Rubin Lab
@therubinlab.bsky.social
News from the Rubin Lab 🧬🧫 We conduct DNA-level editing of microbial communities for understanding and control. Managed by lab members.
@innovativegenomics.bsky.social @ucberkeleyofficial.bsky.social 🔬🌁
🔗 therubinlab.org
@innovativegenomics.bsky.social @ucberkeleyofficial.bsky.social 🔬🌁
🔗 therubinlab.org
Pinned
Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
Reposted by Rubin Lab
Today in Nature Communications, a team of IGI researchers from The Banfield Lab and Pam Ronald's labs uncover a new way to reduce #methane emissions from rice by influencing the activity of rice paddy soil #microbes. Read more: https://ow.ly/45j150Y3WsI
February 10, 2026 at 3:25 PM
Today in Nature Communications, a team of IGI researchers from The Banfield Lab and Pam Ronald's labs uncover a new way to reduce #methane emissions from rice by influencing the activity of rice paddy soil #microbes. Read more: https://ow.ly/45j150Y3WsI
Reposted by Rubin Lab
Featured Article: Chemical inhibition of a bacterial immune system
Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. IP6C improves phage-therapy against P. aeruginosa & acts against Thoeris in polymicrobial communities
www.cell.com/cell-host-mi...
Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. IP6C improves phage-therapy against P. aeruginosa & acts against Thoeris in polymicrobial communities
www.cell.com/cell-host-mi...
Chemical inhibition of a bacterial immune system
Bacteriophages are promising alternatives to antibiotics for treating bacterial infections.
However, bacteria possess immune systems that neutralize bacteriophages. Zang et al.
discover small molecule...
www.cell.com
February 11, 2026 at 7:24 PM
Featured Article: Chemical inhibition of a bacterial immune system
Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. IP6C improves phage-therapy against P. aeruginosa & acts against Thoeris in polymicrobial communities
www.cell.com/cell-host-mi...
Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. IP6C improves phage-therapy against P. aeruginosa & acts against Thoeris in polymicrobial communities
www.cell.com/cell-host-mi...
Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
February 12, 2026 at 12:42 AM
Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
Reposted by Rubin Lab
Check out this cool new preprint from @therubinlab.bsky.social led by @jnvmartinson.bsky.social
They shielded recipient strains from lethal zygosis (conjugative killing of the recipient) by encoding protective DNA cargo via CASTs 🧪🦠🧬🧫
They shielded recipient strains from lethal zygosis (conjugative killing of the recipient) by encoding protective DNA cargo via CASTs 🧪🦠🧬🧫
Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1
February 11, 2026 at 4:55 AM
Check out this cool new preprint from @therubinlab.bsky.social led by @jnvmartinson.bsky.social
They shielded recipient strains from lethal zygosis (conjugative killing of the recipient) by encoding protective DNA cargo via CASTs 🧪🦠🧬🧫
They shielded recipient strains from lethal zygosis (conjugative killing of the recipient) by encoding protective DNA cargo via CASTs 🧪🦠🧬🧫
Reposted by Rubin Lab
Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1
February 11, 2026 at 4:16 AM
Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1
We're honored and grateful to have a project accepted by @nsfexfab.bsky.social BioFoundry, spearheaded by our amazing postdoctoral researcher Dr. Madeline Hayes @chucksbiscuit.bsky.social (co-advised by @cresslab.bsky.social and Dr. Michelle O'Malley from UCSB)! 🦠🔍🤩
February 9, 2026 at 9:43 PM
We're honored and grateful to have a project accepted by @nsfexfab.bsky.social BioFoundry, spearheaded by our amazing postdoctoral researcher Dr. Madeline Hayes @chucksbiscuit.bsky.social (co-advised by @cresslab.bsky.social and Dr. Michelle O'Malley from UCSB)! 🦠🔍🤩
Wrapping up 2025's progress, milestones, and goals for the future at our lab's Year-End Review meeting!🍾 We're excited for an upcoming awesome year of science in 2026😉
February 9, 2026 at 7:28 PM
Wrapping up 2025's progress, milestones, and goals for the future at our lab's Year-End Review meeting!🍾 We're excited for an upcoming awesome year of science in 2026😉
Reposted by Rubin Lab
ICYMI Out Now! Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function #MicroSky
Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function
Nature Microbiology, Published online: 05 February 2026; doi:10.1038/s41564-026-02259-wA covariate-aware analysis reveals that microbiome changes in the gut of patients with chronic kidney disease are better explained by intestinal transit time than by kidney function.
go.nature.com
February 9, 2026 at 1:00 AM
ICYMI Out Now! Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function #MicroSky
Reposted by Rubin Lab
Also a big thanks to @cresslab.bsky.social and @therubinlab.bsky.social who came up with the idea to start this meeting and were instrumental in making it happen! And congratulations to @therubinlab.bsky.social and @paulwilmes.bsky.social for their elections as vice-chairs for the next one!
