Matteo Ciciani

An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...

great to be at the #EMBOMobileGenome meeting in Heidelberg with a wonderful bunch of colleagues, speakers and attendees.
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org

Wow 🤯 crAssphage is a linear phage-plasmid!

🧬🖥️ Postdoc positions available SOON!!
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics

Barbara McClintock portrait

🧬🌽 Happy Transposon Day! 🌽🧬

Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...

🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!

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

🧵⬇️

1/6

Global genetic structure of human gut microbiome species is related to geographic location and host health The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...

🥁 NEW

@vheidrich.bsky.social @mireiavallesc.bsky.social and Nicola Segata described the state-of-the-art of human microbiome transmission, including approaches and challenges associated with microbiome transmission analysis!

New #preprint from the lab! Do you want to see the invisible? So did we! When DNA genomes get broken, cells somehow find related sequences to fix the break. But how do they find it? We developed a way to look at sequence *search*, not just sequence usage.
doi.org/10.1101/2025...

a sign that says `` join us '' on a black background . Alt: a sign that says `` join us '' on a black background .

JOIN US!

✍️Two predoc positions:

lavoraconnoi.unitn.it/en/research-...

✍️Two postdoc positions:

lavoraconnoi.unitn.it/en/research-...

lavoraconnoi.unitn.it/en/research-...

Deadline for application: January 31

Feel free to contact Nicola Segata for any Qs!

In a great collaboration with @hummerlab.bsky.social and the Kräusslich lab: HIV capsid doesn't break at the NPC; instead, it cracks open the NPC itself! Details in Cell: authors.elsevier.com/sd/article/S... @mpibp.bsky.social @uniheidelberg.bsky.social A thread below:

Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals - Nature Microbiology Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.

🧵 How does being a #vegan, #vegetarian or omnivore impact your gut #microbiome? 🥦 Find out in our new paper on gut microbiome signatures of vegan, vegetarian & omnivore diets & associated health outcomes across 21,561 individuals in @naturemicrobiol.bsky.social!🎉 1/10

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

The gut microbiome signature from different diets in 20,000 individuals. Red meat intake correlated with reduced cardiometabolic health; the opposite for plant-based foods or in omnivores with enriched plant-based intake
www.nature.com/articles/s41...

Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons Nature Microbiology - Structural and phylogenetic analyses show that programmable RNA modifications ubiquitous in archaea and eukarya arose from bacterial transposons.

🦠Bacteria serve as an amazing reservoir of immune genes for eukaryotes but also of essential cellular functions!

⬇️New exaptation example : euk RNA-guided RNA modification originated from "bridge RNA" IS110 transposons.

Led by @hugovaysset.bsky.social and C. Meers from Sternberg lab! rdcu.be/d5ovZ

Very excited to share the first story from my postdoc where we uncover the structural basis for slow Cas9 turnover!

We use kinetics-guided cryo-EM to capture 25 conformational states of SpCas9 from a single dataset - including the first look at Cas9 releasing product.

biorxiv.org/content/10.1...

This is figure 1, which shows the consistent global links between coffee consumption and the human gut microbiome.

Coffee consumption is associated with the presence and abundance of a specific member of the human gut microbiome, Lawsonibacter asaccharolyticus, and changes to the plasma metabolome, according to a paper in Nature Microbiology. https://go.nature.com/3CIl4as 🧪