Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸

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/...

Also, as always, 16S rRNA gene amplicon sequencing != metagenomics

A case for absolute gene expression estimates in microbiome studies using metatranscriptomics Metatranscriptomics is widely used to study the functional dynamics of microbial communities in their natural environment [1–6]. Changes in gene expression

case for absolute gene expression estimates in microbiome studies using metatranscriptomics | The ISME Journal | Oxford Academic https://academic.oup.com/ismej/article/19/1/wraf188/8239678?login=true

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

Postdoctoral researcher: avian microbiomes and reproduction We are looking for a postdoctoral researcher to join our team working on avian reproductive microbiomes at the Netherlands Institute of Ecology (NIOO-KNAW) in the group of Dr. Melissah Rowe. The postd...

3.5-year #Postdoc position on avian microbiomes and reproduction @animalecol-nioo.bsky.social @niooknaw.bsky.social on a fully-funded ERC project focused on understanding the significance of reproductive microbiomes for host biology and fitness. Reach out for more info!

nioo.knaw.nl/en/vacancies...

Want to name a real virus? I have recently discovered 9 new phages which now need names! To enter, you simply need to donate to the Cystic Fibrosis Trust on my JustGiving page (£2 = 1 entry) and share your email with me on donation (see link info). Please share 💚 www.justgiving.com/page/meaghan-c-1

ExcludonFinder: mapping transcriptional overlaps between neighboring genes Abstract. Bacteria regulate neighboring genes via overlapping transcription in untranslated regions (UTRs), forming excludons. This overlap leads to transc

🚨🚨 New paper in @narjournal.bsky.social! 🍾

Excludons are pairs of overlapping genes that block each other’s expression (basically, reverse operons).

We built a tool to identify them in bacterial genomes using transcriptomic data, in an awesome collab led by Iñigo Lasa and Álvaro San Martín.

👇

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments journals.asm.org/doi/full/10.... #jcampubs

Functional amyloid proteins confer defence against predatory bacteria - Nature Escherichia coli uses curli fibres, oligomers of the functional amyloid CsgA, as a barrier to protect against the predatory bacteria Bdellovibrio bacteriovorus and Myxococcus xanthus in a mechanism th...

www.nature.com/articles/s41...

Congratulations, Maryse!

A panel of speakers talking to an audience.

Today at #ASMicrobe, 240 early career scientists from around the world gathered to learn about essential tools and insights to successfully launch and develop their professional careers. Looking to unlock your career potential? Explore ASM's resources! asm.social/2t4

Plasmids, prophages, and defense systems are depleted from plant microbiota genomes - Genome Biology Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. He...

Our new paper is online in Genome Biology:
"Plasmids, prophages, and defense systems are depleted from plant microbiota genomes"
genomebiology.biomedcentral.com/articles/10....

Biofilm architecture determines the dissemination of conjugative plasmids | PNAS Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic res...

Biofilm architecture determines the dissemination of conjugative plasmids: We measured the spatiotemporal spread of plasmids in biofilms and found that plasmids only spread in some biofilm regions!

Collab with lab of @sbigot.bsky.social & Christian Lesterlin
www.pnas.org/doi/10.1073/...

Single-tooth prediction of childhood caries:

• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy

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

The four classes of guanidine riboswitches

Various classes of riboswitches bind the nitrogen-rich compound guanidine, but its physiological significance remains elusive. In #JBacteriology, discover what we know so far about this important compound and open questions to guide future research: asm.social/2rW

New paper out! We searched for cargo across thousands of Type 11 Secretion Systems (T11SS) in Proteobacteria and uncovered 2,500+ predicted secreted proteins, including 6 novel cargo types, with experimental verification of a new surface lipoprotein, Pls. doi.org/10.1099/mgen.0.001406

Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria | mSphere We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in ...

Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria | mSphere https://journals.asm.org/doi/full/10.1128/msphere.00996-24?af=R

Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly

#ISMEJournal from Roman Stocker, Mary Ann Moran labs

academic.oup.com/ismej/advanc...

Sequence-based prediction of intermolecular interactions driven by disordered regions Intrinsically disordered regions (IDRs) in proteins play essential roles in cellular function. A growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of amino acids but is instead ...

Sequence-based prediction of intermolecular interactions driven by disordered regions | Science https://www.science.org/doi/full/10.1126/science.adq8381?af=R

CABO-16S—a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples

CABO-16S—a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples | NAR Genomics and Bioinformatics | Oxford Academic https://academic.oup.com/nargab/article/7/2/lqaf061/8136480?login=true

Functional synonymous mutations and their evolutionary consequences - Nature Reviews Genetics Synonymous mutations, once deemed neutral, have been shown to influence gene expression and organismal fitness by affecting transcription, mRNA processing, translation and protein folding. In this Perspective, the authors highlight evidence for fitness effects of synonymous mutations and discuss resulting implications for evolutionary and disease genetics.

Functional synonymous mutations and their evolutionary consequences | Nature Reviews Genetics https://www.nature.com/articles/s41576-025-00850-1

Complex archaea that bridge the gap between prokaryotes and eukaryotes - Nature This study identifies a clade of archaea that is the immediate sister group of eukaryotes in phylogenetic analyses, and that also has a repertoire of proteins otherwise characteristic of eukaryotes—pr...

On this day, 10 years ago, my lab published the @nature.com paper reporting the discovery of the Asgard archaea (Lokiarchaeota at the time), revealing the archaeal nature of eukaryotic cells, and reshaping the Tree of Life. What a ride it has been since then... www.nature.com/articles/nat...

LoVis4u: a locus visualization tool for comparative genomics and coverage profiles Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task

Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...