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...

Apologies, forgot to add the actual paper link!!!!! www.science.org/doi/10.1126/...

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

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...

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

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...

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...

#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 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.

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

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...

#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...

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

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

Tomorrow begins #GloMiNe2025 organized by @microbiotavault.bsky.social & #MVIF Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social Pacific session by Safarina Malik & Célio Dias Santos Júnior Both sessions will be LIVE! Check the details: cassyni.com/s/mvif-glomi...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations. www.biorxiv.org/content/10.1... #microbesky #microbiomesky

Season 5 is going to start 🔜 Check out the program and feel free to join the keynotes by presenting your work–abstract submission is open www.microbiome-vif.org/en-US/-/info... @kathlemon.bsky.social ‬ @saramitri.bsky.social @simrouxvirus.bsky.social @halllab.bsky.social @deepaagashe.bsky.social

Our @i2sysbio.es team published in #ISME Communications @isme-microbes.bsky.social 🥳 our new versatile tool #CleanBar for demultiplexing of split-and-pool barcoding in #singlecell omics. #microsky 🧬🖥️🦠🧪👩‍🔬 🌐 academic.oup.com/ismecommun/a... 🧵⬇️

Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social ‬and #MVIF is OUT: cassyni.com/s/mvif-glomi... 1/3

🥁 We’re thrilled to announce the beginning of #MVIF Season 5 with #GloMiNe2025 event jointly organized by @microbiotavault.bsky.social and #MVIF Save the date: 9 & 10/11 September 2025 & register here: cassyni.com/s/mvif-glomi...

This is a major issue is that the incentives are to output false positives in your tools If you need to survive on having many citations to your tools, it is better if your tool gives users lots of results so that they cite it! open.substack.com/pub/luispedr...

Our work on direct @nanoporetech.com sequencing of non-canonical bases in now out in @natcomms.nature.com! Read all about it here: nature.com/articles/s41... Great collab with Chew and Hirao lab x.com/NiranjanTW/s...

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob #phagesky #microsky journals.asm.org/doi/epub/10....

Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports... PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.

GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction. #Genomics #Rust #GenomeAnnotation #GFF #GenomicFeatures @biorxiv-bioinfo.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

skani v0.3.0 is released. github.com/bluenote-157... - 30-40% potential reduction in memory with approximately the same runtime. - Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.

Very happy to announce our new paper on the evolution of metabolism is out now! royalsocietypublishing.org/doi/10.1098/... With @tweethinking.bsky.social @sabifo4.bsky.social @ssolo.bsky.social Davide Pisani, Tim Lenton and @phil-donoghue.bsky.social (1/2)

In our ongoing saga of description of new protists, we are happy to introduce Multisulcus malaysiensis, a deep-branching heterolobosean that forms highly unusual multiflagellated cells with multiple ventral grooves. Great work by @kristina-prokina.bsky.social onlinelibrary.wiley.com/doi/epdf/10....

At the request of @bradleyph.bsky.social, we have now added the Bacterial and Archaeal trees (credit to @aroneys.bsky.social) used to infer the GlobDB taxonomy to the website globdb.org Feel free to reach out if there's other resources you'd like to see added. No promises, but happy to chat 🖥️🧬🦠

New preprint up now! Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota www.biorxiv.org/content/10.1...

Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota

Synteny-aware functional annotation of bacteriophage genomes with Phynteny https://www.biorxiv.org/content/10.1101/2025.07.28.667340v1

Biologist folk (especially in evolutionary biology and/or ecology, but it don’t matter): Can you give me your favorite examples of trade offs in biology? Organism or system don’t matter. Primary literature or reviews preferred.

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1... and GH repo: github.com/refresh-bio/...

Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications. www.pnas.org/doi/10.1073/...

Back in 1962 microscopy was used to pen a hypothesis about eukaryote-microbe relationships. ~65 years later we have coupled the latest advancements in long read MetaG, MetaP and EUK SAGs to help explain what this means for wider rumen microbiome function www.nature.com/articles/s41...

New sylph pre-built databases + taxonomy available for: - GTDB-R226 (143k prok. species) - GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social ) - UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social ) Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)

Are any of my followers aware of microbes that code for aerobic metabolism but can not grow aerobically? That is are there physiologically obligate anaerobes that contain genetic machinery for oxidative metabolism? #microsky

Our new preprint is out! www.biorxiv.org/content/10.1... In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide. @podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social

@ace-gtdb.bsky.social R226-based profiles from 700k public metagenomes are at sandpiper.qut.edu.au. Search for your fave microbe by GTDB taxonomy there and see to get prevalence and community profiles. Got something novel? Get in touch.

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

If you missed some of the talks from Season 1️⃣, 2️⃣, 3️⃣ OR 4️⃣ you can find most of them on the #MVIF YouTube channel www.youtube.com/@MicrobiomeV... and @cassyni.bsky.social platform: cassyni.com/c/mvif/series (🤫 we are preparing Season 5️⃣) See you in September!