Tami Lieberman
@contaminatedsci.bsky.social
Associate Professor, MIT
Still thinking about the 10^9 mutations generated in your microbiome today.
Website: http://lieberman.science
Still thinking about the 10^9 mutations generated in your microbiome today.
Website: http://lieberman.science
Pinned
Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...
Reposted by Tami Lieberman
High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1
December 26, 2025 at 1:16 AM
High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1
Reposted by Tami Lieberman
So incredibly proud of this work, and thankful to everyone who makes it possible!
Pittsburgh Phage Program — 2025 Wrapped!
To our patients, clinicians, researches,
regulators, and partners— this work doesn’t happen without you. We screened, treated, delivered, learned—and even laid the groundwork for a 2026 trial!
#pittsburghphageprogram #phagetherapy #P3
To our patients, clinicians, researches,
regulators, and partners— this work doesn’t happen without you. We screened, treated, delivered, learned—and even laid the groundwork for a 2026 trial!
#pittsburghphageprogram #phagetherapy #P3
December 23, 2025 at 5:57 PM
So incredibly proud of this work, and thankful to everyone who makes it possible!
Reposted by Tami Lieberman
A new #ScienceImmunology study has identified motile gut bacteria with specific flagellin genes that have the potential to cause intestinal inflammation and are expanded in patients with #CrohnsDisease. https://scim.ag/4p00Dbj
Divergent immune responses to commensal bacteria bearing distinct motility signatures
Motile commensal bacteria that induce immune hyperactivation and colon inflammation are identified.
scim.ag
December 23, 2025 at 4:13 PM
A new #ScienceImmunology study has identified motile gut bacteria with specific flagellin genes that have the potential to cause intestinal inflammation and are expanded in patients with #CrohnsDisease. https://scim.ag/4p00Dbj
Reposted by Tami Lieberman
New from AFI researchers Jennifer Gundrum and Drs. Tabita Ramirez-Puebla, Jessica L. Mark Welch, and Gary G. Borisy:
Novel FISH method overcomes cell wall barriers, enabling clearer insight into complex microbial communities.
Learn more: journals.asm.org/doi/10.1128/...
Novel FISH method overcomes cell wall barriers, enabling clearer insight into complex microbial communities.
Learn more: journals.asm.org/doi/10.1128/...
December 23, 2025 at 2:50 PM
New from AFI researchers Jennifer Gundrum and Drs. Tabita Ramirez-Puebla, Jessica L. Mark Welch, and Gary G. Borisy:
Novel FISH method overcomes cell wall barriers, enabling clearer insight into complex microbial communities.
Learn more: journals.asm.org/doi/10.1128/...
Novel FISH method overcomes cell wall barriers, enabling clearer insight into complex microbial communities.
Learn more: journals.asm.org/doi/10.1128/...
Reposted by Tami Lieberman
I love this plot illustrating the famous generation-time effect on mutation rates with modern data!
In fact, they appear to be eerily similar. The per generation mutation rate seems to lay between 10-9 and 10-8 per bp in all animal taxa surveyed to date–despite vast differences in environments, life histories, and three orders of magnitude variation in the generation time: 4/n
December 22, 2025 at 4:18 PM
I love this plot illustrating the famous generation-time effect on mutation rates with modern data!
Reposted by Tami Lieberman
She let me know that they recently received guidance that, ONLY for the January EI deadline (1/27/2026) and the February ESI deadline (2/3/2026), PIs can submit MIRAs even if their previous application (R35, R01, R15, R21, and R37) is still considered under review.
December 19, 2025 at 7:17 PM
She let me know that they recently received guidance that, ONLY for the January EI deadline (1/27/2026) and the February ESI deadline (2/3/2026), PIs can submit MIRAs even if their previous application (R35, R01, R15, R21, and R37) is still considered under review.
Reposted by Tami Lieberman
Q&A
Budget contd
May not hear about awards or status until CR resolved
Q&A
What are current priorities?
within Bio: 1) advancing biotech 2) accelerating interactions between biology and AI 3) building workforce and bio literacy
Budget contd
May not hear about awards or status until CR resolved
Q&A
What are current priorities?
within Bio: 1) advancing biotech 2) accelerating interactions between biology and AI 3) building workforce and bio literacy
December 18, 2025 at 6:33 PM
Q&A
Budget contd
May not hear about awards or status until CR resolved
Q&A
What are current priorities?
within Bio: 1) advancing biotech 2) accelerating interactions between biology and AI 3) building workforce and bio literacy
Budget contd
May not hear about awards or status until CR resolved
Q&A
What are current priorities?
within Bio: 1) advancing biotech 2) accelerating interactions between biology and AI 3) building workforce and bio literacy
Reposted by Tami Lieberman
Gene-specific selective sweeps for the win!
