Shaul Pollak
@envsysmicro.at
Assistant Professor Environmental Systems Microbiology. Genetics, Genomics, Evolution, Ecology w: https://www.envsysmicro.at @dome-vienna.bsky.social @cemess.bsky.social @univie.ac.at.
Non-canonical gene amplifications facilitate adaptive evolution in bacteria www.nature.com/articles/s41...
Non-canonical gene amplifications facilitate adaptive evolution in bacteria - Nature Microbiology
Transposon-associated amplifications are dominated by a previously underappreciated architecture, where the transposon is found only between, not flanking, the amplicons. These amplifications facilita...
nature.com
(1/2) Hiring! 🦠🧠 Postdoc position in my group @univie.ac.at on microbiome-brain interactions as part of the ERC-funded project “MemoryLane: Neural plasticity through the lens of gut-brain interactions”. 📍 Vienna, Austria 📅 Application deadline: 2 Aug 2026 ℹ️ shorturl.at/2E4sf
New paper out today in Nature Microbiology: "Epistatic interactions inform rational design of synthetic microbial communities for bioremediation." 🧵https://www.nature.com/articles/s41564-026-02386-4 @kiseokmicro.bsky.social @nitmb.bsky.social
How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6...
There is a postdoctoral position available in our group: jobs.univie.ac.at/job/Universi... Please repost.
University Assistant postdoctoral
University Assistant postdoctoral
jobs.univie.ac.at
Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...
Genome-wide sweeps create ecological units in the human gut microbiome - Nature
Genome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.
nature.com
Bacterial immune proteins have repeatedly evolved to become parts of eukaryotic immunity. But how? Our new preprint uncovers a recent horizontal transfer event & shows how eukaryotes co-opted a toxic bacterial immune protein 🦠🧪🧵 1/
New paper out in Nature Comms 🎉 Congrats to first author @sekid.bsky.social & thanks team & collaborators We show that B. bifidum & E. coli can cooperate in the breastfed infant gut through nutrient cross-feeding, helping shape early-life microbiome development 🦠👶 www.nature.com/articles/s41...
Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum - Nature Communications
Escherichia coli is widespread in healthy breastfed infants, yet its ecological role is unclear. Here, the authors provide insights into the mechanisms supporting its persistence and co-existence with...
nature.com
Check out our new manuscript, in collab with Efrat Sheffer, Guy Dovrat and Amir Erez, where we looked at shotgun metagenomes of wild legume nodules, providing an unbiased view of the taxonomic genomic content of legume nodules, and how these relate to plant performance.
Moshe Alon@naturalist1986.bsky.social · 4mo agoWild legume performance is shaped by whole nodule microbiome profile, including non-rhizobial endophytes (NREs). Sulfur assimilation by NREs and type VI secretion system in rhizobial symbionts strongly associated with host traits. New Preprint! @finkel-lab.bsky.social www.biorxiv.org/content/10.6...
a cartoon character holding candles and a skull with the words hail science
ALT: a cartoon character holding candles and a skull with the words hail science
media.tenor.com
Cluster of Excellence 'MicroPlanet'@microbesplanet.bsky.social · 5mo agoAdvance your career in microbiome science! Master’s Programme at @univie.ac.at, led by CoE Key Researcher @jillianmpetersen.bsky.social, is open for a new cohort. Explore microbial communities and their impact on health & the environment. Apply by April 7th! studieren.univie.ac.at/en/degree-pr...
1/11 🔥 New preprint alert 🔥 We wanted to know what plants in the wild really care about. So we asked them 🎤. Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations” www.biorxiv.org/content/10.6...
New preprint on the limits of detecting higher-order interactions in microbial communities. www.biorxiv.org/content/10.6... We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.
biorxiv.org
We found a viral Trojan Horse: a virus can hide inside another virus.This one surprised us: deltaviruses don’t just borrow a helper virus. They can travel inside it. A literal Trojan Horse “virus-in-a-virus” route into cells. 🤯 Kudos to 1st author @viroscope.bsky.social and co-authors !
Deltaviruses spread through a viral Trojan Horse
Hepatitis D-like satellite viruses, known as deltaviruses, have been recently discovered in a wide range of animals. These viruses are thought to expr…
sciencedirect.com
Very good
SeppeKuehnLab@seppekuehnlab.bsky.social · 5mo agoA new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...
Our new preprint introduces #kineochelins, a new group of #siderophores produced by the Antarctic soil actinomycete 🦠🔬🧫 #Actinokineospora sp. UV203 Kudos to the amazing Stanislava Králová & a fantastic team of collaborators 🤩 #microbiomesky www.biorxiv.org/content/10.6...
biorxiv.org
🌊Paper announcement! 📣 Viral infections rewire the metabolic makeup of their host and thereby create distinct chemical signatures. Can we use metabolic biomarkers to diagnose infections of algal blooms in the ocean? Well, take a look at our new article led by Conny Kuhlisch in @pnas.org >>
Mapping of the viral shunt across widespread coccolithophore blooms using metabolic biomarkers | PNAS
The viral shunt is a fundamental ecosystem process which diverts the flux of organic carbon fixed through photosynthesis during algal bloom events ...
doi.org
The Abreu lab at NYU is hiring another postdoc! We study microbial ecology and evolution, using yeast/bacteria microcosms, DNA barcoding for evolutionary lineage tracking, and simple mathematical modeling. Apply here: apply.interfolio.com/179949
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The (Yoav) Voichek lab has opened its gates at the Weizmann Institute, and is actively recruiting students and researchers at all levels - come explore gene regulation and computational genomics in a fun, friendly sprouting lab 🤗🥼⚗️🧪 www.weizmann.ac.il/plants/voichek
Apply now: 1 Postdoc + 1 PhD position, Anderson-Wagner group @univie.ac.at Focus: gut microbial effects on hippocampus & memory 🧠🦠 #PostdocJobs #Microbiome #AcademicJobs #PhDposition Postdoc Ad: careers.univie.ac.at/en/postdoc/e... > Psychology PhD Ad: careers.univie.ac.at/en/praedoc/p... > CoBeNe
It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027! See you there!! @wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social #microsky #mevosky
Out after peer-review: www.science.org/doi/full/10.... Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead! We now also account for regression and nested cross-validation, with more extensive benchmarking.
Distributional bias compromises leave-one-out cross-validation
Leave-one-out cross-validation, a common machine learning evaluation method, has a pernicious flaw; a practical fix is presented.
science.org
Tal Korem@tkorem.bsky.social · 2y agoNew preprint! In a few words: we don't think you should use leave-one-out cross-validation (LOOCV). In a lot of words (+RebalancedCV, a LOOCV alternative): arxiv.org/abs/2406.01652 In a thread:
📢 New preprint on bioRxiv! We introduce V4-EXT, a revised 16S rRNA V4 primer set that dramatically improves detection of Patescibacteria and other undersampled lineages ✅ 938 samples ✅ More novel ASVs Primer choice matters 👀 www.biorxiv.org/content/10.1... @ppjevac.bsky.social #HuifengHu
Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins https://www.biorxiv.org/content/10.1101/2025.11.23.689978v1