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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis #363

Closed BarakatAA closed 3 weeks ago

BarakatAA commented 2 months ago

Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis

https://www.spandidos-publications.com/10.3892/ol.2024.14368

Understanding which gut microbial taxa play a significant role in the progression of cancer and liver metastasis can help identify them as potential biomarkers for disease prognosis and treatment response. This study on Fusobacterium alterations and colorectal cancer prognosis does just that and I think it would be an excellent addition to the BugSigDb database.

Happy curating and BugSigDB-ing!

AleruDivine commented 2 months ago

Good morning @SvetlanaUP and @BarakatAA, I'd like to be assigned this paper for curation. Thank you so much!

AleruDivine commented 2 months ago

Thank you so much @SvetlanaUP

AleruDivine commented 2 months ago

Good evening @SvetlanaUP, I'd like to put up this study for review. Link: https://bugsigdb.org/Study_1011

Scholarpat commented 1 month ago

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

Scholarpat commented 1 month ago

Hi @AleruDivine,

Well done on this curation👏👏 👏. Here are my observations and suggestions:

  1. Study design: The study utilizes a cross-sectional observational design, not a prospective design. The data is collected at a single point in time from patients with CRC from different cohorts, comparing those with and without liver metastasis. There is no mention of following patients over time to observe the progression of microbiota changes or the development of liver metastasis, which is a key characteristic of a prospective study. The study observes and compares existing microbiota characteristics without any longitudinal element. Given these characteristics, it can be best described as a cross-sectional observational design.

  2. Antibiotic Exclusion: Recording only the time frame (3 months) here could make it more concise.

  3. Signature source: It was discussed during office hours that heatmaps are sometimes curatable, and in this study, they were used to demonstrate phyla that were enriched in contrasting groups. However, the heatmaps here should not be curated since there was no mention of their statistical significance.

  4. Taxa: In signature 1 of experiment 1, Bacteroidia (rank = class), a heterotypic synonym of Bacteroidetes, was curated. While this may be accurate in some cases, this study originally reported Bacteroidetes as a phylum, not a class. As such, Bacteroidota (rank = phylum), a homotypic synonym, should be curated instead because of the rank.

You've done a great job. I hope this feedback is helpful and I look forward to hearing your thoughts on it.

AleruDivine commented 1 month ago

Thank you so much for the in-depth review, @Scholarpat. I've had quite an eventful week and I am still in the midst of it. I will carefully review your suggestions and make the necessary corrections over the weekend. Thanks again!

SvetlanaUP commented 1 month ago

Great work, take your time @AleruDivine!

AleruDivine commented 3 weeks ago

Thank you once again for your insightful review of this study, @Scholarpat.

I have adjusted the study design based on your feedback.

Regarding the Antibiotic Exclusion, I have decided to keep it as is. While your suggestion was valid, I opted to clarify that the exclusion pertains specifically to antibiotics taken within the three months preceding specimen collection.

The significance level of P<0.05 was established for determining statistical significance in the study. However, it is worth noting that there was no mention of statistical significance for the heatmaps or the LEfSe analysis. I believe this omission could be attributed to the focus on recording only statistically significant taxa, similar to how it was explicitly mentioned for alpha diversity analysis "a discrepancy of alpha-diversity was observed between two groups, but only Chao1 index and Faith's_pd were not significant (P>0.05; [Fig. 2C]".

Lastly, I've corrected the signature 'Bacteroidota'. It can be a bit confusing at times! 😅

If there is no other concern, I believe this review is complete @SvetlanaUP

Thank you so much for your time and patience.

Scholarpat commented 3 weeks ago

Hi @AleruDivine ,

I agree with you, the Bacteroidota taxa can be confusing sometimes. 😅

For the heatmaps, I do see your point. Although I came across this excerpt under the "Bioinformatics analysis" section; "Linear discriminant analysis (LDA) effect size (LEfSe) was applied to analyze significant microbial characteristics." indicating some sort of significance for the LEFse result.

Please @SvetlanaUP , what do you think about this?

SvetlanaUP commented 3 weeks ago

Yes, it's not so clear @AleruDivine @Scholarpat but this curation covered all what's available from the paper and it should stay as it is now recorded. Well done!