Matteo Ciciani
@matteo-ciciani.bsky.social
PhD student @cibiocm.bsky.social and @g-eu-diting.bsky.social | Working on #CRISPR, MGEs and metagenomics.
Reposted by Matteo Ciciani
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/...
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
November 14, 2025 at 2:25 PM
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/...
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Reposted by Matteo Ciciani
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
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.
www.nature.com
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Matteo Ciciani
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
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org
Welcome to Day 1 of 'The mobile genome: genetic and physiological impacts of transposable elements'! 🧬
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
November 4, 2025 at 8:25 PM
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
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!
The prototypic crAssphage is a linear phage-plasmid
New work demonstrates that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid w/ broad host range
www.cell.com/cell-host-mi...
New work demonstrates that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid w/ broad host range
www.cell.com/cell-host-mi...
The prototypic crAssphage is a linear phage-plasmid
Schmidtke et al. demonstrate that C. communis, a ubiquitous human gut phage that evades
conventional plaque-based isolation, predominately replicates as a low-copy linear
phage-plasmid with a broad ho...
www.cell.com
July 29, 2025 at 5:00 PM
Wow 🤯 crAssphage is a linear phage-plasmid!
Reposted by Matteo Ciciani
🧬🖥️ 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
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
July 4, 2025 at 9:11 AM
🧬🖥️ 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
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
Reposted by Matteo Ciciani
🧬🌽 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
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
June 16, 2025 at 3:14 PM
🧬🌽 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
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
Reposted by Matteo Ciciani
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
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 ...
www.nature.com
June 3, 2025 at 10:43 AM
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
Reposted by Matteo Ciciani
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...
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...
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…
www.sciencedirect.com
April 30, 2025 at 4:15 PM
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...
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...
Reposted by Matteo Ciciani
🥁 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!
@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!
Thrilled to share our review (with @mireiavallesc.bsky.social and Nicola Segata) on "Human microbiome acquisition and transmission" just published @naturerevmicro.bsky.social
March 21, 2025 at 6:00 PM
🥁 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!
@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!
Reposted by Matteo Ciciani
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...
doi.org/10.1101/2025...
doi.org
February 12, 2025 at 4:00 PM
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...
doi.org/10.1101/2025...
Reposted by Matteo Ciciani
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!
✍️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!
a sign that says `` join us '' on a black background .
Alt: a sign that says `` join us '' on a black background .
media.tenor.com
January 15, 2025 at 1:17 PM
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!
✍️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!
Reposted by Matteo Ciciani
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:
January 17, 2025 at 6:43 PM
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:
Reposted by Matteo Ciciani
🧵 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...
www.nature.com/articles/s41...
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.
www.nature.com
January 7, 2025 at 9:30 AM
🧵 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...
www.nature.com/articles/s41...
Reposted by Matteo Ciciani
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...
www.nature.com/articles/s41...
January 6, 2025 at 4:07 PM
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...
www.nature.com/articles/s41...
Reposted by Matteo Ciciani
🦠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
⬇️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
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.
rdcu.be
January 6, 2025 at 10:24 AM
🦠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
⬇️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
Reposted by Matteo Ciciani
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...
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...
November 28, 2024 at 12:32 PM
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...
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...
Reposted by Matteo Ciciani
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 🧪
November 24, 2024 at 4:08 PM
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 🧪