Mike Tisza

🚨 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)

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...

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
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medrxiv.org/cgi/content/...

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

Research institutions have some capacity to buffer this in the short term, and that's happening in many places. I believe each institution is estimating the **long term** value of the external funding ecosystem and buffering/cutting research accordingly.
Just a guess fwiw.

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.

GitHub - ricrocha82/cressent: a modular tool to help researchers to automatically annotate ssDNA contigs a modular tool to help researchers to automatically annotate ssDNA contigs - ricrocha82/cressent

CRESSENT is suitable small and large genome collections. We hope that everyone working with these viruses gives it a try. Install with mamba/conda and check out all the documentation on the GitHub repo/ReadTheDocs site:
github.com/ricrocha82/c...
cressent.readthedocs.io/en/latest/

ssDNA virus genomes, especially CRESS-DNA virus genomes, require a unique approach to analysis. We brought together the best methods described in the literature and made CRESSENT. It focuses on recombination, phylogenetics, tanglegrams, motif/stem loop discovery, and preprocessing.

CRESSENT Schematic

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.

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

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

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 ...

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...

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...

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

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

🦠🧪🧬🚨 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-...

📢 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

Gotta be obsidian. There are lots of ways to make the notes beautiful and functional. And i love using templates to increase structure and save time. Version control with github!
Is your issue that you want the code blocks to have a horizontal scroll bar? I imagine there's a plugin for that.

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 ...

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 ...

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/...

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.

Scalable and systematic hierarchical virus taxonomy with vConTACT3 Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

Untargeted longitudinal ultra deep metagenomic sequencing of wastewater provides a comprehensive readout of expected and unexpected viral pathogens Wastewater surveillance has become a powerful tool to monitor circulating viruses at a community level. Currently, most wastewater surveillance efforts use target-based approaches such as quantitative...

Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?

That is the question we asked in our latest pre-print.

Turns out you can.
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www.medrxiv.org/content/10.1...

We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.

Long-read metagenomics for strain tracking after faecal microbiota transplant Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...

Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!

Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/

📄 rdcu.be/eL8mR

Figure 3. (A–N) Sequencing coverage plots of genetic sequences of viruses detected in indoor air samples of a daycare and phylogenetic analyses of sequences of (O) two human bocaviruses and (P) one RSV identified in some samples, Belgium, January–December 2022

New paper out!

We sampled indoor air for a year in a Belgian daycare and used shotgun metagenomics to track viruses. We recovered many viral genomes of interest.

What would you sample next?

Read at @eurosurveillance.org
@emmanuel-microb.bsky.social, @jellematthijnssens.bsky.social
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Wastewater Sequencing Reveals Persistent Circulation and Rising Prevalence of Several Oncogenic Viruses Across Texas https://www.medrxiv.org/content/10.1101/2025.09.17.25335998v1

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

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