January 19, 2026 at 1:58 PM
Also a big thanks to @cresslab.bsky.social and @therubinlab.bsky.social who came up with the idea to start this meeting and were instrumental in making it happen! And congratulations to @therubinlab.bsky.social and @paulwilmes.bsky.social for their elections as vice-chairs for the next one!
Reposted by Rubin Lab
It was a true privilege to co-chair the inaugural GRC meeting on Microbiome Editing together with @jenniferdoudna.bsky.social . The positive energy and quality of the Science presented were truly inspiring. I look forward to the next one chaired by KC Huang and @omalleylab.bsky.social !!!
January 19, 2026 at 1:53 PM
It was a true privilege to co-chair the inaugural GRC meeting on Microbiome Editing together with @jenniferdoudna.bsky.social . The positive energy and quality of the Science presented were truly inspiring. I look forward to the next one chaired by KC Huang and @omalleylab.bsky.social !!!
Reposted by Rubin Lab
A new preprint on expanding the genetic code, from IGI's Jill Banfield, Peter Penev, and collaborators across the country: https://ow.ly/HiYO50XVNXR
January 15, 2026 at 5:05 PM
A new preprint on expanding the genetic code, from IGI's Jill Banfield, Peter Penev, and collaborators across the country: https://ow.ly/HiYO50XVNXR
Reposted by Rubin Lab
How do the ancestors of CRISPR-Cas unwind DNA and how can this lead to better genome editing? With our collaboration between @doudna-lab.bsky.social x @jacobsenucla.bsky.social x Zev Bryant's lab x @savagecatsonly.bsky.social we've uncovered the secrets behind TnpB's dynamics!
www.biorxiv.org
January 15, 2026 at 6:55 AM
How do the ancestors of CRISPR-Cas unwind DNA and how can this lead to better genome editing? With our collaboration between @doudna-lab.bsky.social x @jacobsenucla.bsky.social x Zev Bryant's lab x @savagecatsonly.bsky.social we've uncovered the secrets behind TnpB's dynamics!
Reposted by Rubin Lab
A team of scientists led by UC Berkeley is working on a system that uses probiotics, beneficial bacteria within our bodies, and prebiotics, the nutrients that support these good bacteria, to combat lung pathogens.
Using the microbiome to combat lung pathogens - Berkeley Engineering
Novel approach offers a way to stop deadly infections without using antibiotics
bit.ly
January 13, 2026 at 11:06 PM
A team of scientists led by UC Berkeley is working on a system that uses probiotics, beneficial bacteria within our bodies, and prebiotics, the nutrients that support these good bacteria, to combat lung pathogens.
Reposted by Rubin Lab
Such a privilege to share the Phage Foundry (phagefoundry.org) team’s work at the inaugural GRC meeting on Microbiome Editing 🎉🎊.
January 13, 2026 at 11:56 PM
Such a privilege to share the Phage Foundry (phagefoundry.org) team’s work at the inaugural GRC meeting on Microbiome Editing 🎉🎊.
Reposted by Rubin Lab
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 14, 2026 at 10:14 AM
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Reposted by Rubin Lab
During my postdoc in @therubinlab.bsky.social, @leosong.bsky.social and I aimed to make CRISPR-associated transposons more efficient for editing bacteria.
Couldn’t have done it w/o a CAST of characters at IGI and beyond @innovativegenomics.bsky.social, @cresslab.bsky.social, @doudna-lab.bsky.social
Couldn’t have done it w/o a CAST of characters at IGI and beyond @innovativegenomics.bsky.social, @cresslab.bsky.social, @doudna-lab.bsky.social
Happy New Year from the Rubin Lab! 🎇
We're excited to start 2026 off with a fresh publication at @science.org Advances. Here, we identified a cast (😉) of host factors affecting VchCAST using genome-wide screens and validated their improvement or inhibition of CAST activity. (1/2)
We're excited to start 2026 off with a fresh publication at @science.org Advances. Here, we identified a cast (😉) of host factors affecting VchCAST using genome-wide screens and validated their improvement or inhibition of CAST activity. (1/2)
Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing
Whole-genome screening reveals strategies to boost CRISPR-associated transposase genome editing efficiency.
www.science.org
January 5, 2026 at 9:39 PM
During my postdoc in @therubinlab.bsky.social, @leosong.bsky.social and I aimed to make CRISPR-associated transposons more efficient for editing bacteria.
