Great turnout for the Atlantic #MVIF-Seerave event on Microbiome Modifiers and Cancer Immunotherapy! 🎉 There's still time to catch the Pacific session: cassyni.com/s/mvif-oncob... Help us spread the word, thanks!

The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)

The RAxML-NG v2.0 preprint is out: www.biorxiv.org/content/10.6... v2.0 features integrated model testing, fast branch support metrics, automatic parallelization, phylogenetic difficulty prediction, genotype evolution models, to name but the most important features. And it is A LOT FASTER of course

RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics

RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...

biorxiv.org

Seerave Foundation and #MVIF invite you to their symposium, Microbiome Modifiers and Cancer Immunotherapy, a two-part event designed to move the field from evidence to action. It's free to join, just bring your questions and your curiosity! 🔗 cassyni.com/s/mvif-oncobiome2026 1/3

Our set of new prokaryote-optimized fluorescent proteins is now published ! #microbiology #microsky #microscopy 🧫🦠🔬 www.science.org/doi/10.1126/...

A palette of bright and photostable monomeric fluorescent proteins for bacterial time-lapse imaging

Bright and photostable monomeric fluorescent proteins enable long-term time-lapse imaging in E. coli.

science.org

"The Mobilome in the Mire" DNA sleuths 🕵️‍♀️ @scbagby.bsky.social and 🕵️‍♂️ @simrouxvirus.bsky.social tracked a whole zoo of mobile genetic elements in thawing permafrost ❄️💧 for 8 years. Another Genome Insider podcast from @jgi.doe.gov 🎙️: jgi.doe.gov/user-science...

The Mobilome in the Mire | Joint Genome Institute

Join Sarah Bagby (Case Western Reserve University) and Simon Roux (JGI) as they talk about their recent work on a time series from Sweden’s Stordalen Mire. By looking at Mobile Genetic Elements, or MG...

jgi.doe.gov

Our special issue on the social lives of bacteria is out today 🎉 it was a pleasure to edit this collection over the last year with @friendlymicrobe.bsky.social. Read our editorial here: portlandpress.com/essaysbioche...

Excited to report that our paper 📃 "Predicting the plastic biodegradation potential within microbial lineages and across global ecosystems" by Harmony Douwes, and Zuzanna Dutkiewicz is out! lnkd.in/d2HN2jsj

Microbiology Society@microbiologysociety.org · 3w ago

Check out our latest Micro Briefing highlighting new research, published in Microbial Genomics, mapping out plastic-degrading microorganisms that present an alternative solution for disposing the world's plastic waste. Read the full article🔗 doi.org/10.1099/mgen.0.001814

Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb

Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology

Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...

nature.com

17 AUG — #ISME20 Day 1! 🦠 Today we're exploring AI (machine learning and LLMs), phage phylogeny, novel species recovery and the complex rumen microbiome. Check out our presentations below! 🔬🌏

Which country is the exact antipode of New Zealand? Spain 🇪🇸! Meet the most exotic team at #ISME20 congress in Auckland: microbial #single-cell genomics lab from @i2sysbio.es in Valencia! Check out our posters PS2.13.166, PS.1.06.296 and PS3.16.112 #microsky

1/12 After years of work, we are incredibly excited to share our study, published yesterday in @nature.com : “Maternal influences on gut microbiome and health” 🎉🦠 www.nature.com/articles/s41... A thread on what we found 🧵👇

Maternal influences on infant gut microbiome and health - Nature

The maternal gut microbiome is a predictor of infant eczema.

nature.com

The Centre for Microbiome Research has a large contingent going to #ISME20 in Auckland next week. See below for our talks, posters and panels! 🌏🔬🦠 Discover new tools and methods to uncover microbial diversity, interactions and function, from individual cells and viruses to global microbiomes.

Our paper identifying a stop codon reassignment in Eggerthellaceae species found in mammalian guts is now out! Great collaborative effort with Pierre Chaumeil, Maria Chuvochina, and Phil Hugenholtz (@xrefugee13.bsky.social). www.microbiologyresearch.org/content/jour... @microbiologysociety.org

Stop codon reassignment to tryptophan in members of the bacterial phylum Actinomycetota

Reassignment of stop codons is a significant evolutionary event with recoding of UGA to tryptophan being previously identified in only three bacterial phyla, the Bacillota, Pseudomonadota and Verrucom...

microbiologyresearch.org

After a very long time, I'm very proud that we have now Joachim "magnus opum" on www.biorxiv.org/content/10.6... Protal is a ultra fast metagenomic species profiler. More precise than other profiled software, faster than most (not sylph though), but generates strain resolution instead.

