Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma

[MyleeeA]

@MyleeeA here you could do "Edit" (... on the right upper corner of this comment box) and add all the info for this study:

Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma – Thananya Jinato – Appl Microbiol Biotechnol. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771587/

• Your poor-in-information message below: Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771587/ is deleted now.

[Isioma20]

Hello @SvetlanaUP I'd love to curate this study. Thank you.

[Isioma20]

Thank you!

[Isioma20]

This study has been curated at https://bugsigdb.org/Study_1032 . It is now ready for review. Thank you

[MyleeeA]

Thanks @SvetlanaUP

Can I review this? It might be a slow review though as I have a few things to sort out but I’ll get it done

[SvetlanaUP]

Sure @MyleeeA! Thanks and no worries, take your time.

[MyleeeA]

Thank you 🙏🏾

[MyleeeA]

Hi @Isioma20

Well done on your curation 👏🏾 I didn’t realize how a bit confusing this article was but you did a great job. I have a few observations and would appreciate your thoughts on them:

1. Antibiotics Exclusion: The article says “Within 2 weeks of Fecal sample collection, participants were asked to discontinue antibiotics, prebiotics, probiotic supplements, or proton pump inhibitors (PPIs).” In my opinion this does not clearly say they were excluded based on Antibiotics intake.
2. Experiment: I believe one experiment is missing. The Alpha diversity figure in the Supplemental Material (FigS1) shows alpha diversities for HCV-HCC vs NBNC as Chao1 to be unchanged (p-value 0.31) , Shannon to be unchanged (p-value 0.088) and Simpson to be increased (p-value 0.05). Although the article says P-value <0.05 shows significance, is this why this experiment wasn’t recorded as you took Simpson to also be unchanged?.
3. Group name and description: The topic says “Distinct alterations of gut microbiota between viral and non viral related hepatocellular carcinoma”. And the study was conducted to investigate the differences of the gut microbiota diversity and composition between the viral and NBNC-HCC subgroups. The viral related HCC was subdivided again into the HBV and HCV. From this NBNC-HCC should be Group 0 in Experiment 2,3 and 5 since the NBNC group is said to be the “Non-hepatitis B, Non-hepatitis C related Hepatocellular Carcinoma group”.

What are your thoughts on this points? Also is there a reason why you curated them the way you did? I might be missing something Thank you 😊

[SvetlanaUP]

Wonderful review and clear feedback! Thanks @MyleeeA Let's hear now @Isioma20 ;)

[MyleeeA]

Thank you @SvetlanaUP 😊

[Isioma20]

Hi @MyleeeA. Thank you so much for the review and feedback. For Observation 1, the excerpt you pasted states discontinuation of antibiotics within two weeks by the participants which implies to me, antibiotic exclusion which is why I stated in the curation as such since I interpreted it as stopping the antibiotics i.e. excluding it.

2. Like you stated, I didn't include that experiment because the significance is at 0.049 which is <0.05. since it crossed that threshold it means it is no longer statistically significant so I didn't add the experiment if all the alpha diversity indices would be unchanged and it had no differential abundance.
3. NBNC-HCC is the more severe form of Hepatocellular Carcinoma which was also cited in the article as shown "Overall, NBNC-HCC is frequently diagnosed at more advanced stages than viral-related HCC (Viral-HCC), and the survival time of NBNC-HCC is typically worse than that of viral-related cases" which is why it was chosen as the group 1 instead of viral HCC. I appreciate your thoughts regarding this curation.

[SvetlanaUP]

I agree on all @Isioma20's comments. All points well spotted by @MyleeeA to recheck them. Well done, both!!

https://bugsigdb.org/Study_1032 reviewed.

[MyleeeA]

Okay

Well done again Thank you @SvetlanaUP

[Isioma20]

thank you @SvetlanaUP , @MyleeeA