The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults

SvetlanaUP commented 3 months ago

The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults – Aljumaah MR, Bhatia U, Roach J, Gunstad J, Azcarate Peril MA – Journal Clinical nutrition https://www.clinicalnutritionjournal.com/article/S0261-5614(22)00344-2/abstract

SvetlanaUP commented 3 months ago

Under curation by @joyceqiu23 https://bugsigdb.org/Study_1092

joyceqiu23 commented 3 months ago

@SvetlanaUP I will finish curating this one

SvetlanaUP commented 3 months ago

Aljumaah-etal-1-Clin-Nutri-2022.pdf

@joyceqiu23 please add here the supplementary material of this paper, thanks!

cc @Scholarpat

Scholarpat commented 3 months ago

Thank you @SvetlanaUP

SvetlanaUP commented 3 months ago

Supplementary material sent by the author Mashael Aljumaah Appendix A. Supplementary data.docx

joyceqiu23 commented 2 months ago

I would like to request a review.

SvetlanaUP commented 2 months ago

https://bugsigdb.org/Study_1092 ready for review.

Buraah commented 2 months ago

Hi @SvetlanaUP Can I review this study?

SvetlanaUP commented 2 months ago

@Buraah enjoy reviewing!

Buraah commented 1 month ago

Hi @joyceqiu23 Thank you for curating this paper. It was a bit tricky, but you did well. Here are some observations and suggestions for possible improvement.

The study investigated the gut microbiome composition of individuals with mild cognitive impairment. (MCI), compared to healthy individuals and investigated the impact of probiotic Lactobacillus rhamnosus GG (LGG) on their gut microbiome. This means two (2) separate experiments were carried out in the study.

Condition

"Cognitive Impairment" will work fine for the condition.

Group name & Sample sizes

Figure 1 has all the information for this. There are five groups in total: cognitive impaired, Cognitive intact, Baseline, Placebo, and Probiotic groups. (Record the sample sizes and group names from the Aggregate level.)

Antibiotic exclusion

I couldn't find a specific time frame for this; the study only said, "In the event participants received specific medications, including antibiotics and proton pump inhibitors, they were excluded." So we can leave this blank.

Lab analysis

The study used 16S rRNA and Whole-Genome Shotgun sequencing (WGS), but WGS was only used to capture species diversity within Prevotella after the experiment with 16S was done. This means our attention should be on 16S since that's the sequencing type used for the main experiments.
All curatable results are also from the 16S sequencing.
In the "Amplification and sequencing with 16S rRNA gene" section, you will find the variable region (V4) and sequencing platform (Illumina).

Statistical analysis

Lefse was used in this study. Data transformation is relative abundance.
MHT, Significance and LDA score are all correct.

Alpha diversity

The alpha diversity result is correct.
It is also unchanged for the remaining three experiments.

Signatures

We do not record relatively abundant taxa; we only record differentially abundant ones. So, figure 3 is not curatable.
The curatable figures are Figure 2C and Figure 5D.

Experiments

The total number of experiments for this study is 4
Cognitively Intact vs Cognitively Impaired Group
Baseline vs Placebo Group
Baseline vs Probiotic Group and,
Placebo vs Probiotic Group.

Figures 2 and 5 contain all the information you need for the signatures. I hope I did well explaining. Please feel free to reach out if you need to clarify anything or help with anything.

Thank you, and well done.

Buraah commented 1 month ago

Hi @SvetlanaUP, I am done with my review.

SvetlanaUP commented 1 month ago

Thanks @Buraah for a great and clear review! @joyceqiu23 please make corrections and feel free to contact @Buraah in case of any doubt.

Buraah commented 1 month ago

Thank you! @SvetlanaUP

yokoDots commented 3 weeks ago

Hello, @joyceqiu23 , just wondering if you need some help to finalize this curation? Let me know, thanks!

SvetlanaUP commented 3 weeks ago

This curation is assigned to @Buraah to finalize it.

SvetlanaUP commented 3 weeks ago

Hello, @joyceqiu23 , just wondering if you need some help to finalize this curation? Let me know, thanks!

@yokoDots this curation is out of the current outreachy contribution period (does not have label: outreachy)

Buraah commented 3 weeks ago

Hi @SvetlanaUP, I have finalized this curation.

SvetlanaUP commented 3 weeks ago

https://bugsigdb.org/Study_1092 reviewed.

waldronlab / BugSigDBcuration

The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults #431