All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

Machine learning enables scalable and systematic hierarchical virus taxonomy doi.org/10.1038/s415...

The glycine betaine-cobalamin feedback loop drives cross-feeding between marine bacteria and algae https://www.biorxiv.org/content/10.64898/2025.12.19.695462v1

Microbial rhodopsins are everywhere in the surface ocean, but were assumed to play a role mainly when nutrients are scarce. Our new study reveals unexpected rhodopsin dynamics tightly linked to phytoplankton blooms.

Have you tried the formulation of the accompanying Science paper by Atrandi? www.science.org/doi/10.1126/... What are your comparative thoughts between both technologies?

the "CAGEs" semi-permeable capsule technology from Allon Klein's lab came out in Science yesterday. So many great experiments in this paper. I've been using the CAGE chemistry lately, and it's the best SPC formulation I've tried, out of many! i think their chemical intuition is spot on

Unexpected microbial rhodopsin dynamics in sync with phytoplankton blooms www.nature.com/articles/s41...

A quick microbio present before the holidays 🎁 >150 years after their first description, filamentous "Crenothrix bacteria" are now in stable laboratory culture! In our pre-print, we probe the unique physiology & ecology of the "lacustrine" group of these enigmatic methane-oxidizing microbes... 1/2

“A process which led from the amoeba to man appeared to the philosophers to be obviously a progress - though whether the amoeba would agree with this opinion is not known" - Bertrand Russell, 1976. Time-lapse video of Vampyrella lateritia eating Spirogyra algae from Science Source/Oliver Skibbe. 🦠

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order doi.org/10.1186/s401...

New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales | Nature Communications https://www.nature.com/articles/s41467-025-67043-6

💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...

Functional Unknomics of the SAR11 clade using bioinformatics approaches https://www.biorxiv.org/content/10.64898/2025.12.11.693642v1

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny academic.oup.com/ismej/advanc... #jcampubs

GTDB is now cross-referenced from ENA genome assembly pages. Check it out: www.ebi.ac.uk/ena/browser/.... Thank you to @ebi.embl.org for support with setting up these links!

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes. Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero link.springer.com/protocol/10....

🧪🦠🌊 Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus? #Urea is (part of) the answer! Very happy this fun study led by @mpimarinemicrobio.bsky.social is out: shorturl.at/wajjh Big shout out to Joerdis and Hannah for pushing this over the finish line!

The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani. Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....

Structural basis and evolutionary pathways of glycerol-1-phosphate transport in marine bacteria www.pnas.org/doi/abs/10.1... #jcampubs 🌊

Heterotrophic nanoflagellates in lakes ingest 10–20 bacteria/hour, removing roughly 1/3 of all prokaryotes daily but most remain uncultured and unsequenced. We devised a new cultivation strategy to describe one such predator here 🦖🔬 t.co/TU1fq4eVg2 #MicrobialEcology

A ferritin-like diiron oxygenase BioE initiates bacterial biotin synthesis, a promising antivirulence target www.pnas.org/doi/10.1073/...

Percent‐Level Copper Mineralisation Promoted by Copper‐Tolerant Iron‐Oxidising Bacteria in Circumneutral Mine Drainage enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

Comparative transcriptomes reveal differential effects on host metabolism reprogramming in two different pelagiphage-SAR11 infection systems academic.oup.com/ismecommun/a... #jcampubs

🧬🦠🚨 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...

Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it academic.oup.com/ismecommun/a... #jcampubs

Uniform pre-processing of bacterial single-cell RNA-seq www.biorxiv.org/content/10.6... #jcampubs

eggNOG v7: phylogeny-based orthology predictions and functional annotations | Nucleic Acids Research | Oxford Academic https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1249/8373942?rss=1&login=true

100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...

Our BEHIND THE STORY. A glimpse into the role of auxiliary metabolic genes in cyanophages during infection communities.springernature.com/posts/a-glim...

What would a marine microbiome observing system meant to last decades look like? 🌊🦠 We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations. merenlab.org/workshops/MM...

SciLifeLab researchers Maliheh Mehrshad (SLU) and Camilla Engblom (@ki.se) appointed Wallenberg Academy Fellows ↓ 🧪 “This program gives researchers the chance to pursue high-risk, high-gain research ideas” – @mehrshmali.bsky.social Q&A ↓ www.scilifelab.se/news/long-te... @kawresearch.bsky.social

New preprint! We explore how gutless marine worms and their bacterial symbionts use organosulfur compounds like DMSP and DMS - key molecules in marine sulfur cycling. Our results show that these compounds support carbon and energy metabolism in the Olavius algarvensis symbiosis.

Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea | Nature Communications https://www.nature.com/articles/s41467-025-67002-1

Size-fractionated fungal communities in the sunlit ocean www.nature.com/articles/s42... #jcampubs

Cosmopolitan marine bacteria facilitate a vast phytoplankton-derived sulfonate-based carbon flow through sulfoquinovosidases www.nature.com/articles/s41... #jcampubs 🌊

Proliferation of a bloom-forming phytoplankton via uptake of polyphosphate-accumulating bacteria under phosphate-limiting conditions academic.oup.com/ismecommun/a... #jcampubs 🌊

Respiratory endosymbionts, that allow their ciliate hosts to breathe nitrate instead of (or in addition to) oxygen are frequent members of the wastewater microbiome. 🦠 🖥️🧬 Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations! doi.org/10.1093/isme...

Fresh from our group, a new role for oxygen production in ammonia-oxidizing archaea: Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea Congrats to Thomas Pribasnig for this great work! Check it out here: www.biorxiv.org/content/10.6...

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬 www.nature.com/articles/s41...

Amazing dataset describing the metabolic profiles of 66 E. coli transporter knockouts by @sulheim.bsky.social with Peter Doubleday and @nzamboni.bsky.social. The tool, set up by @lambdapp.bsky.social and Eric Ulrich allows you to explore for yourself. Enjoy! Pre-print here: doi.org/10.1101/2025...

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

🚀 Just launched: GraphBin Visualise (WASM) a browser-based visualisation tool for comparing initial metagenomic binning results vs refined results from GraphBin - all running in your browser, no backend required. (1/n) #bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly

🔊 APPLY NOW for our #MarMic #MSc/#PhD program! Come to #Bremen and take an interdisciplinary approach to #marine #microbiology, #molecularbiology, #biochemistry, #evolution and more. ⏳ Open until Feb 28 2026 ➡ marmic.mpg.de #graduatestudents #marinescience #sciencecareer #IMPRS @maxplanck.de

📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools. 🔥 Apply by Jan 8, 2026 Details: phd.pages.ista.ac.at

I am recruiting graduate students for Fall 2026! The Microbial Ecosystems Lab @hot-mes-asu.bsky.social at ASU studies microbial interactions, spatial ecology, and imaging-driven microbiome science. If you love microbes, microfluidics, or single-cell analysis, let’s talk! www.microbialeco.systems

Redox-constrained microbial ecology dictates nitrogen loss versus retention academic.oup.com/ismecommun/a... #jcampubs

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes url: academic.oup.com/nar/article/...

From Microscale to Microbial Insights: Validating High-Throughput Microvolume Extraction (HiMEx) Methods for Marine Microbial Ecology | ISME Communications | Oxford Academic https://academic.oup.com/ismecommun/advance-article/doi/10.1093/ismeco/ycaf218/8342219

VIRE: a metagenome-derived, planetary-scale virome resource with environmental context | Nucleic Acids Research | Oxford Academic https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007?rss=1&login=false