Samuel Aroney
Postdoc at Centre for Microbiome Research at QUT. Bioinformatics, metagenomics, Bin Chicken, permafrost...
- Reposted by Samuel AroneyNew paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects. www.nature.com/articles/s44...
- Reposted by Samuel AroneyLAUNCH DAY🎙️ We're thrilled to share the very first episode of #MVIFconversations w/ Jack Gilbert 💫 Stefanie Malan-Müller & @cpavloud.bsky.social talked with @gilbertjacka.bsky.social about how microbes shape our health and the invisible living world around us. Give it a listen & spread the word!
- Reposted by Samuel AroneyDISCOVER ZOONIVERSE PROJECTS IN A WHOLE NEW WAY We’re happy to introduce an updated Projects page on Zooniverse, designed to make it easier, faster, and more enjoyable to find projects that match your interests. The new page brings together improved navigation, long-requested features like sorting…
- Reposted by Samuel AroneyIt's Friday! ...and a new #MVIF program is out! 🤩 Free registration: cassyni.com/s/mvif-46 Highlights: 🇺🇸 Rebecca L. Knoll 🇯🇵 Akito Sakanaka Keynote: 🇺🇸 @simrouxvirus.bsky.social ⭐️ Talks: 🇦🇺 @jeremyjbarr.bsky.social 🇨🇦 @erikbakkeren.bsky.social 🇨🇳 Guanxiang Liang
- Reposted by Samuel AroneyThe ISME Early Career Scientist Committee is glad to begin the year by spotlighting @aroneys.bsky.social, a Postdoctoral Researcher at QUT, and his paper, “Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.” doi.org/10.1038/s415... (1/2)
- Reposted by Samuel AroneyPresent your research at the 20th International Symposium on Microbial Ecology in Auckland, from 16 - 21 August 2026! When submitting your abstract, make sure to check whether you are eligible for one of the travel grants. isme-microbes.org/call-for-abs... #microbialecology #isme20
- Reposted by Samuel Aroney🚨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
- Reposted by Samuel AroneyNew paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods. www.biorxiv.org/content/10.6...
- Reposted by Samuel AroneyReally important read for people working with long-read MAGs. www.nature.com/articles/s41...
- Reposted by Samuel AroneyA free, open-access library of high-quality organism illustrations for science communication
- Reposted by Samuel AroneyLandmark study in @Nature! 🇩🇰 The "Microflora Danica" project has created the first-ever national microbiome atlas. Led by Aalborg University, @fwf-at.bsky.social CoE Microplanet's Director @michiwagner4.bsky.social, and @daanspeth.bsky.social, Andrew Giguere @cemess.bsky.social analyzed nitrifiers.
- Reposted by Samuel AroneyNew preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...
- Reposted by Samuel AroneyOur Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!
- Reposted by Samuel Aroney
- Reposted by Samuel AroneyGTDB 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!
- Reposted by Samuel AroneyFrom @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓 ⬇️ academic.oup.com/nar/advance-...
- Reposted by Samuel AroneyA lucky year in 2025, and now I've a QUT Faculty of Health Researcher of the Year to prove it. Thank you to the many non-myself people who made it happen.
- Reposted by Samuel AroneySome archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science. The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. scim.ag/4omApQ7
- Reposted by Samuel AroneyAn Asgard Archaeon (Lokiarchaeum ossiferum) growing and retracting its arms
- Reposted by Samuel AroneyMicroflora 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...
- Reposted by Samuel AroneyHappy December! Join #MVIF 44 – we will discuss diverse #microbiome topics: human urinary, gut, oral and nasal microbiomes, extreme environments, and a new sequence alignment tool.
- Reposted by Samuel AroneymetaTraits: a large-scale integration of microbial phenotypic trait information academic.oup.com/nar/advance-...
- Reposted by Samuel AroneyOut after peer-review: www.science.org/doi/full/10.... Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead! We now also account for regression and nested cross-validation, with more extensive benchmarking.
- Reposted by Samuel Aroney🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.” Explore the full study: doi.org/10.1093/bioadv/vbaf280
- Reposted by Samuel AroneyCelebrating Excellence at the Centre for Microbiome Research! We’re thrilled to share that Gene Tyson, @benjwoodcroft.bsky.social and @luispedrocoelho.bsky.social have once again been named Highly Cited Researchers for 2025 by Clarivate! #HighlyCited2025
- Reposted by Samuel AroneyOur paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠
- Reposted by Samuel AroneyCongrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published! proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
- Reposted by Samuel AroneySoils 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...
- Reposted by Samuel AroneySingleM v0.20.2 - ONT/PacBio input reads now supported (if somewhat inefficiently), plus improved Lyrebird database for phage profiling. Microbial fraction is now prokaryotic fraction, easier to specify input genomes.
