It’s that wonderful time of year again. A new GTDB release is out :)

ace-gtdb.bsky.social@ace-gtdb.bsky.social · 4mo ago

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.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration www.nature.com/articles/s41...

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology

FAMSA2 accurately aligns millions of protein sequences at high speed.

nature.com

🦠🧪🧬🚨 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-...

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

academic.oup.com

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

Soils contain an amazing diversity of functions encoded in plasmids. The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples. Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov www.nature.com/articles/s41...

🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes

Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

academic.oup.com

A BLAST update adding support for compressed files and csv output with headers is a Good Friday night surprise! blast.ncbi.nlm.nih.gov/doc/blast-ne...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

Preprint alert from the group 🚨 super fast grep-like sequence selection

Antoine Limasset@npmalfoy.bsky.social · last yr.

A common approach is to use k-mer indexes to identify datasets that share a significant number of k-mers with a query sequence. This problem has been studied extensively, and I recommend the survey of @camillemrcht.bsky.social, a great introduction to the subject genome.cshlp.org/content/31/1...

Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41... #jcampubs

Scaling laws of bacterial and archaeal plasmids - Nature Communications

The capacity of a plasmid to express genes is constrained by parameters such as its length and copy number. Here, Maddamsetti et al. present a computational method that enables rapid and accurate dete...

nature.com

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

The Koonin Law of Computatoinal Biology: Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.

At Tatta Bio, we have been thinking deeply about the sequence-to-function problem. We believe that before AI can power functional prediction, we first need to rethink how we curate, manage, and share sequence data. Here, we share our initial ideas on what we are building next:

Today's sequence data infrastructure is set up for failure in the age of AI.

Building an open and collaborative sequence platform for both Human and AI scientists.

tattabio.substack.com

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

Our new paper is out in @science.org! By exploring the rich genetic diversity of Brazil, we show how fine-scale genomic analyses reveal that this diversity, rooted in Indigenous ancestry and centuries of complex demographic history, plays a key role in population health.

Very proud of my colleagues and friends for their amazing publication out in Science today! Nunes et al. "Admixture’s impact on Brazilian population evolution and health" www.science.org/doi/10.1126/... @hunemeier.bsky.social @macscastro.bsky.social 👏

Admixture’s impact on Brazilian population evolution and health

Brazil, the largest Latin American country, is underrepresented in genomic research despite boasting the world’s largest recently admixed population. In this study, we generated 2723 high-coverage who...

science.org

schaechter.asmblog.org/schaechter/2... #MicroSky #Archaea #ArchaeaSky #SymbioSky

Cultivating the Ancestors (4|4)

by Christoph — Having one or two 'Asgard' archaea under the microscope – after having cultivated them with great effort and even more patience – and looking them in the face is exciting, but a bit uns...

schaechter.asmblog.org

STCmicrobeblog@stcmicrobeblog.bsky.social · last yr.

schaechter.asmblog.org/schaechter/2... #MicroSky #Archaea #ArchaeaSky #SymbioSky

We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue doi.org/10.1093/nar/... Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI: bakta.computational.bio (1/5)

Bakta Web – rapid and standardized genome annotation on scalable infrastructures

Abstract. The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensiv

doi.org

Unique investigation of some errors in long read assemblers. In particular these remarkably chimeric contigs are 😱, if rare.... Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Assemblies of long-read metagenomes suffer from diverse errors https://www.biorxiv.org/content/10.1101/2025.04.22.649783v1

A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2

GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.

Is the genome just a bag of genes? A new paper in Science now reports that for two thirds of an organisms' genes the position along the chromosome is actually very tightly constrained! Amazing work from my favorite night scientist Martin Lercher and his team! www.science.org/doi/10.1126/...

CoverM is published! CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

CoverM: Read alignment statistics for metagenomics

AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r

academic.oup.com

🚨New paper!🚨 A comprehensive take on the origins and evolution of translation factors & how these essential players evolved across the tree of life. 🌍🧬 Led by Evrim Fer @uwmadisonmdtp.bsky.social grad student! 👏 Free access: www.sciencedirect.com/science/arti... @cp-trendsgenetics.bsky.social

The abstract submission & registration for #RdRpSummit2025 is NOW OPEN!!! 🎉🙌 Do you work on RNA virus discovery using RdRps? Are you joining the #ViBioM2025 in Portugal? Consider submitting your research in one of our sessions! More info: RdRp.io

Publishing a paper in Nature while based in Brazil is an incredible achievement. Huge congratulations to the authors! I'm excited to give this a proper read :)

Nature@nature.com · last yr.

Nature research paper: A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion https://go.nature.com/4jODjvX