Samuel Aroney
@aroneys.bsky.social
Postdoc at Centre for Microbiome Research at QUT. Bioinformatics, metagenomics, Bin Chicken, permafrost...
Reposted by Samuel Aroney
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...
www.nature.com/articles/s44...
Priority effects inhibit the repeated evolution of phototrophy - npj Complexity
npj Complexity - Priority effects inhibit the repeated evolution of phototrophy
www.nature.com
February 3, 2026 at 9:37 PM
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...
www.nature.com/articles/s44...
Reposted by Samuel Aroney
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!
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!
January 26, 2026 at 2:57 PM
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!
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 Aroney
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…
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…
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…
blog.zooniverse.org
January 27, 2026 at 8:25 PM
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…
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 Aroney
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
...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
January 23, 2026 at 11:53 AM
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
...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 Aroney
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)
doi.org/10.1038/s415...
(1/2)
January 20, 2026 at 4:49 PM
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)
doi.org/10.1038/s415...
(1/2)
Reposted by Samuel Aroney
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
isme-microbes.org/call-for-abs...
#microbialecology #isme20
January 15, 2026 at 3:15 PM
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
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
- >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
January 12, 2026 at 4:34 PM
🚨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
- >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 Aroney
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...
www.biorxiv.org/content/10.6...
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...
www.biorxiv.org
January 7, 2026 at 6:58 PM
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...
www.biorxiv.org/content/10.6...
Reposted by Samuel Aroney
Really important read for people working with long-read MAGs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
www.nature.com
January 6, 2026 at 6:05 AM
Really important read for people working with long-read MAGs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Samuel Aroney
A free, open-access library of high-quality organism illustrations for science communication
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...
doi.org
December 29, 2025 at 6:03 PM
A free, open-access library of high-quality organism illustrations for science communication
Reposted by Samuel Aroney
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.
December 4, 2025 at 10:17 AM
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.
Reposted by Samuel Aroney
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...
🔗 DOI: www.biorxiv.org/content/10.6...
December 15, 2025 at 8:19 AM
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...
🔗 DOI: www.biorxiv.org/content/10.6...
Reposted by Samuel Aroney
Our Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!
Review: Genomics of host–microbiome interactions in humans by @pamferretti.bsky.social ocial, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social
rdcu.be/etIRy
rdcu.be/etIRy
Genomics of host–microbiome interactions in humans
Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...
rdcu.be
December 15, 2025 at 9:54 PM
Our Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!
Reposted by Samuel Aroney
🎉 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.
This achievement marks a major step forward in the adoption and impact of the SeqCode within the scientific community.
December 13, 2025 at 6:11 AM
Reposted by Samuel Aroney
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!
Thank you to @ebi.embl.org for support with setting up these links!
ENA Browser
ENA Browser
www.ebi.ac.uk
December 11, 2025 at 3:04 PM
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!
Thank you to @ebi.embl.org for support with setting up these links!
Reposted by Samuel Aroney
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-...
⬇️
academic.oup.com/nar/advance-...
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
academic.oup.com
December 9, 2025 at 1:39 PM
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-...
⬇️
academic.oup.com/nar/advance-...
Reposted by Samuel Aroney
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.
December 9, 2025 at 8:23 AM
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.
Reposted by Samuel Aroney
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
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 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...
scim.ag
November 25, 2025 at 8:24 PM
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
The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7
Reposted by Samuel Aroney
An Asgard Archaeon (Lokiarchaeum ossiferum) growing and retracting its arms
December 3, 2025 at 8:32 PM
An Asgard Archaeon (Lokiarchaeum ossiferum) growing and retracting its arms
Reposted by Samuel Aroney
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...
www.nature.com/articles/s41...
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.
www.nature.com
December 3, 2025 at 8:50 PM
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...
www.nature.com/articles/s41...
Reposted by Samuel Aroney
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.
Join #MVIF 44 – we will discuss diverse #microbiome topics:
human urinary, gut, oral and nasal microbiomes,
extreme environments, and
a new sequence alignment tool.
It's Monday!
...and a new #MVIF program is out! 🤩
Free registration: cassyni.com/s/mvif-44
⭐️ Highlights:
🇺🇸 Vanessa Hale
🇰🇷 Jun Hyung Cha
⭐️ Keynote:
🇺🇸 Katherine Lemon @kathlemon.bsky.social
⭐️ Talks:
🇺🇸 Meenakshi Chakraborty
🇨🇳 Wei Shen @shenwei356.bsky.social
🇺🇸 Johanna Gutleben
...and a new #MVIF program is out! 🤩
Free registration: cassyni.com/s/mvif-44
⭐️ Highlights:
🇺🇸 Vanessa Hale
🇰🇷 Jun Hyung Cha
⭐️ Keynote:
🇺🇸 Katherine Lemon @kathlemon.bsky.social
⭐️ Talks:
🇺🇸 Meenakshi Chakraborty
🇨🇳 Wei Shen @shenwei356.bsky.social
🇺🇸 Johanna Gutleben
December 1, 2025 at 12:21 PM
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.
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 Aroney
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
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
academic.oup.com
November 30, 2025 at 4:47 AM
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Samuel Aroney
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.
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.
November 28, 2025 at 7:32 PM
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.
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: https://doi.org/10.1093/bioadv/vbaf280
Explore the full study: https://doi.org/10.1093/bioadv/vbaf280
November 26, 2025 at 10:01 AM
🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.”
Explore the full study: https://doi.org/10.1093/bioadv/vbaf280
Explore the full study: https://doi.org/10.1093/bioadv/vbaf280
Reposted by Samuel Aroney
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
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
bsky.app
November 23, 2025 at 10:59 PM
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
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