(Not that anyone is keeping score. Genome-wide sweeps and soft sweeps are also great)
(Not that anyone is keeping score. Genome-wide sweeps and soft sweeps are also great)
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 7:45 PM
Gene-specific selective sweeps for the win!
(Not that anyone is keeping score. Genome-wide sweeps and soft sweeps are also great)
(Not that anyone is keeping score. Genome-wide sweeps and soft sweeps are also great)
Reposted by Tami Lieberman
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 17, 2025 at 12:46 AM
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Reposted by Tami Lieberman
"The only kind of thinking that matters in science is structured thinking. The only way to give structure and substance to your thoughts is to write them down. Writing. Is. Thinking."
Thinking about this in the context of AI tools....
Thinking about this in the context of AI tools....
An open letter to graduate students and other procrastinators: it’s time to write - Nature Biotechnology
Nature Biotechnology - An open letter to graduate students and other procrastinators: it’s time to write
www.nature.com
March 25, 2025 at 2:46 PM
"The only kind of thinking that matters in science is structured thinking. The only way to give structure and substance to your thoughts is to write them down. Writing. Is. Thinking."
Thinking about this in the context of AI tools....
Thinking about this in the context of AI tools....
Reposted by Tami Lieberman
An MIT lab director was killed in a shooting at his home in Brookline, Massachusetts Monday night, the school confirmed.
No one is in custody, Brookline police deputy superintendent said.
No one is in custody, Brookline police deputy superintendent said.
MIT professor Nuno Loureiro killed in shooting at his Brookline, Massachusetts home
MIT professor Nuno F.G. Loureiro was killed in a shooting at his home in Brookline, Massachusetts.
cbsn.ws
December 16, 2025 at 6:30 PM
An MIT lab director was killed in a shooting at his home in Brookline, Massachusetts Monday night, the school confirmed.
No one is in custody, Brookline police deputy superintendent said.
No one is in custody, Brookline police deputy superintendent said.
Reposted by Tami Lieberman
From @semianalysis.com.web.brid.gy, Nvidia $NVDA acquires SchedMD, makers of SLURM, a widely used open source workload scheduler. Many AI companies such as Mistral, Thinking Machines, parts of Meta's FAIR division, university academic labs use SLURM.
December 16, 2025 at 8:52 AM
From @semianalysis.com.web.brid.gy, Nvidia $NVDA acquires SchedMD, makers of SLURM, a widely used open source workload scheduler. Many AI companies such as Mistral, Thinking Machines, parts of Meta's FAIR division, university academic labs use SLURM.
Great example of warfare mechanisms targeting fitness determining genes.
An electron transport complex required in the gut sensitizes Bacteroides to a pore-forming type VI secretion toxin (*Or "Return of the Rnf Complex*) www.pnas.org/doi/abs/10.1...
An electron transport complex required in the gut sensitizes Bacteroides to a pore-forming type VI secretion toxin | PNAS
Data suggest that antagonism between bacteria is prevalent within the gut microbiome.
Such antagonism could have profound consequences on the fitne...
www.pnas.org
December 13, 2025 at 5:02 PM
Great example of warfare mechanisms targeting fitness determining genes.
Reposted by Tami Lieberman
🚨New faculty job opportunity 🚨
Please share this ad for a faculty position in our department at UC Irvine, in the fields of microbiology and infectious disease. MD/PhDs and PhDs are desired and should apply!
recruit.ap.uci.edu/JPF09954
Please share this ad for a faculty position in our department at UC Irvine, in the fields of microbiology and infectious disease. MD/PhDs and PhDs are desired and should apply!
recruit.ap.uci.edu/JPF09954
Pediatric Infectious Diseases/Microbiology - Professor Series (tenure track/tenure), Open Rank
University of California, Irvine is hiring. Apply now!
recruit.ap.uci.edu
December 12, 2025 at 8:55 PM
🚨New faculty job opportunity 🚨
Please share this ad for a faculty position in our department at UC Irvine, in the fields of microbiology and infectious disease. MD/PhDs and PhDs are desired and should apply!
recruit.ap.uci.edu/JPF09954
Please share this ad for a faculty position in our department at UC Irvine, in the fields of microbiology and infectious disease. MD/PhDs and PhDs are desired and should apply!
recruit.ap.uci.edu/JPF09954
Reposted by Tami Lieberman
I think some folks might be happy to see this. NIGMS MIRA R35 for EI/NI has been published. PAR-26-121 files.simpler.grants.gov/opportunitie...
PAR-26-121: Maximizing Investigators' Research Award (MIRA) (R35 - Clinical Trial Optional)
files.simpler.grants.gov
December 11, 2025 at 6:48 PM
I think some folks might be happy to see this. NIGMS MIRA R35 for EI/NI has been published. PAR-26-121 files.simpler.grants.gov/opportunitie...
Reposted by Tami Lieberman
MAGAZINER: How many veterans have you deported?