BioShell is live! 🧬💻 A ready-to-use command-line virtual environment for #bioinformatics Co-managed with SIH @sydney-crf.bsky.social & powered by @ardc.edu.au, @nci-australia.bsky.social & originally developed by @pawseycentre.bsky.social #NCRISImpact Read more 🔗

BioShell opens a new gateway to national compute for life science researchers — Australian BioCommons

A new ready-to-use virtual environment offers researchers immediate access to a curated set of bioinformatics tools and datasets. BioShell provides a command line interface that is preconfigured for bioinformatics and uses national computer resources, at no cost to researchers.

biocommons.org.au

"Writers have been using me long before AI. I am the punctuation equivalent of a cardigan—beloved by MFA grads, used by editors when it’s actually cold, and worn year-round by screenwriters. I am not new here. I am not novel. I’m the cigarette you keep saying you’ll quit."

The Em Dash Responds to the AI Allegations

“Writers have been using me long before the advent of AI. I am the punctuation equivalent of a cardigan—beloved by MFA grads, used by editors when it’s actua...

buff.ly

Tragic and - according to scientists quoted in the article — avoidable.

Exclusive: Death of girl in Chinese gene-editing trial was never made public

Parents want accountability after study went disastrously wrong, Science and Retraction Watch investigation reveals

science.org

New preprint! 🧵 Best #Cercozoa genome alert! For a decade, I’ve studied protist ecology through questions like who eats whom. But beyond “they eat this, they eat that,” what do #protists do to their environment, biochemically speaking? #protistsonsky @huesnaoeztoprak.bsky.social

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

Our new work @natecoevo.nature.com shows Karenia cristata produces brevetoxins and is the dominant player in the prolonged bloom & mass mortality event in Southern Australia. Glad to be part of this work with Shauna Murray & the whole team! rdcu.be/fse9r The Conversation: tinyurl.com/3rnyxrnj

A catastrophic marine mortality event caused by a complex algal bloom including the brevetoxin producer Karenia cristata

Nature Ecology & Evolution - Genomic characterization and toxicity assays identify Karenia cristata as a brevetoxin-producing species that is the dominant component of the prolonged microalgal...

rdcu.be

Nature Ecology & Evolution@natecoevo.nature.com · 3mo ago

Genomic characterization and toxicity assays identify Karenia cristata as a brevetoxin-producing species that is the dominant component of the prolonged microalgal bloom causing mass marine mortality in South Australia 🧪 www.nature.com/articles/s41...

Genuine question for folx who look at bacterial phylogenies: How do you interpret the bootstrap support and posterior probabilities that you get on your tree estimates? Do you take them seriously? Do you think: "Wow, all 99%, that must be a reliable tree!"? 1/

Walk through our July issue! Read about 💊Microbiome and AMR 🧊Permafrost microbes 🦠Phages and flagella ⚕️Cholera protection 💉Poxvirus vaccine design 🍄Commensal skin yeast and much more! www.nature.com/nmicrobiol/v... #MicroSky

@jgi.doe.gov's Genome Insider podcast has posted an episode about our paper now too, featuring @simrouxvirus.bsky.social and me: jgi.doe.gov/user-science...

The Mobilome in the Mire | Joint Genome Institute

Join Sarah Bagby (Case Western Reserve University) and Simon Roux (JGI) as they talk about their recent work on a time series from Sweden’s Stordalen Mire. By looking at Mobile Genetic Elements, or MG...

jgi.doe.gov

New tool sracat-rs extracts .sra format files from NCBI - streaming, flexible, as fast as anything else I know of. github.com/wwood/sracat...

GitHub - wwood/sracat-rs: Flexible streaming .sra format extraction

Flexible streaming .sra format extraction. Contribute to wwood/sracat-rs development by creating an account on GitHub.

github.com

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

1) Dereplication of the datasets is now done using Galah (github.com/wwood/galah), which takes into account checkM2 quality scores. This means a lot of species representative genomes have changed relative to release 226.

GitHub - wwood/galah: More scalable dereplication for metagenome assembled genomes

More scalable dereplication for metagenome assembled genomes - wwood/galah

github.com

@aroneys.bsky.social and @benjwoodcroft.bsky.social generated the full 7-level taxonomy, and a singleM metapackage and two sylph databases are available for profiling metagenome datasets using the GlobDB.

I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets. More info globdb.org 🦠🖥️🧬

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357