Samuel Aroney

Priority effects inhibit the repeated evolution of phototrophy - npj Complexity npj Complexity - Priority effects inhibit the repeated evolution of phototrophy

New 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...

LAUNCH 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!

DISCOVER 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 by language, and a refreshed visual design that aligns with Zooniverse’s evolving front-end experience. Read on to learn more or go explore the new Projects page at…

DISCOVER 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…

mvif 46 program

It'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

The 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)

Present 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

🚨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

Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...

New 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...

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Really important read for people working with long-read MAGs.
www.nature.com/articles/s41...

A free, open-access library of high-quality organism illustrations for science communication We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...

A free, open-access library of high-quality organism illustrations for science communication

Landmark 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.

New 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...

Our Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!

🎉 The #SeqCode has reached a significant milestone: with the validation of the genus Skiveiella, a total of 1,000 #names have now been validly published under the SeqCode.

This achievement marks a major step forward in the adoption and impact of the SeqCode within the scientific community.

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!

eggNOG v7: phylogeny-based orthology predictions and functional annotations Abstract. The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database is a phylogenomic resource for orthology inference, evol

From @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-...

trophy backlit by coloured lights

Researcher of the year slide

A 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.

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

Some 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. https://scim.ag/4omApQ7

An Asgard Archaeon (Lokiarchaeum ossiferum) growing and retracting its arms

The Microflora Danica atlas of Danish environmental microbiomes - Nature Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.

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...

Happy 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.

metaTraits: a large-scale integration of microbial phenotypic trait information Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is

metaTraits: a large-scale integration of microbial phenotypic trait information

academic.oup.com/nar/advance-...

Out 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.

🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.” 

Explore the full study: https://doi.org/10.1093/bioadv/vbaf280

Celebrating 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

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our 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
🖥️🧬🦠

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob

Congrats @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/...

A stylized infographic showing the workflow for building a global soil plasmidome resource on the left and a textured world map on the right. The workflow depicts three input data streams from metagenomic datasets and isolate plasmids, which pass through steps like quality control, clustering, functional annotation, CRISPR analysis, host assignment, and detection of gene categories such as biosynthetic clusters, antimicrobial resistance, antimicrobial peptides, and CAZymes. All outputs feed into a central SQL database. The world map shows sample locations across the globe as teal circles of varying size, highlighting regions from many plasmids were recovered. Adapted from Fig 1A and 1B in Fiamenghi et al., doi:10.1038/s41467-025-65102-6

Soils 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...

SingleM 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.

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

Curious 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 👇