Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸

Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉

How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬
www.nature.com/articles/s41...

A jumbo cyanophage encodes the most complete ribosomal protein set in the known virosphere www.biorxiv.org/content/10.1...

The plastic pollution crisis and unanswered questions about the increased risk of
—Cancer
jci.org/articles/vie...
—Neurodegenerative diseases
jci.org/articles/vie...

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself.

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

Photoholes within cyanobacterial mats can account for the origin of #anammox bacteria and ancient #nitrogen loss link.springer.com/article/10.1...

The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term use and broad ad...

A must read! The constant and often irrational renaming of microbes is out of control, and bad for microbiology and microbiologists.
journals.asm.org/doi/10.1128/...

Visualizing pairwise genome comparisons? No need to run BLAST separately anymore! 🧬
​#gbdraw has implemented #LOSAT, a WASM-powered Rust reimplementation of BLASTN/TBLASTX.
​✅ No local installation
✅ No data transfer (Serverless)
​Try it here: gbdraw.app

Organohalide respiration by a Desulforhopalus-dominated community academic.oup.com/ismej/advanc... #jcampubs

A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...

How bacteria evolved thousands of precision nanoinjectors?

Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).

Bacteriophages mobilize bacterial defense systems via lateral transduction Bacteriophages and PICIs spread bacterial defenses via lateral transduction, shaping microbial immunity and pathogen evolution.

Very interesting paper. www.science.org/doi/10.1126/...

The Shingles vaccine has outperformed all expectations. Why?
erictopol.substack.com/p/spotlight-...

GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate

🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.

libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix

github.com/ebiggers/lib...

Tuberculosis: A surprising new hiding place for a dangerous pathogen

The bacterium that causes TB can hide in liver cells called hepatocytes and reprogram their metabolism for its own benefit.

buff.ly/DjdnT51

A commensal bacterium secretes effector proteins to establish population heterogeneity in the gut Zagieboylo and colleagues demonstrate that the human commensal Bacteroides thetaiotaomicron secretes two self-targeting proteins that induce heterogeneity within its own population. Differential expre...

#microsky 😳

www.cell.com/cell-host-mi...

Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda infection and uncover a conserved phage-encoded sRNA that activates host replication machinery. Their findings re...

Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...

This is a disaster. I would not be where I am today without the constructive (and yes, sometimes frustrating) reviews my NSF proposals received as a young investigator. This feedback didn't come from the POs but rather the peer reviewers and panelists who saw how I was trying to enter the field

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?

doi.org/10.1093/narg...

Phages are full of genes of unknown function that are likely adaptive in specific conditions.
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh

Systematic discovery of TIR-based immune signaling systems in bacteria Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...

I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life.

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-...

anvi-report-circularity An anvi'o program. Predict contig circularity from paired-end read alignments in a given BAM file.

Need to predict whether a given contig in your assembly was circular in the environment?

Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity:

anvio.org/help/main/pr...

All the world’s a phage | PNAS A renewed interest in bacteriophages has emerged from the explosive discovery of the complex pan-immune bacterial defense system and a revival of t...

#microsky #phagesky
Mycobacterium #phage review by Graham Hatfull covering the state of the art

www.pnas.org/doi/10.1073/...

The Penicillin Myth Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.

Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?

Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Plastic degradation by enzymes from uncultured deep sea microorganisms Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are

A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT.

We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)

Genome-wide bacterial genetic interaction mining by dual Tn-seq | Nature Methods https://www.nature.com/articles/s41592-025-02921-x

Pull requests · hadley/genzplyr dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

Y’all these genzplyr PRs are off the hook: github.com/hadley/genzp...

"If you think research is expensive, try disease!"
🧪 #NIH #CDC #PEPFAR #NIHR @who.int

Microbes without borders: uniting societies for climate action | mBio The climate crisis is one of the most urgent and complex challenges of our time. Although often overlooked in models and policy, microorganisms play a critical role in climate dynamics. They are sensi...

Microbiology societies from five continents recently met at @asm.org HQ in DC for the inaugural Global Strategy Meeting on Microbes and Climate Change. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.
journals.asm.org/doi/10.1128/...