PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation

[SvetlanaUP]

PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation – Guangping Huang et al. – Microbiome 2023

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01657-0

[lwaldron]

Cool! @SvetlanaUP would you add the host species at https://bugsigdb.org/Help:Admin? ("Host species). Species names should match the NCBI taxonomy browser.

[SvetlanaUP]

Ailuropoda melanoleuca added! @lwaldron

[Davidlred]

can i have this paper assigned to me please, although i have done a second contribution already..

[SvetlanaUP]

@Davidlred please see the other types of contribution that you can do while waiting your review report: https://community-bioc.slack.com/archives/C04RATV9VCY/p1697144958544289

[Omabekee]

@SvetlanaUP May I curate this? Chioma Onyido.

[Davidlred]

alright, so i can't curate this yeah?

[Omabekee]

Hi @cmirzayi @SvetlanaUP currently looking for papers to curate, this doesn't look assigned yet. 🙏🏾

[Shruti700]

Hey @SvetlanaUP can you assign this to me? -Shruti Pal

[JigzG]

Can I curate this?

[lwaldron]

@JigzG @Shruti700 @Omabekee @Davidlred please let us know if you still want to curate this even though it's no longer during the Outreachy contribution period.

[Davidlred]

that wont be a problem sir

[Omabekee]

I would still love to @lwaldron, however seems @Davidlred already claimed it, Not a probelm because I just posted a request on another issue #157 to curate. :)

[JigzG]

I am in for contributing!

[SvetlanaUP]

@Davidlred assigned.

[Davidlred]

thanks

On Wed, 8 Nov 2023 at 12:10, Svetlana Ugarcina Perovic < @.***> wrote:

@Davidlred https://github.com/Davidlred assigned.

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/123#issuecomment-1801673359, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZN2FIVGJZHMKNW6DHSEWQLYDNSCXAVCNFSM6AAAAAA534BTP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBRGY3TGMZVHE . You are receiving this because you were mentioned.Message ID: @.***>

[Dindihub]

Hi @SvetlanaUP. Can I be assigned this study to curate? Thanks

[abziatwrite]

I would like to claim this article @SvetlanaUP @lwaldron @Peacesandy @Omabekee. My name is Abiola Fausat. Thank you.

[Dindihub]

Hi @SvetlanaUP. Please review my curation of this study. https://bugsigdb.org/Study_892

Thanks

[SvetlanaUP]

Hi @Dindihub, unfortunately, this curation is poorly done:

• First, this study is a whole genome metagenomic study, not with a 16S rRNA gene sequencing approach.

• Also, other study design elements are not correctly identified, such as condition, contrast groups, statistical analysis etc.

• Figure 4A is not curatable since we are not interested in relative abundances. Thus, we curated Figure 3A for significant differential abundances.

CURATION RESULTS

All elements marked "Needs review" (none "Incomplete") (1 point): 1 Correct study design (1 point): 1 Entered all relevant experiments and no irrelevant experiments (1 point): 0 Body site correctly identified (i.e. does not include multiple sites) (1 point): 1 Condition entered according to contrast (correct EFO ontology) (1 point): 0 Contrast groups correctly identified (1 point): 0 Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 0 Antibiotic exclusion correctly identified (1 point): 1 Correctly identified sequencing details (2 points): 1 Identified correct statistical test (1 point): 0 Identified MHT correction (1 point): 0 Correctly recorded matched on factors (1 point): 0 Entered correct number of statistical tests per experiment (1 point): 0 All diversity measures identified (1 point): 0 Diversity results correctly entered as increased/decreased/unchanged (1 point): 0 All signature sources correctly identified (-1 for each error) (2 points): 0 Abundance direction correctly selected (1 point): 0 Members of Signatures identified correctly (2 points): 0 Correct use of NCBI taxonomy (2 points): 0 Total (maximum 23 points): 5

https://bugsigdb.org/Study_892 reviewed and corrected ✅

[Dindihub]

Thanks for the review @SvetlanaUP . I admit the study was overwhelming because I don't have a scientific background. I've seen your correction and will apply the specifics to future studies. Thank you.

[omojokunoluwatomisin10]

@SvetlanaUP can i work on this

[SvetlanaUP]

@omojokunoluwatomisin10 yes please

[fiddyhamma]

Hello @SvetlanaUP @omojokunoluwatomisin10 reached out to me to collaborate in correcting this study and I noticed fig 2A and supplemental S7A showing statistically significant alpha diversity (Shannon and Simpson’s index) wasn’t curated in these groups MIN, QXL and QIN. The increase is shown in the image and supported in the texts too.

Also, this excerpt “Here, we present a comprehensive panda gut microbiome catalog (termed pandaGUT), established with Nanopore, Pacbio, and Illumina sequencing data across highly diverse samples to address host-microbe coevolution and improve conservation efforts.” Only Illumina was recorded in this study and I want to confirm if it’s okay to add both Nanopore and Pacbio

Lastly, do you think It's okay to contact the researchers to shed more light on fig 3A?

[SvetlanaUP]

@fiddyhamma @omojokunoluwatomisin10 In the end of my feedback is stated "https://bugsigdb.org/Study_892 reviewed and corrected ✅" that means that this curation did not need any changes. Corrections were made. Please put back this curation as it was before your changes.

[SvetlanaUP]

@fiddyhamma Thank you for adding alpha diversity. Illumina is main sequencing method in this study. The other two are used for selected and/or pooled samples. We are not contacting the authors of the paper to interpret their study. The paper should be interpreted by the curator as it is written.

[SvetlanaUP]

@fiddyhamma @omojokunoluwatomisin10 I made the curation back to corrected version. Please do not make any changes. https://bugsigdb.org/Study_892 is reviewed and corrected ✅

[fiddyhamma]

Okay, noted @SvetlanaUP

@omojokunoluwatomisin10 reached out to me and I noticed it was reviewed but since you assigned her to it and I noticed the alpha diversity, I thought it should be curated

[omojokunoluwatomisin10]

Noted @SvetlanaUP