📢 Applications open! Join us for our upcoming Viromics Workshop! 🧬 Learn cutting-edge metagenomic assembly, viral identification, and annotation pipelines. 🗓️ Dates: Oct 14-16 ⏰ (Extended) Deadline: Aug 20, 2026 🔗 Apply here: forms.gle/pJFLDCNEBvAe... #Viromics #Bioinformatics #AcademicSky

After four years, several updates and a handful of CRAN releases, 𝗹𝘁𝗰 𝗰𝗼𝗹𝗼𝗿 𝗽𝗮𝗹𝗲𝘁𝘁𝗲 𝗥-𝗽𝗮𝗰𝗸𝗮𝗴𝗲, reached a version I feel genuinely good about sharing with the community. github.com/loukesio/ltc...

🚨VIROMICS WORKSHOP 2026🚨 Application is now OPEN for the 8th International Viromics Workshop, Oct. 14-16, 2026, in-person at Ohio State University. Application closes Aug. 7. Apply: forms.gle/pJFLDCNEBvAe... Full details: u.osu.edu/viruslab/vir... #viromics #viruses #ecology #workshop

Introducing nail - a Rust implementation of profile HMM sequence alignment for proteins. Near-HMMER sensitivity, but a lot faster: www.biorxiv.org/content/10.1... github.com/TravisWheele...

Happy to share a new preprint on work from the past few months: In this work, we define the Min-Frame Transformation (MFT), which allows us to transform nucleotide sequences such that mutations between sets of sequences can be effectively masked. www.biorxiv.org/content/10.6... 1/n

Glad that our paper is out today in @cp-cellhostmicrobe.bsky.social A baby received a routine course of amoxicillin. In that infant's #gut 💩, we could see something remarkable, already present **before** the antibiotic arriveda single strain 🦠 of #Akkermansia muciniphila was already running 1/n

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

Ni et al. show that epigenetic phase variation (ePV)—gene expression changes mediated by bacterial DNA methylation—is prevalent in the human gut microbiome and associated with fluctuating environments...

cell.com

I worry that we scientists aren't thinking enough about lab notebooks. Most setups are a headache and don't faithfully preserve the scientific record. Why aren't we just running everything on markdown? Blog 📣: tiszalab.github.io/posts/markdo... Lab Notebook Framework 📓: github.com/tiszalab/obs...

🚨 preprint alert! check out our new pub on an unusual summer flu outbreak among shorebirds traced with targeted metagenomic sequencing of wastewater. more like this coming soon from our team at @wastewaterscan.bsky.social !

medRxivpreprint@medrxivpreprint.bsky.social · 4mo ago

Divergent avian strains drive an off-season influenza A peak in municipal wastewater https://www.medrxiv.org/content/10.64898/2026.04.02.26350079v1

Cenote-Taker 3's manuscript has now been reviewed and published in @peercomjournal.bsky.social ! 🎉 I love the mission and ethics of PCJ, focusing on rigorous peer review, open access, and author involvement in publishing. I highly recommend it to others! 🧬🖥️ peercommunityjournal.org/item/10.2407...

Mike Tisza@miketisza.bsky.social · 12mo ago

I'm very excited to share our manuscript for Cenote-Taker 3. We show that (1) CT3 quickly and accurately annotates previously uncatalogued virus genomes and (2) finds divergent virus genomes in contiguous assemblies. Virome benchmarks are SO hard, but I think we came up with clever and useful ones.

Studying DNA modification in microbes shouldn't be limited by methodology. 🧬 We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

rdcu.be

Nature Biotechnology@natbiotech.nature.com · 4mo ago

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

_720 Gbp_ marine nanopore metagenome -> 328 circular prokaryotic contigs: using myloasm! Insane work by Lui and Nielsen. Also shows how modern long read assemblies can disentangle coexisting strains and reveal ecological insights.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5mo ago

Contrasting population structures coexist in a strain-resolved estuarine microbiome https://www.biorxiv.org/content/10.64898/2026.03.20.713316v1

