 2, 3, and 4 appear to be incorrect and I'm not sure where this info is coming from.
• The signatures still contain mistakes and missing taxa. For instance, Bifidobacteriaceae was increased in experiment 1 but is not included. There are many taxa missing from each experiment it appears. All taxa in the figures/tables need to be accounted for in the curation.

[chrisawoke]

Hi, @Rukaya-lab. How are you doing today? I’d be happy to join you in reviewing your curation and assist wherever you might be facing a challenge.

@SvetlanaUP suggested I offer help if you need any support.

Please, let me know where I can collaborate with you. I'm currently going through your work.

[MyleeeA]

Happy to collaborate on effecting the corrections on this as well @chrisawoke and @Rukaya-lab If this is okay @SvetlanaUP

[Rukaya-lab]

@chrisawoke Thank you for message. I'll be very glad for your help. Do we need to set up a meeting to discuss? Let me know when you're available. @MyleeeA Sure, It's okay by me if you want to also help. We can set up the meeting so. Thank you both.

[chrisawoke]

@Rukaya-lab, thanks for the opportunity! Please let me know what time works best for you. Today or tomorrow works for me.

In the meantime, I'm already going through the study.

@MyleeeA, welcome aboard!

[Rukaya-lab]

@chrisawoke Is 3pm today okay? Or we could do tomorrow by 11am. GMT +1 timezone

[chrisawoke]

Hello, @Rukaya-lab. I'm sorry I’m just seeing your message now. I've sent you a message via the Slack channel.

[MyleeeA]

Thank you @chrisawoke and @Rukaya-lab

I am @ Mildred Anashie on slack

[Rukaya-lab]

@chrisawoke I didn't see your message, my name on slack is Ruqayyah

[SvetlanaUP]

@MyleeeA @chrisawoke @Rukaya-lab enjoy your collaboration! Please continue your communication in Slack.

[MyleeeA]

Noted @SvetlanaUP Thank you 🙏🏾

[SvetlanaUP]

@chrisawoke what's the status of this collaboration and curation?

[MyleeeA]

Hi @SvetlanaUP

We are currently working on it With permission from @Rukaya-lab, I am done making the necessary corrections to the experiment and including the omitted ones while @chrisawoke is adding the signatures

[chrisawoke]

Hello, @SvetlanaUP,

As @MyleeeA mentioned, we're almost done. I'm almost finished adding the signatures.

[SvetlanaUP]

@MyleeeA @chrisawoke ok, just wanted to check if you are stuck :) Keep up the good work!

[Rukaya-lab]

@cmirzayi @SvetlanaUP Thank you for your feedback so far. We have the curation for review now. Kindly go through it.

[cmirzayi]

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	0
14	All diversity measures identified	1	0
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	2
	TOTAL	23	22

This is nearly there! Great improvement! You've fixed every outstanding issue that I could find, except I am still noticing some missing taxa and other issues in the signatures--for instance in Experiment 1, Signature 2 Phocea (NCBI taxonomy name: Merdimmobilis) is missing. Similarly, in experiment 1, signature 1 Actinobacteria (NCBI: Actinomycetota) is not actually increased in the prebiotic group (which is why it has a white/empty bar in Figure 2). I think with a review to ensure that the taxa are curated correctly this will be a perfect curation.

[chrisawoke]

Oh, great. Thanks so much, @cmirzayi.

We'll fix that ASAP.

Thanks again for the review.

[MyleeeA]

Hi @cmirzayi @SvetlanaUP

Thank you for your patience

We have effected the corrections @Rukaya-lab @chrisawoke

[cmirzayi]

There were some minor outstanding issues with the signatures but I have resolved them. Study marked as reviewed.

[MyleeeA]

Thank you again @cmirzayi 🙏🏾

[chrisawoke]

Thank you so much, @cmirzayi.