- Reposted by Samuel AroneyCurious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨 doi.org/10.1038/s414... We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
- “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
- Bin Chicken compares marker gene sequences across metagenomic reads to group samples into coassemblies 🧬🧬 predicted to recover novel genomes 🦠. It can recover rare lineages that can’t be recovered from single-samples and target recovery of particular lineages of interest. 2/
- We used Bin Chicken to screen public 🌍 metagenomes, choosing the best 800 sample-sets for coassembly, and recovered 24,028 novel species 🦠 of Bacteria and Archaea, including the first representatives of 6 phyla and 41 classes. 3/
-
View full threadShoutout to @georginajoyce.bsky.social for creating the amazing Bin Chicken logo! www.georginajoyce.com And thanks to everyone at @cmrqut.bsky.social for your support and @emerge-bii.bsky.social for funding this research!
- Reposted by Samuel AroneyAmazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology www.cell.com/trends/micro...
- Reposted by Samuel Aroney🚨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 👇
- Reposted by Samuel AroneyAnother key challenge in virome research is that most viruses lack taxonomic classification, leading to ad hoc approaches that hinder cross-study comparisons. To address this, we developed a taxonomy-like framework and a tool for assigning user's genomes to UHGV clusters. (4/8)
- Reposted by Samuel AroneyTo facilitate adoption by the community, we provide online tools to allow users to explore UHGV in the browser. If you don't mind using the command line, we also provide all of the data for download :) 🌐 uhgv.jgi.doe.gov (8/8)
- Reposted by Samuel Aroney
- Reposted by Samuel AroneyScientists 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
- Reposted by Samuel AroneyGreat 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-...
- Reposted by Samuel AroneyThe average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology. I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
- Reposted by Samuel Aroney🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"? It said a restriction map was "extremely unlikely to have arisen by random evolution.” I took its claims seriously. The "synthetic fingerprint" hypothesis collapses. My new preprint explains why. arxiv.org/abs/2510.23833
- Reposted by Samuel AroneyWhat can the current global bacterial taxonomy knowledge reveal about the actual (past and present) ecological success of each lineage? | bioRxiv biorxiv.org/content/10.1101/202…
- Reposted by Samuel Aroneymicrofabricated stamps, fresh off the printer :)
- Reposted by Samuel AroneyOur @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-...
- Reposted by Samuel AroneyMicrobes sustain all ecosystems yet they’re nearly absent from conservation frameworks. The @IUCN Microbial Conservation Specialist Group aims to change that. Honored to co-chair this global effort. Great @nytimes piece by Carl Zimmer: www.nytimes.com/2025/10/17/s...
- Reposted by Samuel AroneyAnother great edition of Environmental #Metagenomics is wrapping up! Huge thanks to @oskolkov.bsky.social , @aroneys.bsky.social and all the amazing participants who joined us this week. 🙌 We wish you all the best with your research projects!
- Reposted by Samuel AroneyVery excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
- Reposted by Samuel AroneyIf you feel like contributing your microbial growth data, take a look at μGrowthDB mgrowthdb.gbiomed.kuleuven.be You can also read the preprint: www.biorxiv.org/content/10.1... 🧬🖥️🧪🦠🧫
- Reposted by Samuel AroneyTHIS WEEK see you at #MVIF 42! Tuesday/Wednesday – check the Pacific time and date in your time zone: www.timeanddate.com/worldclock/c... Thursday – check the Atlantic time and date in your time zone: www.timeanddate.com/worldclock/c...
- Reposted by Samuel AroneySuperb news to kick off the week! 🎉 Our new paper is out today in @natcomms.nature.com 𝗣𝗿𝗼𝗙𝗹𝗲𝘅 𝗮𝘀 𝗮 𝗹𝗶𝗻𝗴𝘂𝗶𝘀𝘁𝗶𝗰 𝗯𝗿𝗶𝗱𝗴𝗲 𝗳𝗼𝗿 𝗱𝗲𝗰𝗼𝗱𝗶𝗻𝗴 𝗽𝗿𝗼𝘁𝗲𝗶𝗻 𝗱𝘆𝗻𝗮𝗺𝗶𝗰𝘀 𝗶𝗻 𝗻𝗼𝗿𝗺𝗮𝗹 𝗺𝗼𝗱𝗲 𝗮𝗻𝗮𝗹𝘆𝘀𝗶𝘀
- Reposted by Samuel Aroney@oskolkov.bsky.social & @aroneys.bsky.social have just kicked off the Environmental Metagenomics course! We will cover both read- and assembly-based methods, focusing on the strength of each of these methods depending on the research question, using both #illumina & @nanoporetech.com data
- Reposted by Samuel AroneyThe Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...
