Samuel Aroney

Save the Whales. But Save the Microbes, Too.

Microbes 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...

Another 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!

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very 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.

If 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...

🧬🖥️🧪🦠🧫

THIS 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...

Nature Communications paper: 𝗣𝗿𝗼𝗙𝗹𝗲𝘅 𝗮𝘀 𝗮 𝗹𝗶𝗻𝗴𝘂𝗶𝘀𝘁𝗶𝗰 𝗯𝗿𝗶𝗱𝗴𝗲 𝗳𝗼𝗿 𝗱𝗲𝗰𝗼𝗱𝗶𝗻𝗴 𝗽𝗿𝗼𝘁𝗲𝗶𝗻 𝗱𝘆𝗻𝗮𝗺𝗶𝗰𝘀 𝗶𝗻 𝗻𝗼𝗿𝗺𝗮𝗹 𝗺𝗼𝗱𝗲 𝗮𝗻𝗮𝗹𝘆𝘀𝗶𝘀

Superb 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

@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

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

The 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...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...

🚨 Join us for the Environmental Metagenomics course (Oct 13–17, online) with @oskolkov.bsky.social & @aroneys.bsky.social !

🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data.

shorturl.at/HOm6X

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

I'm grateful to be part of Data Reuse Consortium contributing to the paper "A roadmap for equitable reuse of public microbiome data" published in Nature Microbiology @natmicrobiol.nature.com. It proposes solutions for the data recycling🧵⬇️
www.nature.com/articles/s41...
#microsky 🧪🦠💻🧬👩‍🔬
@i2sysbio.es

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

Autocycler: long-read consensus assembly for bacterial genomes AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

If you generate or reuse #microbiome data, check out these guidelines for equitable sequence data reuse. Grateful to @alexjprobst.bsky.social and his team for leading this important work and for bringing together 160+ microbiome scientists (myself included) to contribute!

doi.org/10.1038/s415...

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

Apologies, forgot to add the actual paper link!!!!!

www.science.org/doi/10.1126/...

microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis - Genome Biology Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. No...

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published

A Cytoscape app is also available to make your life easier (and prettier)

#microbiome #metabolic-modeling #networks

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

Finally, the results of my postdoc at the
@bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.

See our new preprint:
www.biorxiv.org/content/10.1...

Number of genes, domains and pathways gained at every node of a cladogram of 508 species

Pleased to announce that our #preprint on the evolutionary history of gene functions is now online at #bioRxiv! We overlayed functional annotations on the evolutionary history of ~4.5M genes from 508 species across the tree of life and found some very cool stuff!

tinyurl.com/FuncEvol

🧵 1/10

MVIF 42 program

It's Monday!
...and a new #MVIF program is out! 🤩

Free registration: cassyni.com/s/mvif-42

⭐️ Highlights:
🇦🇺 @gbouras13.bsky.social
🇺🇸 Danica Schmidtke

⭐️ Keynote:
🇺🇸 Peter Turnbaugh

⭐️ Talks:
🇸🇬 Minghao Chia
🇺🇸 @arzamasovalex.bsky.social ‪
🇳🇿 Brooke Wilson

Autocycler: long-read consensus assembly for bacterial genomes. #LongRead #SequneceData #GenomeAssembly #ConsensusAssembly #BacterialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out!

Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases

doi.org/10.1101/2025...

A nitrogen-fixing bacterium forms symbioses on land and at sea - Nature Microbiology Discovery of a marine diatom-associated Bradyrhizobium that nodulates a terrestrial legume expands our understanding of the environmental and host range of nitrogen-fixing symbioses.

#News&Views

A marine diatom-associated Bradyrhizobium can nodulate a terrestrial legume, expanding understanding of nitrogen-fixing symbioses

www.nature.com/articles/s41...

#microsky

Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky

GloMiNe 2025 by Microbiota Vault and MVIF - 9th/11th September 2025 - YouTube

#GloMiNe recordings now available!!

@cassyni.bsky.social ▶️ cassyni.com/s/mvif-glomi...

YouTube ▶️ www.youtube.com/playlist?lis...

@microbiotavault.bsky.social #MVIF

Thanks @tosina.bsky.social for putting all up.

Iron-respiring microbes could have a role in sulfur cycling A species of bacteria grows when both ferrihydrite and sulfide are present, but not when either is absent.

Nice summary from Songcan & Marc 🙏 on our discovery of a new microbial energy metabolism 🦠 🧫 ⚡ 🔌

Microbial Iron oxide respiration coupled to Sulfide Oxidation (MISO)

@nature.com Research Briefing 😍 doi.org/10.1038/d415...

📰 Original paper www.nature.com/articles/s41...

#microsky #microbiomesky

🚨 New tool for viral genomics!

Meet CLAE: a high-fidelity Nanopore sequencing strategy that pushes accuracy to Q30, boosts throughput >800 Mb/100 pores, and recovers full-length viral genomes from complex samples 🌊🦠

👉 [https://doi.org/10.1002/advs.202505978]

#viromics #nanopore #genomics

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...