Lightnews — Scholar-powered news

Reposted by Samuel Aroney

Michael Brockhurst @brockhurstlab.bsky.social · 3d

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 · 10d

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 · 9d

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 · 10d

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 · 12d

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 · 13d

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 · 16d

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 · 16d

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 · 16d

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 · 17d

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 · 17d

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 · 18d

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 · 21d

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 · 21d

#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 · 22d

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 · 22d

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 · 24d

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 · 24d

#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 · 28d

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 · 26d

🚨 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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Reposted by Samuel Aroney

Jim Shaw @jimshaw.bsky.social · Sep 7

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

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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Reposted by Samuel Aroney

Zamin Iqbal @zaminiqbal.bsky.social · 29d

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...

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.

www.nature.com

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Reposted by Samuel Aroney

Microbiome Virtual International Forum @microbiomevif.bsky.social · 28d

#MVIF abstract submission is always open:

- OCTOBER: Pacific-first event w/ Peter Turnbaugh
Deadline: 13/09/2025

- NOVEMBER: Atlantic-first event w/ @deepaagashe.bsky.social
Deadline: 12/10/2025

For any question, feel free to write to us [email protected]

docs.google.com/forms/d/e/1F...

MVIF Abstract Submission

More info on the MVIF website https://microbiome-vif.org, if you have any questions, please email us at [email protected] You can always submit your work. Check which events are accepting abs...

docs.google.com

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Reposted by Samuel Aroney

Lingchen He 何灵尘 @lingchenhe.bsky.social · 29d

We discovered a new horizontal gene transfer mechanism: tail-less cf-PICIs hijack free phage tails extracellularly, forming infectious chimeric virions that drive both intra- and inter-species transfer among bacteria. @jonaszpatkowski.bsky.social @tcostalab.bsky.social @jrpenades.bsky.social

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Reposted by Samuel Aroney

Falk Hildebrand @bioinf.bsky.social · 29d

How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1...

Massive thanks to Klara for driving this

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