Samuel Aroney
@aroneys.bsky.social
Postdoc at Centre for Microbiome Research at QUT. Bioinformatics, metagenomics, Bin Chicken, permafrost...
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
Reposted by Samuel Aroney
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
🖥️🧬🦠
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
🖥️🧬🦠
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
doi.org
November 21, 2025 at 4:21 PM
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
🖥️🧬🦠
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 Aroney
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/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
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
academic.oup.com
November 20, 2025 at 8:50 AM
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/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
Reposted by Samuel Aroney
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...
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...
November 18, 2025 at 7:18 PM
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...
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 Aroney
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.
Microbial fraction is now prokaryotic fraction, easier to specify input genomes.
November 17, 2025 at 4:49 AM
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.
Microbial fraction is now prokaryotic fraction, easier to specify input genomes.
Reposted by Samuel Aroney
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 👇
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 👇
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...
doi.org
July 2, 2025 at 10:07 AM
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 👇
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
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
November 13, 2025 at 10:09 AM
“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
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Reposted by Samuel Aroney
Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology
www.cell.com/trends/micro...
www.cell.com/trends/micro...
November 12, 2025 at 2:10 AM
Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology
www.cell.com/trends/micro...
www.cell.com/trends/micro...