I'm sorry, what? In writing my first monograph, I spent six weeks trying to track down a citation in TWO languages I didn't know. And good thing too, because the citation was wrong. That's scholarship. That's research. You know, the thing we're trained to do?!?
Our study describing `microntology` and annotations for >300k metagenomes is now online in Bioinformatics @academic.oup.com :
academic.oup.com/bioinformati...
Congratulations to @fullam.bsky.social @vishnuprasoodanan.bsky.social & @biocs.bsky.social !
See the thread below for more details.
Our May issue with a focus on technological advances in microbiology is out now!
Read about
🌱defence evasion by plant pathogens
🦠E. coli capsule revival
💻multiomic microbiome integration
🐁chronic chikungunya infection
🦀 bacteria in cancer immunotherapy
and much more: shorturl.at/Wtzkp
#MicroSky
How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well.
In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵
www.biorxiv.org/content/10.6...
More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form:
"The elusive resistome: a global comparison reveals large discrepancies among detection pipelines"
www.biorxiv.org/content/10.6...
Hostage taker to hostages: This is your hostage crisis, too. Don’t just sit there waiting for me to negotiate, stand up and do something to get us all out of here!
A clearer way to describe microbial habitats helps researchers compare #microbiome data.
A new paper in #𝐁𝐢𝐨𝐢𝐧𝐟𝐨𝐫𝐦𝐚𝐭𝐢𝐜𝐬 introduces microntology: 148 terms and curated annotations for 305,626 #metagenomic samples.
@tsbschm.bsky.social @embl.org @vishnuprasoodanan.bsky.social
📰 buff.ly/FD1SYYJ
Our new paper „Variations in the latitudinal diversity gradients of the ocean microbiome“ was just published in @cp-cellhostmicrobe.bsky.social 🥳
We present a global analysis of prokaryotic #biodiversity in the surface and mesopelagic layers of the ocean 🦠🌊
www.cell.com/cell-host-mi...
Darwin approves.
Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
Eriksson et al. conduct a global marine microbiome diversity analysis and demonstrate
how the surface ocean latitudinal diversity gradient is disproportionately shaped
by a few species-rich taxa. Mask...
www.cell.com
Sebastian Schmidt
AbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and
We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data.
Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al:
1/
www.biorxiv.org/content/10.6...
Summary. We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k m...