Couldn’t have done it w/o a CAST of characters at IGI and beyond @innovativegenomics.bsky.social, @cresslab.bsky.social, @doudna-lab.bsky.social
Couldn’t have done it w/o a CAST of characters at IGI and beyond @innovativegenomics.bsky.social, @cresslab.bsky.social, @doudna-lab.bsky.social
Reposted by Rubin Lab
New in Science Magazine Science Advances from the Doudna Lab, Rubin Lab and Cress Lab —Identification of proteins influencing #CRISPR-associated #transposases for enhanced #GenomeEditing. Read here: https://ow.ly/U0s450XS82n
January 5, 2026 at 7:23 PM
New in Science Magazine Science Advances from the Doudna Lab, Rubin Lab and Cress Lab —Identification of proteins influencing #CRISPR-associated #transposases for enhanced #GenomeEditing. Read here: https://ow.ly/U0s450XS82n
Happy New Year from the Rubin Lab! 🎇
We're excited to start 2026 off with a fresh publication at @science.org Advances. Here, we identified a cast (😉) of host factors affecting VchCAST using genome-wide screens and validated their improvement or inhibition of CAST activity. (1/2)
We're excited to start 2026 off with a fresh publication at @science.org Advances. Here, we identified a cast (😉) of host factors affecting VchCAST using genome-wide screens and validated their improvement or inhibition of CAST activity. (1/2)
Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing
Whole-genome screening reveals strategies to boost CRISPR-associated transposase genome editing efficiency.
www.science.org
January 5, 2026 at 6:45 PM
Happy New Year from the Rubin Lab! 🎇
We're excited to start 2026 off with a fresh publication at @science.org Advances. Here, we identified a cast (😉) of host factors affecting VchCAST using genome-wide screens and validated their improvement or inhibition of CAST activity. (1/2)
We're excited to start 2026 off with a fresh publication at @science.org Advances. Here, we identified a cast (😉) of host factors affecting VchCAST using genome-wide screens and validated their improvement or inhibition of CAST activity. (1/2)
Reposted by Rubin Lab
Nature Microbiology turns 10! 🎂
As a special treat, we take you back to the editorial team that started it all and then fast forward to take a peek into the future of microbiology through some brilliant microbiologists.
#MicroSky 🦠
www.nature.com/nmicrobiol/v...
As a special treat, we take you back to the editorial team that started it all and then fast forward to take a peek into the future of microbiology through some brilliant microbiologists.
#MicroSky 🦠
www.nature.com/nmicrobiol/v...
January 5, 2026 at 4:44 PM
Nature Microbiology turns 10! 🎂
As a special treat, we take you back to the editorial team that started it all and then fast forward to take a peek into the future of microbiology through some brilliant microbiologists.
#MicroSky 🦠
www.nature.com/nmicrobiol/v...
As a special treat, we take you back to the editorial team that started it all and then fast forward to take a peek into the future of microbiology through some brilliant microbiologists.
#MicroSky 🦠
www.nature.com/nmicrobiol/v...
Reposted by Rubin Lab
🚨 Our Lab is HIRING! If you are interested in characterizing model microbiomes using genome-resolved methods, statistical/metabolic modeling, and/or machine learning please submit an application here: aprecruit.berkeley.edu/JPF05234
#postdoc #sciencejobs #biology #microbiome
#postdoc #sciencejobs #biology #microbiome
Postdoc - Microbiome - Innovative Genomics Institute
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
January 5, 2026 at 6:19 PM
🚨 Our Lab is HIRING! If you are interested in characterizing model microbiomes using genome-resolved methods, statistical/metabolic modeling, and/or machine learning please submit an application here: aprecruit.berkeley.edu/JPF05234
#postdoc #sciencejobs #biology #microbiome
#postdoc #sciencejobs #biology #microbiome
Reposted by Rubin Lab
#NewResearch
Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.
#MicroSky 🦠
www.nature.com/articles/s41...
Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.
#MicroSky 🦠
www.nature.com/articles/s41...
Large-scale analysis of bacterial genomes reveals thousands of lytic phages - Nature Microbiology
Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.
www.nature.com
January 2, 2026 at 2:06 PM
#NewResearch
Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.
#MicroSky 🦠
www.nature.com/articles/s41...
Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.
#MicroSky 🦠
www.nature.com/articles/s41...
Reposted by Rubin Lab
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed.
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
www.biorxiv.org
December 15, 2025 at 9:49 PM
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed.
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Reposted by Rubin Lab
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
go.nature.com
January 2, 2026 at 4:39 PM
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Reposted by Rubin Lab
Congrats to #BioEGSB affiliate scientist Ben Rubin and team on publication of @therubinlab.bsky.social's first lead paper!
New in Nucleic Acids Research from the Rubin Lab — OriGen, a language model that can generate plasmid origins of replication. 🔄🦠 The model makes sequences that are remarkably different from wild type origins, yet still replicate in vivo. Read here: https://ow.ly/jjOt50XIBxb
December 19, 2025 at 6:35 PM
Congrats to #BioEGSB affiliate scientist Ben Rubin and team on publication of @therubinlab.bsky.social's first lead paper!