ICYMI: New online! The paradox of immune systems conservation between prokaryotes and eukaryotes

Everyone knows that space and spatial structure is super important in shaping the Microverse 🌎🌍🌏 Check out this amazing review where @marcelbaecker.bsky.social and @bramvandijk.bsky.social et al bring together a huge body of knowledge @microverse.bsky.social @binfutrecht.bsky.social

AlphaGenome is out! Input 1 Mb DNA -> predict gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chromatin contact maps, ..., up to single-base-pair resolution! Trained on human and mouse data 🧪🧬🖥️🦠✨ www.nature.com/articles/s41...

Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)

New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...

Application of Nanopore sequencing to intact caspid-packaged DNA reveals that bacterial DNA encapsulation is widespread in the human gut #microbiome www.nature.com/articles/s41...

Genomic rearrangements occur at varying rates across Archaea and Bacteria, but are typically enriched near the ori region. While gene synteny is widely conserved, some species show highly flexible genomic layouts. #Microevo #evolution #genomics academic.oup.com/gbe/advance-...

A nice study showing that community conservatism is common in microbial communities across different environments #microecoevo #microbes www.nature.com/articles/s41...

Bacteriophages mobilize bacterial defense systems via lateral transduction #phage #virus #microecoevo www.science.org/doi/10.1126/...

Do you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research? Then come and join our group !

Our latest. Led by the very talented @ahoiching.bsky.social Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊

Subsurface oxygen maxima in oligotrophic oceans are catalyzed by the viral shunt - www.nature.com/articles/s41...

Identifying Fundamental Gaps in Functional Metagenomics: A Step Towards Unlocking Microbiome Research Potential www.biorxiv.org/content/10.6... #jcampubs

microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats https://www.biorxiv.org/content/10.64898/2026.01.12.698811v1

Microbes and DOM molecules both exhibit strong seasonality, with the largest majority of recurrent signals occuring in summer journals.asm.org/doi/10.1128/...

Don’t forget that the 1961 triplet code paper only became elegant when it was written! The experiments were all a bit of a mess... I suspect the same was true of the other classic papers!

Urea-driven nitrification contributes up to 40% of the total N2O produced through nitrification processes in the oligotrophic oceans academic.oup.com/ismej/articl...

The microbial keystone concept is a very cool topic in microbiome ecology. This review summarises mechanisms, prediction methods and implications, with "keystoneness" being highly context/time dependent + new methods approaches suggested. Very nice read! www.nature.com/articles/s41...

Two articles published in concert in Nature Microbiology indicate that lytic phages may be prevalent and persistent in isolated microbes - www.nature.com/articles/s41... & www.nature.com/articles/s41...

Three weeks of relaxing, travelling to see family and friends, eating lots and not opening my laptop...feeling refreshed and excited for the year ahead 😁

Feeling grateful to end this year by contributing to a commentary on bioengineering the coral holobiont. This is my first manuscript as a professor and a dream come true to team up with leaders in coral probiotics, Raquel Peixoto and @reefgenomics.bsky.social. 🪸🧪🧬🦠 www.cell.com/one-earth/ab...

#Phage resistance in a marine bacterium through surface protein and intracellular mutations that impact the cell's stickiness and increases sinking rate - potential wider impact on carbon cycling - www.nature.com/articles/s41...

Isolation of 81 new strains combined with a comprehensive genomic and ecological analysis revealed 29 monophyletic ecotypes (genera) within the Pelagibacterales www.nature.com/articles/s41...

Conjugative plasmids help spread AMR genes. @andrewmatthews.bsky.social @sonjalehtinen.bsky.social & @tatianadimitriu.bsky.social show that #AMR loss in evolving populations involves streamlined #plasmids that gain a transmission advantage by deleting AMR genes @plosbiology.org 🧪 plos.io/48NM0BL

Ecogenomics and functional biogeography of the Roseobacter group in the global oceans link.springer.com/article/10.1...

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...

Landmark study in @Nature! 🇩🇰 The "Microflora Danica" project has created the first-ever national microbiome atlas. Led by Aalborg University, @fwf-at.bsky.social CoE Microplanet's Director @michiwagner4.bsky.social, and @daanspeth.bsky.social, Andrew Giguere @cemess.bsky.social analyzed nitrifiers.

#NatMicroPicks A new protist with remnants of ancient mitochondrial DNA 🧬🦠 The eukaryotic tree of life grows with the addition Solarion arienae - a unique and peculiar protist species #MicroSky www.nature.com/articles/s41...

📢 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

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠

The core genomic backbone of bacteria is not necessarily resilient to gene flow! A new study shows that introgression impacts, on average, 2% of the core genes of species - www.nature.com/articles/s41... #microevo #microeco #evolution

Very cool study - a new approach for single cell genomics that captures a wealth of #virus diversity in only 300 nanolitres of #ocean water, including viruses that use non-canonical bases www.nature.com/articles/s41...

🚨vConTACT3 preprint live!🚨(Peer Review soon...!) vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification. 🔗 Read the preprint: doi.org/10.1101/2025... Improvements details below 👇

Scientists still have a very limited understanding of #marine #biodiversity. Jonathan Belmaker explores a new @plosbiology.org study that uses unprecedented global environmental DNA #eDNA sampling to reveal the extent of our ignorance 🧪 Paper: plos.io/47yRnEk Primer: plos.io/3XeJ2kl

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com rdcu.be/eLtCH

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

The evolutionary and ecological consequences of cooperation -in American Naturalist by @stuwest.bsky.social, @annadewar.bsky.social, @ryosukeiritani.bsky.social, Laurence Belcher, and @asgriffin.bsky.social www.journals.uchicago.edu/doi/abs/10.1...

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...

Postdoc vacancy: Microbial dormancy in the cryosphere @erc.europa.eu #ERC_SIESTA 📢 PLEASE RT 🧬 Single cell microbial activity measurements, flow cytometry, cell sorting, omics, ecological interpretation ☀️ Marseille, France ‼️ Apply ASAP & before 7 Nov Link: emploi.cnrs.fr/Offres/CDD/U...

Phytoplankton blooms at the marginal ice zone in the central Arctic support elevated nitrogen fixation by non-cyanobacterial diazotrophs - www.nature.com/articles/s43...

I'm delighted our paper is out: doi.org/10.1093/isme... With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠

The ecological and phylogenetic partitioning of coastal and offshore SAR11 is underpinned by a handful of distinct metabolic traits under high selective pressure - academic.oup.com/ismej/advanc...

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues. @mkrupovic.bsky.social @yifanzhou.bsky.social @deemteam.bsky.social www.nature.com/articles/s41...

Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology! @mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social www.nature.com/articles/s41...

This is not good. Positive feedbacks adding to warming.... www.theguardian.com/environment/...

Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

Our latest work reveals that arbitrium phages cross-communicate across species! These tiny viruses “listen” to signals from others, coordinating lysis-lysogeny decisions across species. Original idea from @albertomarina.bsky.social and, as usual, he was right. www.biorxiv.org/content/10.1...

Bacteria in hot springs can move against fast water flow without flagella. Instead, they use pili like grappling hooks to crawl upstream, revealing a surprising survival strategy in extreme environments. isme-microbes.org/hot-spring-b... #microbes #bacterialmotility #extremophiles #hotsprings

Interested in how microbial #diversity is structured across the global #oceans? Check out our newest preprint! We show that latitudinal diversity gradients are taxon-specific, reflecting differing ecological strategies and their responses to environmental gradients www.biorxiv.org/content/10.1...