Our new MSCA-Doctoral Network project ML4Plankton will kick off soon. 14 PhD students will start in March 2027 to work on plankton big data, i.e., machine learning. Get in touch if you are interested. Coordinator: Sakina-Dorothée Ayata @norwichmicro.bsky.social www.normalesup.org/~ayata/DN_ML...

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

My ANDV #Hantavirus @nextstrain.org phylogenies now pull directly from @pathoplexus.org to incorporate all seqs I'll continue to improve them, & will keep them updated Change the Tip Labels in the left-hand menu. You can see links to all builds, plus tanglegrams at: nextstrain.org/groups/hodcr...

I was investigating the genomes that I didn't manage to convert to near-complete MAGs in my assembly graph (the components in gray). The circle on top left is actually a complete genome but with 40% completeness (both in metaMDBG and myloasm)

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

www.nature.com/articles/s41...

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...

AI is starting to look like pseudoscience

Not all of it, but some scientists are too eager to believe their own hype

stevensalzberg.substack.com

www.lemonde.fr/planete/arti...

Des pôles aux abysses, les nouveaux explorateurs scientifiques font rêver mais irritent le monde de la recherche

Les expéditions mêlant aventure, sport et recherche se multiplient dans les zones extrêmes du globe. Très médiatisées, elles suscitent pourtant des réserves chez les chercheurs académiques, qui dénonc...

lemonde.fr

Researchers Uncover Hidden Genetic World in Antarctic Waters "at least a third of the genes identified are missing from existing marine gene catalogs" @loimai.bsky.social #microbiome #oceans

Researchers Uncover Hidden Genetic World in Antarctic Waters

The discovery of vast numbers of previously unknown microbial genes in Antarctic waters could improve understanding of how the ocean shapes Earth’s climate.

dlvr.it

Exciting new methane research: Huge credit to @annajwallenius.bsky.social & Andy Leu for using nifty bioinformatics to disentangle 8 novel MAGs of 'Candidatus Methanoborealis' This is version 1 of our #bioRxiv preprint. Aanalysis is ongoing & we welcome your feedback! doi.org/10.64898/202...

Living patescibacterial (CPR) cells are a rare sight! Meet Strigamonas methylophilicida, a parasite of methylotrophic proteobacteria we just described in our latest paper: doi.org/10.1128/mbio...

New paper from my 2nd PostDoc is now published in The ISME Journal by @isme-microbes.bsky.social! #Sulfur disproportionation occurs globally across anoxic habitats & has multiple mechanisms of independent evolutionary origin academic.oup.com/ismej/advanc... #Bacteria #Microbes #Evolution #DeepSea

I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...

Genomic perplexity and the evolution of context-dependent function

Abstract. The fundamental principle that selection acts on a gene's function often assumes implicitly that this function is fixed and intrinsic. However, e

academic.oup.com

Very happy to share the latest paper of our group (et al.)! rdcu.be/e7zyX . This one has a special place… 1/n

Water mass specific genes dominate the Southern Ocean microbiome

Nature Communications - Southern Ocean microbial communities are less well studied. Here, the authors generate a circumpolar-scale gene catalog from 218 metagenomics samples revealing broadscale...

rdcu.be

Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/ Bonus: beautiful seascape and friendly spirit!

Antarctica InSync will host two webinars, bringing together the science community to discuss the draft White Papers currently available on our website. · 20 January, 17:00–19:00 (CET) · 21 January, 09:00–11:00 (CET) 📌 Register: lnkd.in/epX4_JiA 📝 Provide input to the draft papers: lnkd.in/eYfJgTUV

Now published in Nature Biotechnology: go.nature.com/44P7nSm If you missed it, the TL;DR is in my April thread below

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology

Long-read sequence assemblies from metagenomes contain frequent errors.

go.nature.com

Florian Trigodet@floriantrigodet.bsky.social · last yr.

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

1/ The overturning circulation is a network of ocean currents transporting heat, carbon, oxygen and nutrients around the world. At the heart of this circulatory system is the global pumphouse of #Antarctica and the Southern Ocean. Animation: NASA-SVS

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....

Virome Analysis

Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...

link.springer.com

www.nature.com/articles/s41... Thrilled to share our new study! We show that mirusviruses include lineages packed with spliceosomal introns and likely replicating in the nucleus of unicellular eukaryotes—a sharp contrast to most large and giant eukaryotic viruses that replicate in the cytoplasm.

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology

Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.

nature.com

Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea

a man walking in a field with an umbrella

ALT: a man walking in a field with an umbrella

media.tenor.com

I am very excited to announce that a fully funded PhD position is available in my group. Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia Please RT or forward this information to interested candidates. Deadline: 11.01.26 More info: shorturl.at/f1TuF

New GEOTRACES Science Highlight! 🌊 Long-range transport of iron via the #Agulhas Current and counter-current: a boon for the phytoplankton www.geotraces.org/long-range-t... Paper first authors: Eva Bucciarelli & Pierrick Penven, LEMAR #oceanscience #traceelements @scor-int.bsky.social

Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6

This meeting will be great! Abstract submission open now See you 26-27 Nov in Liverpool microbiologysociety.org/event/societ...

Understanding and predicting microbial evolutionary dynamics - 2025 meeting

microbiologysociety.org

Come join us at @mcgill.ca as an assistant professor in virus-host interactions! Please share widely. mcgill.wd3.myworkdayjobs.com/en-US/McGill...

Assistant Professor (Research), Department of Microbiology & Immunology, (C2-240724)

Please refer to the How to Apply for a Job (for External Candidates) job aid for instructions on how to apply. If you are an active McGill employee (ie: currently in an active contract or position at ...

mcgill.wd3.myworkdayjobs.com

#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025. A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay! Apply here until June 1: maignienlab.gitlab.io/ebame

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience