Paolo Stincone
@paolosti.bsky.social
Postodoc at Cluster of Excellence GreenRobust, previous MSCA Fellow, exploring plant - microbiome interactions via multi-omics approaches.
Reposted by Paolo Stincone
Congrats to @turgutmesut.bsky.social @canerbagci.bsky.social and Semih Erdoğmuş for the update and major improvement of ARTs-DB academic.oup.com/database/art... 🥳 Now also including fungal data and a much improved and more intuitive interface!! happy #targetdirectedgenomemining #secmet
ARTS-DB 2.0: an expanded database for target-directed genome mining across bacteria and fungi
Abstract. The increasing prevalence of antimicrobial resistance requires efficient strategies to prioritize biosynthetic gene clusters (BGCs) that may enco
academic.oup.com
September 26, 2026 at 3:19 PM
Congrats to @turgutmesut.bsky.social @canerbagci.bsky.social and Semih Erdoğmuş for the update and major improvement of ARTs-DB academic.oup.com/database/art... 🥳 Now also including fungal data and a much improved and more intuitive interface!! happy #targetdirectedgenomemining #secmet
Reposted by Paolo Stincone
New GreenRobust publication by the group of Eric Kemen on using machine learning to identify beneficial microbiota:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Machine learning reveals biocontrol agents shaping disease outcome in natural Arabidopsis populations - Nature Communications
Plants can recruit beneficial microbes to suppress pathogens, offering a route to rational biocontrol beyond empirical screening. Here, the authors use machine learning to identify disease-associated ...
www.nature.com
July 29, 2026 at 6:03 AM
New GreenRobust publication by the group of Eric Kemen on using machine learning to identify beneficial microbiota:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Paolo Stincone
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies www.biorxiv.org/content/10.6... #jcampubs
July 27, 2026 at 2:57 PM
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies www.biorxiv.org/content/10.6... #jcampubs
Reposted by Paolo Stincone
ENVnet provides a global molecular resource of dissolved organic matter - @berkeleylab.lbl.gov @jgi.doe.gov www.nature.com/articles/s41...
July 21, 2026 at 1:58 PM
ENVnet provides a global molecular resource of dissolved organic matter - @berkeleylab.lbl.gov @jgi.doe.gov www.nature.com/articles/s41...
Reposted by Paolo Stincone
Can the probabilistic reasoning that leads to LLM hallucinations be harnessed for scientific discovery? This work demonstrates that agentic AI can become another tool in the structural elucidation toolbox, generating testable hypotheses for new metabolites. #metabolomics
Preprint: lnkd.in/gJpDdXkP
Preprint: lnkd.in/gJpDdXkP
June 27, 2026 at 3:25 PM
Can the probabilistic reasoning that leads to LLM hallucinations be harnessed for scientific discovery? This work demonstrates that agentic AI can become another tool in the structural elucidation toolbox, generating testable hypotheses for new metabolites. #metabolomics
Preprint: lnkd.in/gJpDdXkP
Preprint: lnkd.in/gJpDdXkP
Reposted by Paolo Stincone
Out Now! Phages tame plant pathogens #MicroSky
Phages tame plant pathogens
Nature Microbiology, Published online: 23 June 2026; doi:10.1038/s41564-026-02395-3Predicting infection heterogeneity requires looking beyond the host. Phage–bacteria coevolution in tomato fields maintains diverse bacterial strategies and explains uneven disease occurrence across plant populations.
go.nature.com
June 24, 2026 at 2:10 AM
Out Now! Phages tame plant pathogens #MicroSky
Reposted by Paolo Stincone
Our study on Bacteroides iron piracy is now out in @pnas.org. We show how surface-exposed lipoproteins bind xenosiderophores with different iron-chelating chemistries and propose a mechanism for xenosiderophore import across the outer membrane. Lots of structures (mostly X-ray this time)!
Structural basis of iron piracy by human gut Bacteroides | PNAS
Iron is an essential element that can be growth-limiting in microbial communities,
particularly those present within host organisms. To acquire iro...
doi.org
May 2, 2026 at 9:22 AM
Our study on Bacteroides iron piracy is now out in @pnas.org. We show how surface-exposed lipoproteins bind xenosiderophores with different iron-chelating chemistries and propose a mechanism for xenosiderophore import across the outer membrane. Lots of structures (mostly X-ray this time)!
Reposted by Paolo Stincone
New Article: "Rice roots recruit Bacillus via the secretion of heptadecanoic acid" rdcu.be/ff7vo
With Research Briefing: rdcu.be/ff2X0
Rice plants facing fungal infection mobilize a soil-borne defence force via a previously unknown mechanism. MAPK inside.
With Research Briefing: rdcu.be/ff2X0
Rice plants facing fungal infection mobilize a soil-borne defence force via a previously unknown mechanism. MAPK inside.
April 29, 2026 at 4:56 PM
New Article: "Rice roots recruit Bacillus via the secretion of heptadecanoic acid" rdcu.be/ff7vo
With Research Briefing: rdcu.be/ff2X0
Rice plants facing fungal infection mobilize a soil-borne defence force via a previously unknown mechanism. MAPK inside.
With Research Briefing: rdcu.be/ff2X0
Rice plants facing fungal infection mobilize a soil-borne defence force via a previously unknown mechanism. MAPK inside.
Reposted by Paolo Stincone
Cooperative siderophore use stabilizes a protective leaf microbiome https://www.biorxiv.org/content/10.64898/2026.03.18.712463v1
March 19, 2026 at 2:18 AM
Cooperative siderophore use stabilizes a protective leaf microbiome https://www.biorxiv.org/content/10.64898/2026.03.18.712463v1
Reposted by Paolo Stincone
📅 Save the Date – CMFI Conference 2027
Feb 17–19, 2027
📍 Tuebingen, Germany
Confirmed speakers:
Benoit Chassaing · Eran Elinav · Neha Garg · Kiran Patil · Bertrand Routy · Nina van Sorge
Subscribe to stay updated and join us in Tuebingen:
www.cmfi.uni-tuebingen.de/en/cmfi2027
Feb 17–19, 2027
📍 Tuebingen, Germany
Confirmed speakers:
Benoit Chassaing · Eran Elinav · Neha Garg · Kiran Patil · Bertrand Routy · Nina van Sorge
Subscribe to stay updated and join us in Tuebingen:
www.cmfi.uni-tuebingen.de/en/cmfi2027
March 3, 2026 at 2:43 PM
📅 Save the Date – CMFI Conference 2027
Feb 17–19, 2027
📍 Tuebingen, Germany
Confirmed speakers:
Benoit Chassaing · Eran Elinav · Neha Garg · Kiran Patil · Bertrand Routy · Nina van Sorge
Subscribe to stay updated and join us in Tuebingen:
www.cmfi.uni-tuebingen.de/en/cmfi2027
Feb 17–19, 2027
📍 Tuebingen, Germany
Confirmed speakers:
Benoit Chassaing · Eran Elinav · Neha Garg · Kiran Patil · Bertrand Routy · Nina van Sorge
Subscribe to stay updated and join us in Tuebingen:
www.cmfi.uni-tuebingen.de/en/cmfi2027
Reposted by Paolo Stincone
Reposted by Paolo Stincone
We are looking for candidates to apply for the Junta de Andalucía PhD and Postdoc fellowships.
Interested in T6SS and plant–microbe interactions for biotech applications using metabolomics, genetic engineering and molecular biology? Get in touch! More info www.ihsm.uma-csic.es/investigador...
Interested in T6SS and plant–microbe interactions for biotech applications using metabolomics, genetic engineering and molecular biology? Get in touch! More info www.ihsm.uma-csic.es/investigador...
Carlos Molina Santiago
Instituto de Hortofruticultura Subtropical y Mediterránea
www.ihsm.uma-csic.es
January 5, 2026 at 10:16 AM
We are looking for candidates to apply for the Junta de Andalucía PhD and Postdoc fellowships.
Interested in T6SS and plant–microbe interactions for biotech applications using metabolomics, genetic engineering and molecular biology? Get in touch! More info www.ihsm.uma-csic.es/investigador...
