Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients

[AleruDivine]

Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients https://onlinelibrary.wiley.com/doi/full/10.1002/advs.202205058

[AleruDivine]

I found this paper interesting because it explores the oral fungal microbiota in COVID-19 patients and those who have recovered. This offers a fresh perspective because it sheds light on an area I had not previously explored.

[Buraah]

Hi @SvetlanaUP , @AleruDivine I'd love to curate this paper...Please assign it to me. Thank you

Victoria.

[Buraah]

Hi @SvetlanaUP I am done curating this study and it's ready for a first review. Link to study: https://bugsigdb.org/Study_940

[AleruDivine]

I'd like to review this study @SvetlanaUP. Thank you so much!

[AleruDivine]

Thank you so much @SvetlanaUP 😊

[AleruDivine]

Well done on your curation! 👏👏 @Buraah! You have done a great job with this.

I have a few observations and suggestions that I'd like you to consider:

Phenotype Studied:

• It seems that the experimental condition or phenotype being studied is the oral microbiome, specifically in the context of COVID-19, rather than COVID-19 itself. The paper indicates an interest in understanding how the composition of fungal microorganisms in the oral cavity differs between individuals with and without COVID-19.

Antibiotic Exclusion:

• The paper states that the controls had not taken antibiotics in the past 8 weeks. Could this be considered as antibiotic exclusion? I have raised this question on Slack and am awaiting responses from the mentors.

Signature 1 in Experiment 1:

• Signature 1 in Experiment 1 is missing a fungi: Fantasmomyces.

Signature 1 in Experiment 3:

• I believe that Signature 1 in Experiment 3 should indicate increased abundance in the post-COVID-19 group.

Supplemental Material - Figure S4:

• While reviewing the supplemental material, I noticed Figure S4 (titled "The characterization of oral fungi among COVID-19-N, COVID-19-C, and control groups") can be curated. The paper states: "The 71 COVID-19 patients from Henan were divided into COVID-19 patients without comorbidities (COVID-19-N, n = 56) and COVID-19 patients with comorbidities (COVID-19-C, n = 15). Then we analyzed the oral fungal characteristics of COVID-19-N, COVID-19-C, and control (n = 132) groups." I believe this information should be included in the study as Figure S4 provides relevant data.

I hope my suggestions are helpful. I am very open to hearing your thoughts on them.

Thank you so much.

[SvetlanaUP]

Thanks @AleruDivine! I agree with all the point.

As for Antibiotic exclusion: Yes, it should be reported, with a note. That's not surprising, since it can be challenging to recruit "non-healthy" participants without any recent antibiotic treatment.

@Buraah can you correct your curation for details mentioned above?

[Buraah]

Thank you for your review @AleruDivine I'll indicate here when I'm done making corrections.

[Buraah]

Hi @AleruDivine, Thank you again for your review. I agree with the condition and antibiotic exclusion. I totally missed supplemental figure 4S while curating initially, even after the peer review.

For the signatures in experiment 3 signature 1, I recorded them as decreased because of this text from the first paragraph of the Discussion section: After the first specimen was collected at the time of admission, some Post‐COVID‐19 patients received antibiotic therapy. The results of the analysis showed that the oral fungal diversity of the recovered patients was significantly lower than that of the control group, and the oral bacterial diversity gradually returned to normal, indicating that fungi require a longer recovery time than bacteria. I thought it was a valid reason for the decision.

I've made corrections, but there's an issue. The new experiments I added are not showing. I've reported this here: https://github.com/waldronlab/BugSigDB/issues/221 It looks like someone is checking it out too.

To help you review, I will link each of the 3 experiments I just added. Experiment 4: https://bugsigdb.org/Study_940/Experiment_4 Experiment 5: https://bugsigdb.org/Study_940/Experiment_5 Experiment 6: https://bugsigdb.org/Study_940/Experiment_6

Thank you...

[AleruDivine]

Well done, @Buraah. I completely understand your point.

I believe this issue of invisible experiments will be resolved soon.

Thank you for adding the links—that is so thoughtful! 😅

[SvetlanaUP]

@AleruDivine @Buraah great job, thanks! https://bugsigdb.org/Study_940 reviewed.

[SvetlanaUP]

@Buraah ha, here it is https://bugsigdb.org/Study_940 please correct the condition ;)

[Buraah]

Yes😀Doing that now.

[Buraah]

Done... @SvetlanaUP