Daniel Podlesny

metaTraits: a large-scale integration of microbial phenotypic trait information Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is

metaTraits: a large-scale integration of microbial phenotypic trait information

academic.oup.com/nar/advance-...

Get in touch if you have feedback or would like to see other data on metaTraits. metaTraits is fully Open Access and FAIR and was supported by a Flex Fund from nfdi4microbiota.de @nfdi4microbiota.bsky.social within @nfdi.de. Many thanks to all co-authors! 8/8

A figure comparing gut microbiome composition across three groups: Gut infection (pre-FMT), post-FMT, and Healthy control. Stacked bar charts show a high relative abundance of aerotolerant bacteria (blue) in the infection group, which decreases drastically after FMT to match the healthy control group (dominated by anaerobes in dark grey). Box plots below quantify the mean abundance dropping from 42.8% to 11.8%.

2️⃣ sumTraits computes community-level trait summaries from taxonomic profiles (mOTUs, MetaPhlAn, etc.). Trait shifts can mirror environmental context: Here, aerotolerant microbes, abundant in rCDI, decrease after FMT, likely reflecting the restoration of low oxygen availability in the gut. 7/8

1️⃣ porTraits predicts traits for your genomes/MAGs (currently BacDive‑AI, GenomeSPOT, Traitar, MICROPHERRET) & pulls metaTraits context for the detected taxa. Also available on the free ☁️ workflow platform CloWM.de, or via @nextflow.io github.com/grp-bork/por.... 6/8

Bring your own data! 💻 We provide two workflows for the annotation of user-submitted data. Have a look at the examples and try them out on our metaTraits website: 5/8

Most microbial diversity is uncultured. metaTraits bridges the gap by combining culture-based trait data (@bacdive.bsky.social, @bvbrc.bsky.social, JGI/GOLD/IMG) with predictions for MAGs and genomes (SPIRE, proGenomes). All trait summaries come with provenance and links to their original data. 4/8

Search 🔍 metaTraits by NCBI or GTDB taxonomy, or directly by IDs in the underlying DBs. Filter data sources to consider in your query: You can include/exclude genome-based predictions or toggle specific culture collections to strictly control the level of evidence you need. 3/8

View traits 📊 for individual microbes, or summarized at species, genus, or family level. Explore traditional culture-based traits (e.g. aerotolerance, pH, motility), alongside metrics derived from (meta)genomics (e.g. genome size, pangenome openness, generalism, population diversity). 2/8

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.

Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

Alcohol-related liver disease disrupts bile acid synthesis and is associated with compensatory gut microbiota changes Background: Alcohol overuse disrupts liver function and alters microbial gut communities, with alcohol-related liver disease (ALD) accounting for half of all liver-related deaths worldwide. Bile acids...

Super happy to share our latest preprint in #liverdisease & #gut microbiota mechanisms.

www.medrxiv.org/content/10.1...

New preprint from the lab: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" analysing 85k metagenomes across the world, e.g. looking into generalism across habitats www.biorxiv.org/content/10.1... – see the thread below for more details!

#MicroSky 🖥️🧬🦠

Planetary microbiome structure and generalist-driven gene flow across disparate habitats Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...

Our new preprint is out!
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social

The team's first preprint is out!

Led by ‪
‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?

A 🧵.

The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...

Europe’s choice is clear.

To put science at the heart of its economy.

To become the home of scientific freedom and collaboration.

And to welcome talent from all over the world.

I’m glad to present the first elements of our Choose Europe Initiative.

→ europa.eu/!TTbWbJ

Live in 2h: Metagenomic microbial strain tracking in the cloud! I'll be doing a quick demo showing how to use the SameStr workflow on the @nfdi4microbiota.bsky.social Cloud-based Workflow Platform (CloWM) - GUI / no-install / scalable / free for scientific use.

Efficient and robust search of microbial genomes via phylogenetic compression Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

1/

Schon wieder Der Aufstieg der NSDAP/AfD

Die Faschisten sind auf dem Vormarsch - schon wieder - und wir machen genau die gleichen Fehler - schon wieder.
datajournal.org/schon-wieder/

Screenshot von Google News: Zeit Online schreibt von vermeintlichem Hitlergruß, NTV sagt Geste ähnelt, SZ von möglichem Hitlergruß, Welt spricht von römischen Gruß oder Geste von Herzen

Weitere Screenshots von Google News. ZDF spricht von fragwürdiger Geste, T-Online schreibt Mast ihre Tiere mit Geste, BR schreibt von Hitlergruß ähnlicher Geste und so weiter

Weitere Screenshots von anderen Medien im selben Ton

Weiteres Screenshots, diesmal aber mit Watson, die als einziges Medium den Hitlergruß als solchen benennen

Dass nur eine einzige Redaktion sich hier traut, zu schreiben, was jeder sehen konnte: "Musk macht Hitlergruß" – das ist so dystopisch, ihr werft uns denen zum Fraß vor.

Die deutschen Mainstream-Medien sind soweit nach links gerutscht, dass sie einen Hitlergruß nicht mehr Hitlergruß nennen.

A phylogenetic approach to comparative genomics Nature Reviews Genetics, Published online: 08 January 2025; doi:10.1038/s41576-024-00803-0Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests.…

NEW ONLINE! New online! A phylogenetic approach to comparative genomics

A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy - Nature Communications Here, the authors show that higher levels of the gut bacterial clade TANB77 associate with better response to cancer immunotherapy, and further demonstrate in mice that a conserved pilin from TANB77 p...

I’m excited to share our new paper published in Nature Communications!
In our work, we discovered TANB77, a bacterial clade previously obscured by a polyphyletic grouping in conventional taxonomy, as a reliable biomarker across diverse immunotherapy recipient groups.
www.nature.com/articles/s41...

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...

Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...

🚨 New review in @natrevgastrohep.bsky.social:
Should you take probiotics with antibiotics?
www.nature.com/articles/s41...

Bottom line: current evidence does not support the common perception that probiotics can facilitate the gut microbiome's recovery from antibiotics. BUT! 1/🧵

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

YouTube video by Microbiome Virtual International Forum Vedanth Ramji - argNorm: Normalization of antibiotic resistance gene annotations to ARO | S04 MVIF34

If you missed #MVIF 34, no worries, here is Vedanth's talk and other amazing talks! www.youtube.com/watch?v=SnDy...

About one week left to apply! Open postdoc position for analysing environmental microbiome data, e.g. from @embl.org 's TREC expedition along the coastlines of Europe www.embl.org/about/info/t...

Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti...

See below for @suguru-nishijima.bsky.social 's thread on the preprint!

#microsky #microbiome

AI protein-prediction tool AlphaFold3 is now open source The code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics.

1/AlphaFold 3 code now available, following researcher criticism for not providing it with the initial publication. www.nature.com/articles/d41...