Samuel Aroney

🚨 New preprint 🚨 We’ve discovered millions of viruses from sequencing data but we don’t always know who they infect. Our new tool, VHAMSTeR generates broad virus host predictions across the tree of life (prokaryote, plant, animal, fungi and protist hosts) A thread 🧵👇 www.biorxiv.org/content/10.6...

For this year's #WorldPhageDay we wanted to highlight the historical importance of #phage in Biology So we asked a panel of experts* for their favorite phage-based contributions accross history Here is their top 5 *members of the BBH lab (List of choices was based on doi: 10.1002/bies.201400152)

Love 🦤radEmu🦤? You'll love ☄️fastEmu☄️! Fantastic work by @steichman.bsky.social fastEmu replaces a computationally expensive piece of hypothesis testing in radEmu with a cheaper approximation. Especially beneficial for large datasets & complex designs! Software: statdivlab.github.io/fastEmu Enjoy!

Always wanted to fix microbial cells while still enabling downstream DNA sequencing? Try the new microbial fixative: DSP Preprint is out! doi.org/10.64898/202... Huge thanks to my collaborators @kennethwasmund.bsky.social & @loyteam.bsky.social & supervisors @sjmcilroy.bsky.social & Gene Tyson!

Reversible fixation of microbial cells for targeted genomics www.biorxiv.org/content/10.6... #jcampubs

Skani (github.com/bluenote-157...) is now v0.4.0! Big performance update: **~2.5x faster** and ~30-40% less RAM for average nucleotide identity (ANI) comparison of genomes. The database format has changed (breaks forward compatibility; watch out!).

The archaeon Sukunaarchaeum mirabile, associated with dinoflagellates, has a genome of only 238 kbp🧬🤯 #archaea #symbiosis #eukaryotes #protists #MicroSky @currentbiology.bsky.social www.cell.com/current-biol...

🚀 Excited to introduce Agar3000 - our open‑source tool for automatic colony counting! Developed by Vadym Sokhan, Agar3000 detects & counts microbial colonies directly from smartphone photos. We’ve validated it across multiple datasets, growth media, and illumination setups: lnkd.in/dAX2qdkB

We just released Polars 2.0. It removed many of our legacy decisions makes the streaming engine our default and promotes SQL to a first class citizen within Polars. pola.rs/posts/releas...

How do redox conditions in an Asgard archaea-rich environment determine their vertical distribution? Find out in our latest paper about the amazing Catherine crater lake microbial mat: www.nature.com/articles/s41...

Juan Inda (@bigdatabiology.bsky.social) will discuss how the choice of ARG annotation tool influences resistome profiles derived from metagenomic data. (More context in the thread below) See you at #MVIF 52! cassyni.com/s/mvif-52

Have a look at all the cute #nudibranchs pictures in our article just published in Microbiome! 🤩 We applied #museomics to a large collection of nudibranchs and discovered novel symbionts @i2sysbio.es @uv.es @csic.es #microsky #bioinformatics 👩‍🔬🦠🧪🧬🖥️🦑 🧵⬇️ link.springer.com/article/10.1...

Great work by @georginajoyce.bsky.social @sjmcilroy.bsky.social and team. The metabolic flexibility/ease of HGT in Methanoperedenaceae keeps us on our toes :). Arsenate reduction coupled to anaerobic oxidation of methane by members of the Methanoperedenaceae academic.oup.com/ismej/articl...

A genomic catalog of Earth’s bacterial and archaeal symbionts #symbiosis www.nature.com/articles/s41...

Interested in #archaea, #methane, #cell-envelopes? New paper out @nature.com ! We discovered an enzyme that specifically cleaves the cell wall of methanogens, revealing a new chemical structure of archaeal peptidoglycan, 50 yrs after its first description www.nature.com/articles/s41... #MicroSky 🧵👇

Our description of fire amoeba, 𝘐𝘯𝘤𝘦𝘯𝘥𝘪𝘢𝘮𝘰𝘦𝘣𝘢 𝘤𝘢𝘴𝘤𝘢𝘥𝘦𝘯𝘴𝘪𝘴, is now online at Cell! Thanks @oliverio.bsky.social and amazing team for questioning the limits of eukaryotes! 🔥 www.cell.com/cell/fulltex...

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

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/...

"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...

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

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

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 🧵👇

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

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 🔗

"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."

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

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

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...

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

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.

@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

The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...

Global warming boosts freshwater methane production. Now, a study shows that methane oxidizing bacteria cannot increase their methane consumption rates enough in response to warming-induced enhancement of methane availability, leading to higher emissions. www.nature.com/articles/s41...

A bit delayed announcement, but we recently released SemiBin 2.30! No big new features, but it contains a large number of small fixes and improvements (include having had all major LLMs audit and improve the code) bioconda & pypi packages have been updated too github.com/BigDataBiolo...

If you do any work with DNA sequencing at some point, you need to assemble the reads. Usually, we just use the contigs, but that ignores important evidence from your data, so @vijinim.bsky.social wrote agtools to explore the assembly graph and learn more! academic.oup.com/bioinformati...