Interested in T6SS and plant–microbe interactions for biotech applications using metabolomics, genetic engineering and molecular biology? Get in touch! More info www.ihsm.uma-csic.es/investigador...
Reposted by Paolo Stincone
A graduate student from southeast Asia, now based in a European country and missing her homeland, agonizes over her next career move
go.nature.com/4pFc6hO
go.nature.com/4pFc6hO
Should I return to my home country after my PhD abroad?
A graduate student from southeast Asia, now based in a European country and missing her homeland, agonizes over her next career move.
go.nature.com
January 1, 2026 at 9:38 AM
A graduate student from southeast Asia, now based in a European country and missing her homeland, agonizes over her next career move
go.nature.com/4pFc6hO
go.nature.com/4pFc6hO
Reposted by Paolo Stincone
This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - @pluskal-lab.org @iocbprague.bsky.social go.nature.com/4k1n5iC
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology
A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.
go.nature.com
May 24, 2025 at 8:21 AM
This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.
Reposted by Paolo Stincone
We are pretty stoked that our paper on chemical shifts in kelp forests in the Gulf of Maine made it onto the front cover of @science.org
Big congratulations to Shane Farrell and everybody involved! ✌️✌️✌️
Big congratulations to Shane Farrell and everybody involved! ✌️✌️✌️
Kelp forests on the coast of Maine are in decline owing to rapid ocean warming and are being replaced by turf algae, which alter the ecosystem’s chemistry, hindering the recovery of kelp forests.
Learn more in this week's issue of Science: scim.ag/4dwzl8j
Learn more in this week's issue of Science: scim.ag/4dwzl8j
May 22, 2025 at 11:03 PM
We are pretty stoked that our paper on chemical shifts in kelp forests in the Gulf of Maine made it onto the front cover of @science.org
Big congratulations to Shane Farrell and everybody involved! ✌️✌️✌️
Big congratulations to Shane Farrell and everybody involved! ✌️✌️✌️
Reposted by Paolo Stincone
Die Universität Tübingen erhält sechs #Exzellenzcluster, die im Rahmen der #Exzellenzstrategie vom 01.01.2026 an sieben Jahre lang gefördert werden! Darunter drei Cluster, die bereits etabliert sind und eine erneute Förderung erhalten. uni-tuebingen.de/universitaet... #ExStra #Forschung #UniTübingen
May 22, 2025 at 5:13 PM
Die Universität Tübingen erhält sechs #Exzellenzcluster, die im Rahmen der #Exzellenzstrategie vom 01.01.2026 an sieben Jahre lang gefördert werden! Darunter drei Cluster, die bereits etabliert sind und eine erneute Förderung erhalten. uni-tuebingen.de/universitaet... #ExStra #Forschung #UniTübingen
Reposted by Paolo Stincone
Kelp forests on the coast of Maine are in decline owing to rapid ocean warming and are being replaced by turf algae, which alter the ecosystem’s chemistry, hindering the recovery of kelp forests.
Learn more in this week's issue of Science: scim.ag/4dwzl8j
Learn more in this week's issue of Science: scim.ag/4dwzl8j
May 22, 2025 at 6:05 PM
Kelp forests on the coast of Maine are in decline owing to rapid ocean warming and are being replaced by turf algae, which alter the ecosystem’s chemistry, hindering the recovery of kelp forests.
Learn more in this week's issue of Science: scim.ag/4dwzl8j
Learn more in this week's issue of Science: scim.ag/4dwzl8j
Reposted by Paolo Stincone
Biology is so cool
- P. syringae produces syringafactin, which is deacylated by amoebae
- Deacylated syringafactin binds to CraR, triggering amoebicidal pyrofactin synthesis
- Cra allows P. syringae to infect Arabidopsis thaliana in the presence of amoebae
#MicroSky
- P. syringae produces syringafactin, which is deacylated by amoebae
- Deacylated syringafactin binds to CraR, triggering amoebicidal pyrofactin synthesis
- Cra allows P. syringae to infect Arabidopsis thaliana in the presence of amoebae
#MicroSky
A chemical radar allows bacteria to detect and kill predators
Pseudomonas syringae can detect and kill microbial predators via a chemical radar
(Cra), which also allows the bacterium to infect plants despite predation pressure.
