Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... 🧬💻🧪 github.com/RasmussenLab...

This piece has *really* *really* *really* good charts. h/t @profraywills.futuresmart.com.au #energysky

More renewables = lower electricity prices. Also: Nyuck Nyuck! youtu.be/FbjiKIKzY3c But, seriously, folks: Gas is flaming out. #energysky The rise of battery storage, and why the grid is rapidly passing gas! reneweconomy.com.au/the-rise-of-...

EIA: 99%+ of new US capacity in 2026 will be solar, wind + storage 🔌💡 electrek.co/2026/01/28/e...

AI Agent Skills Have a Massive Security Problem Someone just proved you can trick developers into running malicious code. 16 people from 7 countries fell for it in 8 hours. Here's what happened:

Host-asssociated, especially human, metagenomics colleagues! Is there a current best-practice pipeline for removing human (long) reads from a metagenome at this point? We usually just map against the host reference, but are their classifiers that really work well for this?

Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...

Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments? My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database. Please share around for visibility.

In reviewing grants and papers lately, as an exp., I have been using LLMs *after* my reviews to see how they stack up. And let me tell you - they're (all) *completely* off the mark. That makes sense if you understand the fundamentals of LLMs, but I'm worried many don't. But, please, don't do this.

Excited to see this published! A big part of why SAR11 is so tricky to grow like "normal" microbes.

“The enormous diversity of fungal genomes...offers catalogs of enzymes, secondary metabolites & other parts lists for biotechnology, bioenergy & biomaterials."—Igor Grigoriev, Fungal & Algal Program Head. 🖥️🧬🍄🍄‍🟫 https://jgi.doe.gov/user-science/science-stories/mapping-earths-hidden-fungal-kingdom

This fits with pretty much everyone i’ve asked trying to implement AI for business purposes. I’m not an expert, but from what I’ve seen, LLMs seem great as coding assistants and ML for research purposes, but the AI slop LLMs create for everything else just requires more people’s time to correct.

Been doing a lot of @nanoporetech.com sequencing for soil and sediment lately and it appears that no matter how much DNA or how little we still get decent yields. So pretty robust performance. Yield clearly depends on pore count.

🚨vConTACT3 now in Nature Biotechnology: - >95% agreement with ICTV for known viruses - Classifies both prokaryotic and eukaryotic viruses - Extends beyond genus → subfamily, family & order - Systematically assigns taxonomy to tens of thousands of previously unclassified viruses

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...

I'm usually skeptical about AI research tools. But Google's new tool for literature search is fantastic - because it does less, not more. New post: substack.com/home/post/p-...

Open up this picture fully. Then look at the surface of Mars. Then look up to the top right. Spot Mars' moon Phobos high in the sky. Then notice the bright spot beside Phobos. That's Earth.

This is a metaphor for the tech industry overall circa 2025

Welcome to another member of the antiSMASH ecosystem of tools. When @marnixmedema.bsky.social and I were putting together antiSMASH version 1.0 15 years ago, I don't think our wildest dreams would have predicted where our little tool would go.

Metagenomics colleagues! Anybody know if a good piece of software to test whether Illumina contigs are circular? @antobeck.bsky.social?

Merry X-SMASH! My first first author paper is out on bioRxiv! 🖥 We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫 1/8

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)

WATCH: Here's the segment CBS News pulled from "60 Minutes" last night

Former NSA employee (16 years) with a pro tip for you. Released controlled document on the left, Epstein on the right. See the difference? In real redactions, some words, headers, and bits will almost always still be visible, but especially classification headers. These documents are UNCLASSIFIED

Team, what tool do you use to adapter clip PacBio data? I’m used to using PoreChop for ONT, but not sure for PacBio.

💾 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...

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...

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

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....

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!

🧬🦠🚨 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...

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...

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...

Holy crap And theoretically, if one size-selected, could even be better? 7kb N50 is good but we’ve seen ~20% output improvement after size selection before.

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...

🦠🧪🧬🚨 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-...

Symbiont-coral partnerships Hologenome of B. pseudoalternata reveals a division of labor between deep-sea coral & symbionts. Host provides habitat & manages immunity, while symbionts recycle waste, supply nutrients, resist viruses & produce antioxidants www.cell.com/cell-host-mi...

Enormous milestone. All thanks to vaccinations!!!

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Hey Team! What do you think are the best free digital notebooks these days. I've used: Evernote--great, but now it's paid TiddlyWiki wasn't bad, but got rid of scrollable code blocks Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki. Suggestions?

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions. Here is a blog that explains my motivation for this and how to schedule a meeting: merenlab.org/2025/11/16/E...

“My magic beans can work miracles, they’re different from all of the fake magic beans out there” has been the sales pitch of charlatans since time immemorial.

I just published my weekly newsletter to >10K subscribers: The truth about AI coding for bioinformatics divingintogeneticsandgenomics.kit.com/posts/ai-po...

The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity academic.oup.com/gbe/article/... 🧬🖥️🧪

Chemical richness and diversity of uncultivated ‘Entotheonella’ symbionts in marine sponges www.nature.com/articles/s41... #jcampubs

Thought i'd show a bit of personality outside of metagenomics talk here. Caught a bit of the aurora in Ohio yesterday. Was my first time seeing one, and also trying to photograph it. I love how these turned out. Anybody else see it?

A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT. We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)