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Reposted by Samuel Aroney

Christina Pavloudi @cpavloud.bsky.social · 1d

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...

🧬🖥️🧪🦠🧫

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Reposted by Samuel Aroney

Microbiome Virtual International Forum @microbiomevif.bsky.social · 2d

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...

Microbiome Virtual International Forum @microbiomevif.bsky.social · 22d

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

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Reposted by Samuel Aroney

Timofey Skvortsov @timskvortsov.bsky.social · 2d

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

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

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Reposted by Samuel Aroney

Physalia-courses@Online @physaliacourses.bsky.social · 2d

@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

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Reposted by Samuel Aroney

Rob Patro @robp.bsky.social · 6d

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...

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.

www.nature.com

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Reposted by Samuel Aroney

Michael Brockhurst @brockhurstlab.bsky.social · 9d

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...

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...

www.biorxiv.org

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Reposted by Samuel Aroney

Physalia-courses@Online @physaliacourses.bsky.social · Jun 30

🚨 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

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Reposted by Samuel Aroney

Maria Dzunkova @dzunkovam.bsky.social · 16d

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

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.

www.nature.com

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Reposted by Samuel Aroney

Tami Lieberman @contaminatedsci.bsky.social · 16d

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...

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...

www.biorxiv.org

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Reposted by Samuel Aroney

Ryan Wick @rrwick.bsky.social · 16d

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

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

doi.org

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Reposted by Samuel Aroney

Pamela Ferretti @pamferretti.bsky.social · 18d

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...

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Reposted by Samuel Aroney

Zamin Iqbal @zaminiqbal.bsky.social · 19d

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

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

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...

www.science.org

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Reposted by Samuel Aroney

Haris Zafeiropoulos @hariszaf.bsky.social · 22d

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

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...

doi.org

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Reposted by Samuel Aroney

Anna Cusco @annacusco.bsky.social · 22d

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...

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...

www.biorxiv.org

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Reposted by Samuel Aroney

Gaurav Diwan @gddiwan.bsky.social · 22d

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

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

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Reposted by Samuel Aroney

Microbiome Virtual International Forum @microbiomevif.bsky.social · 23d

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

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Reposted by Samuel Aroney

Javier Santoyo @jsantoyo.bsky.social · 24d

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

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Reposted by Samuel Aroney

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 24d

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

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...

www.nature.com

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Reposted by Samuel Aroney

Luis Pedro Coelho @luispedrocoelho.bsky.social · 27d

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...

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Reposted by Samuel Aroney

Nature Microbiology @natmicrobiol.nature.com · 27d

#News&Views

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

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

#microsky

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.

www.nature.com

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Reposted by Samuel Aroney

Ruoshi @ruoshiz.bsky.social · 29d

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🧵

Nature Methods @natmethods.nature.com · 29d

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social

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

De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

www.nature.com

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Reposted by Samuel Aroney

AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · Sep 15

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

Alignment algorithms represent a balance between speed and accuracy. We evaluated this balance across aligners, with accuracy measured by suboptimal alignments. We found that the relationship between alignment time (with 30 threads) and suboptimal alignment rates exhibits diminishing returns, where X-Mapper stands out as an outlier, offering the highest accuracy with competitive speed.

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Reposted by Samuel Aroney

Microbiome Virtual International Forum @microbiomevif.bsky.social · Sep 15

#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.

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

www.youtube.com

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Reposted by Samuel Aroney

Alex Loy @loyteam.bsky.social · Sep 11

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

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.

doi.org

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Reposted by Samuel Aroney

Sullivan Lab at OSU @sullivan-lab.bsky.social · Sep 12

🚨 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

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