Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries

[Nana-Habiba]

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries - Vivianne Cruz - frontiers https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.683685/full

[Rahila-me]

@SvetlanaUP may i curate this paper, thank you

[Nana-Habiba]

I have to update this study because the first one already exist

[SvetlanaUP]

@Rahila-me please see message by @Nana-Habiba. My apologies to you on behalf of @Nana-Habiba.

[Rahila-me]

@SvetlanaUP yes i have to reach out to @Nana-Habiba that the former study already exist but she can just update a new study so i will still create the new one but it will still have same issue tag. so it's not a problem. I have started working on the recent one

[Rahila-me]

@SvetlanaUP This study is ready for a review: https://bugsigdb.org/Study_1013

[Scholarpat]

Good morning @SvetlanaUP , I'll like to review this curation. Thank you

[Scholarpat]

Hi @Rahila-me,

Well done on your curation. Here are a few observations and suggestions I have after reviewing your study:

1. Body site: Dental plaque can be either subgingival or supragingival. Although the term "dental plaque" was repeatedly used in the study, "supragingival plaque" should be used as one of the body sites since it is more specific. This excerpt from Sample Collection explains it better: "Supragingival plaque samples were collected from all available tooth surfaces with a sterile interdental... For simplicity, supragingival plaque samples are referred to as dental plaque."

2. Condition: Oral microbiome measurement seems like a more accurate term than "Mouth disease."

3. Group 1 definition: Altering this section could make it more descriptive and clearer. For example:

   • Exp. 1: "Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC)" would be better than "The differences between the dental plaque and oral swab bacteriome and mycobiome of children with severe early childhood caries (S-ECC)"
   • Exp. 2: "Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination" as opposed to "The differences between the dental plaque and oral swab bacteriome and mycobiome of children that are in the Caries-free groups"

4. Data transformation: This should be raw counts based on the statistical test used.

5. Signature source definition: Source definitions should be consistent for both signatures. For example:

   • Exp. 1: "Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group"
   • Exp. 2: "Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group"

6. Additional experiments: 16S rRNA and ITS sequencing types were both used in this study for bacterial and fungal microbiomes, respectively. You curated the bacterial microbiomes (16S) but not the fungal microbiomes (ITS). I believe Table 2 (fungal microbiomes) should be curated as follows:

   • Supragingival plaque vs. oral swab in children with S-ECC (alpha diversity - Fig. 4A)
   • § Supragingival plaque vs. oral swab in caries-free children (alpha diversity - Fig. 4A)

   • S-ECC vs. caries-free in oral swab samples.

The symbols (*, §, and #) below Table 2 denote the taxa that are differentially abundant in each experiment. The Fungal Community Analysis section also explains which taxa are increased/decreased.

I hope this is helpful. Please let me know your thoughts on this. Thank you.

[Scholarpat]

Hi @SvetlanaUP,

I have made the corrections to this curation and added the experiments/signatures that were not previously curated.

During the curation process, some of the experiments and signatures intermittently failed to display. Reloading the page sometimes resolves this issue, but not consistently.

I have included this report here.

Additionally, please delete Signature 3 of Experiment 1, as it was curated in error.

Thank you very much!

[SvetlanaUP]

https://bugsigdb.org/Study_1013 reviewed.

[Scholarpat]

Hi @SvetlanaUP, this curation has one signature that is still not displaying with the others; https://bugsigdb.org/Study_1013/Experiment_3/Signature_2

[SvetlanaUP]

Thanks for letting me know @Scholarpat!