www.cell.com
April 5, 2025 at 1:13 PM
Biology is so cool
- P. syringae produces syringafactin, which is deacylated by amoebae
- Deacylated syringafactin binds to CraR, triggering amoebicidal pyrofactin synthesis
- Cra allows P. syringae to infect Arabidopsis thaliana in the presence of amoebae
#MicroSky
- P. syringae produces syringafactin, which is deacylated by amoebae
- Deacylated syringafactin binds to CraR, triggering amoebicidal pyrofactin synthesis
- Cra allows P. syringae to infect Arabidopsis thaliana in the presence of amoebae
#MicroSky
Reposted by Paolo Stincone
Happy to share our paper from a new research line led by @camolsan.bsky.social, where we engineered the T6SS of Pseudomonas putida to deliver effectors against bacterial competitors and fungal pathogens like Botrytis cinerea. @ihsmumacsic.bsky.social
jbioleng.biomedcentral.com/articles/10....
jbioleng.biomedcentral.com/articles/10....
Engineering the T6SS of Pseudomonas for targeted delivery of antibacterial and antifungal effectors - Journal of Biological Engineering
Background Bacteria employ diverse molecular systems, such as the type VI secretion system (T6SS) to outcompete other microorganisms and adapt to ecological niches. The T6SS is a versatile nanomachine...
jbioleng.biomedcentral.com
April 3, 2025 at 6:00 PM
Happy to share our paper from a new research line led by @camolsan.bsky.social, where we engineered the T6SS of Pseudomonas putida to deliver effectors against bacterial competitors and fungal pathogens like Botrytis cinerea. @ihsmumacsic.bsky.social
jbioleng.biomedcentral.com/articles/10....
jbioleng.biomedcentral.com/articles/10....
Reposted by Paolo Stincone
Excited to share our latest, out today in @naturemicrobiol.bsky.social Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium www.nature.com/articles/s41... @idpittstop.bsky.social
Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium - Nature Microbiology
Genomic and functional analyses of healthcare-associated vancomycin-resistant Enterococcus faecium reveal that bacteriocin T8 is enriched in emergent lineages and provides a competitive advantage in v...
www.nature.com
March 21, 2025 at 1:46 PM
Excited to share our latest, out today in @naturemicrobiol.bsky.social Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium www.nature.com/articles/s41... @idpittstop.bsky.social
Reposted by Paolo Stincone
February 24, 2025 at 6:28 PM
Reposted by Paolo Stincone
Composing a microbial symphony: synthetic communities for promoting plant growth
Composing a microbial symphony: synthetic communities for promoting plant growth
Plant microbiomes are pivotal for host development, influencing growth, health, fitness, and evolution, and have emerged as promising resources for sustainable agriculture. However, leveraging these microbiomes to improve crop yield and resilience is…
dlvr.it
February 18, 2025 at 12:37 AM
Composing a microbial symphony: synthetic communities for promoting plant growth
Reposted by Paolo Stincone
We will be hosting the first @mzmine.bsky.social Community Meeting at @iocbprague.bsky.social. Please register if you wish to learn about the latest developments in mzmine. More info: docs.google.com/document/d/1...
February 17, 2025 at 4:21 PM
We will be hosting the first @mzmine.bsky.social Community Meeting at @iocbprague.bsky.social. Please register if you wish to learn about the latest developments in mzmine. More info: docs.google.com/document/d/1...
Reposted by Paolo Stincone
New preprint from our collaboration with @aliciaperezlorente.bsky.social from Diego Romero's group, who spend some time with us at @cmfi.bsky.social. It's great to see all the puzzle pieces coming together, providing a detailed snapshot of the molecular interplay between Bacillus and and Botrytis.
February 12, 2025 at 1:18 AM
New preprint from our collaboration with @aliciaperezlorente.bsky.social from Diego Romero's group, who spend some time with us at @cmfi.bsky.social. It's great to see all the puzzle pieces coming together, providing a detailed snapshot of the molecular interplay between Bacillus and and Botrytis.