Ever wondered if your favorite bacteria 🧫🦠 produce exopolysaccharides? You can now easily check that with epsSMASH, our new bioinformatic tool built on the antiSMASH framework. It detects both known and novel exoPS BGCs. Check out and share the preprint! www.biorxiv.org/content/10.6...

Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...

Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated! Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking. Thanks to all co-authors for such a great collaboration!

Authors published a paper in Biorxiv, they used GTDB-Tk in the study. Including #RRIDs will make this less ambiguous. SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID

If you want an example of gold standard genomics across every aspect of a paper, read this. It levelled me up. Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too. www.nature.com/articles/s41...

Discovery of the most intron-rich eukaryotic genome phys.org/news/2025-12... New #ISEPpapers: Nuclear #genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis academic.oup.com/dnaresearch/... #Protists #Algae #Microbes #Genomics

@peterfineran.bsky.social and colleagues develop Tn-seq for phages by leveraging anti-CRISPR (Acr) as a positive selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs www.biorxiv.org/content/10.6...

Wait, is this a new taxonomy??

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!

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....

More on ARC job cuts & restructure: ARC’s spending $374k on consultants for organisational “review” & “planning & development”. They’re also spending $765k on “risk management”. That’s $1.1 million on consultants being spent over 1 year. Un. Believable. Slow clap, ARC.

The Metagenome Stability Diagram uses gene markers across ecosystems to understand how environmental conditions constrain metabolic activity in microbiomes. 🖥️🧬🦠 https://jgi.doe.gov/user-science/science-stories/data-discovery-tool-helps-identify-microbial-roles-within-metagenomes

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

ARC says they’ll announce Centres of Excellence outcomes tomorrow (Tuesday 9th Dec). This is more than 2 months late, most likely due to the new security checking requirements for ARC grants. Centres of Excellence grants also need to have been approved by the Minister.

Excited to share our new @natecoevo.nature.com paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8) www.nature.com/articles/s41...

github.com/bede/deacon For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️

Eukaryogenesis was a billion year spree, but the acquisition of mitochondria happened when the party was winding down www.nature.com/articles/s41...

interesting side project picked up during development of gTranslate - discussed in the preprint

Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters. Pre-print: www.biorxiv.org/content/10.1... 🧵👇(1/n)

pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences https://www.biorxiv.org/content/10.1101/2025.11.27.689987v1

metaTraits: a large-scale integration of microbial phenotypic trait information academic.oup.com/nar/advance-...

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses www.nature.com/articles/s41... @luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social

Our institute @i2sysbio.es published news on our article published in #ISME Communications. We developed a #bioinformatics tool to demultiplex reads from #Atrandi microfluids platform @atrandi.bsky.social for microbial #single-cell genomics, great for detection of #phages & #viruses 👩‍🔬🧬🧪🦠🧫🖥 #microsky

@arc-tracker.bsky.social - any intel on CoE announcements?

📢 New preprint on bioRxiv! We introduce V4-EXT, a revised 16S rRNA V4 primer set that dramatically improves detection of Patescibacteria and other undersampled lineages ✅ 938 samples ✅ More novel ASVs Primer choice matters 👀 www.biorxiv.org/content/10.1... @ppjevac.bsky.social #HuifengHu

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...

According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.

www.sciencealert.com/newly-discov... 🧪 #endosymbiosis #mitochondria

www.nature.com/articles/s41... #protistsonsky

High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules. academic.oup.com/ismecommun/a...

Deep-branching eukaryotes and early events in protist evolution #evolution #eukaryotes #protists onlinelibrary.wiley.com/doi/10.1111/...

@katharinasures.bsky.social @probstlab.bsky.social et al. analysed CRISPR-Cas systems of metagenome-assembled genomes from two subsurface environments, shedding new light on the diversity of CRISPR spacers in natural microbial communities. 🔗 doi.org/10.1093/gbe/evaf201 #genome #evolution #CRISPR

FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT). #Kmers #MaskedBWT #Genomics #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...

Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge #microbiology #bacteria enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Synteny plot quality control with SyntenyQC. #SyntenyPlots #Grnomivd #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

We are delighted to let you know that your Plants, People, Planet article 'Demystifying Fungal Systematics: A Gateway to Fungal Literacy and Societal/Ecological Relevance Through Familiar Species' has been published on Early View. nph.onlinelibrary.wiley.com/doi/10.1002/...

Augmenting microbial phylogenomic signal with tailored marker gene sets www.nature.com/articles/s41... #jcampubs

The core genomic backbone of bacteria is not necessarily resilient to gene flow! A new study shows that introgression impacts, on average, 2% of the core genes of species - www.nature.com/articles/s41... #microevo #microeco #evolution

The diderm cell envelope is not a stack of layers but a unified scaffold of Inner Membrane–Peptidoglycan–Outer Membrane. We discuss how tethering the OM to the PG in E. coli preserves integrity — and extend the concept across diderm bacteria. Curr Opin Microbiol: doi.org/10.1016/j.mi... #microsky 🔬

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

Half of microbial eukaryote literature focuses on only twelve human parasites #microbiology #protists #eukaryotes @isme-microbes.bsky.social academic.oup.com/ismej/articl...

🚨vConTACT3 preprint live!🚨(Peer Review soon...!) vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification. 🔗 Read the preprint: doi.org/10.1101/2025... Improvements details below 👇

Scientists still have a very limited understanding of #marine #biodiversity. Jonathan Belmaker explores a new @plosbiology.org study that uses unprecedented global environmental DNA #eDNA sampling to reveal the extent of our ignorance 🧪 Paper: plos.io/47yRnEk Primer: plos.io/3XeJ2kl

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

#CentresOfExcellence #CE26 ARC has "postponed" announcement of Centres of Excellence outcomes! It says "due diligence checks" are still being carried out on some applications. www.arc.gov.au/news-publica...

We have had some amazing abstracts submitted to the free @official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com rdcu.be/eLtCH

Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...