New paper 🔔 Collaboration @sullivan-lab.bsky.social Marissa Gittrich led the work Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

🚨 𝗡𝗲𝘄 𝗽𝗿𝗲𝗽𝗿𝗶𝗻𝘁! After years of work, I'm excited share our manuscript "𝗣𝗿𝗲𝗴𝗻𝗮𝗻𝗰𝘆 𝗮𝗻𝗱 𝗘𝗮𝗿𝗹𝘆-𝗟𝗶𝗳𝗲 𝗚𝘂𝘁 𝗩𝗶𝗿𝗼𝗺𝗲 𝗶𝗻 𝘁𝗵𝗲 𝗟𝗶𝗳𝗲𝗹𝗶𝗻𝗲𝘀 𝗡𝗘𝗫𝗧 𝗰𝗼𝗵𝗼𝗿𝘁: 𝗢𝗿𝗶𝗴𝗶𝗻, 𝗣𝗲𝗿𝘀𝗶𝘀𝘁𝗲𝗻𝗰𝗲, 𝗜𝗻𝗳𝗹𝘂𝗲𝗻𝗰𝗶𝗻𝗴 𝗙𝗮𝗰𝘁𝗼𝗿𝘀 𝗮𝗻𝗱 𝗛𝗲𝗮𝗹𝘁𝗵 𝗜𝗺𝗽𝗹𝗶𝗰𝗮𝘁𝗶𝗼𝗻𝘀". doi.org/10.64898/202... A thread🧵👇 (1/11)

Happy to report that we submitted a new manuscript this week. The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social 1/ medrxiv.org/cgi/content/...

Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States

Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this cap...

medrxiv.org

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza. Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.

Worried your ssDNA virus genomes aren't getting enough love? Now they can, thanks to CRESSENT, a new software package from Ricardo Pavan, @sullivan-lab.bsky.social, and I! 🧬💻🧪 Out now: doi.org/10.1099/mgen...

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

Thrilled to share our labor of love over the last 5 years 🤩 Leveraging long-read metagenomics (@nanoporetech.com) we identified some of the most prevalent gut phage families that have previously been overlooked in short-read based studies. [1/5] Read more here: www.biorxiv.org/content/10.6...

What's the science behind our paper? A thread 🧵 1/10 The human gut microbiome plays a major role in immunity, metabolism, and disease risk—but we still don’t fully understand how gut bacteria communicate with our cells.

Pascal Falter-Braun@interactome.bsky.social · 6mo ago

Very happy and proud that our paper “Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation” is out today in #NatureMicrobiology @natmicrobiol.nature.com Paper 👉 t1p.de/v42xb #microbiome #commensal #pathomechanism #T3SS #immune #health #IBD

Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology

Long-read sequence assemblies from metagenomes contain frequent errors.

nature.com

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

nature.com

Check out this work enabling genetic variation analysis at the whole-virome scale. 🧬🖥️ I'm really grateful for getting to play a supporting role behind @ryandoughty.bsky.social and @treangen.bsky.social www.biorxiv.org/content/10.6...

Ryan Doughty@ryandoughty.bsky.social · 8mo ago

Some of my work from the first year of my PhD is out as a preprint, please check it out! Virus evolution is rapid and prolific both across and within individuals. However, a significant amount of variation remains hidden due to computational bottlenecks in read-alignment and variant calling 1/n

Preprint out! Check out our new long-read metagenomic SNP-caller, SNooPy 😀. Work with Chris Quince. Thread 🧵 👉 www.biorxiv.org/content/10.6...

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

academic.oup.com

📢 New preprint is out on bioRxiv 📢: How much does virome prep influence our view of the human gut virome? Short answer: a lot. Long answer: doi.org/10.1101/2025... Different methods lead to distinct community structures, richness, and major virus-host abundance patterns. 🧵 1/5

1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge. Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases

Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

science.org

Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️ www.science.org/doi/10.1126/...

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases

Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

science.org

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 9mo ago

Functional genomics in a microbe that degrades and metabolizes PET plastic https://www.biorxiv.org/content/10.1101/2025.11.11.687616v1