NOEM: We haven't deported veterans
MAGAZINER: We are now joined on Zoom by a combat veteran you deported to Korea
NOEM: We haven't deported veterans
MAGAZINER: We are now joined on Zoom by a combat veteran you deported to Korea
December 11, 2025 at 4:22 PM
MAGAZINER: How many veterans have you deported?
NOEM: We haven't deported veterans
MAGAZINER: We are now joined on Zoom by a combat veteran you deported to Korea
NOEM: We haven't deported veterans
MAGAZINER: We are now joined on Zoom by a combat veteran you deported to Korea
Reposted by Tami Lieberman
🧬 Microbiome researchers: Dec. 30 is the last day to submit poster abstracts for the Keystone Symposium on Human Microbiome! Learn why this meeting is a hub for collaboration: youtu.be/RmK-4P4CZL4
Submit: keysym.us/KSMicrobiome26
@contaminatedsci.bsky.social #KSMicrobiome26 #microbiome
Submit: keysym.us/KSMicrobiome26
@contaminatedsci.bsky.social #KSMicrobiome26 #microbiome
KSQA: Dr. Harry Sokol (Human Microbiome)
YouTube video by KeystoneSymposia
youtu.be
December 10, 2025 at 6:23 PM
🧬 Microbiome researchers: Dec. 30 is the last day to submit poster abstracts for the Keystone Symposium on Human Microbiome! Learn why this meeting is a hub for collaboration: youtu.be/RmK-4P4CZL4
Submit: keysym.us/KSMicrobiome26
@contaminatedsci.bsky.social #KSMicrobiome26 #microbiome
Submit: keysym.us/KSMicrobiome26
@contaminatedsci.bsky.social #KSMicrobiome26 #microbiome
Reposted by Tami Lieberman
✨New preprint!
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
December 9, 2025 at 7:52 AM
✨New preprint!
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
Reposted by Tami Lieberman
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research
The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...
research.pasteur.fr
December 8, 2025 at 8:53 AM
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Reposted by Tami Lieberman
can't stop watching this clip of a tesla Optimus teleoperator taking his headset off before properly logging out the robot
December 8, 2025 at 9:29 AM
can't stop watching this clip of a tesla Optimus teleoperator taking his headset off before properly logging out the robot
Reposted by Tami Lieberman
My first lead author paper is out with Ben Kerr and @alisonfeder.bsky.social! We found that making an antiviral too strong can sometimes make resistance easier to evolve. This has implications for how we design drugs, choose doses, and think about viral evolution in the face of treatment. (1/n)
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback - Nature Ecology & Evolution
A model of intrahost poliovirus replication shows that, after several rounds of replication, pocapavir, a poliovirus capsid inhibitor, collapses viral density, preventing intracellular interactions th...
www.nature.com
December 8, 2025 at 5:15 PM
My first lead author paper is out with Ben Kerr and @alisonfeder.bsky.social! We found that making an antiviral too strong can sometimes make resistance easier to evolve. This has implications for how we design drugs, choose doses, and think about viral evolution in the face of treatment. (1/n)
Reposted by Tami Lieberman
Pretty cool! Engineered periplasmic binding proteins+fluorophore sensors (for sugars+AAs) are used to report real-time extracellular metabolite dynamics in E. coli + many others species after 24h in plate readers, showing hierarchical substrate use.
journals.asm.org/doi/full/10....
journals.asm.org/doi/full/10....
Real-time simultaneous monitoring of multiple analytes in bacterial cultures | Applied and Environmental Microbiology
Real-time monitoring of metabolites in bacterial cultures is crucial for advancing our understanding of microbial physiology, metabolic fluxes, and dynamic responses to environmental changes. This capability enables researchers to capture transient metabolic states that are often missed in endpoint measurements. The use of engineered periplasmic binding proteins as biosensors for this real-time metabolite monitoring represents a groundbreaking approach. By leveraging the natural specificity and high affinity of PBPs for small molecules, these biosensors can be engineered to detect a wide range of metabolites with exceptional sensitivity and temporal resolution. The integration of PBP-based biosensors into microbial research not only enhances our ability to study real-time metabolism but also provides a versatile tool for optimizing industrial bioprocesses and exploring bacterial infections and complex microbial ecosystems
journals.asm.org
December 8, 2025 at 3:37 PM
Pretty cool! Engineered periplasmic binding proteins+fluorophore sensors (for sugars+AAs) are used to report real-time extracellular metabolite dynamics in E. coli + many others species after 24h in plate readers, showing hierarchical substrate use.
journals.asm.org/doi/full/10....
journals.asm.org/doi/full/10....
Reposted by Tami Lieberman
The #1 organism used to make biocement has never been engineered... until now! Excited to share our work on Sporosarcina pasteurii! Esp. since it's the first project I've contributed to here at Cultivarium :)
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
A genetic platform for a biocementation bacterium
Sporosarcina pasteurii is the most widely studied bacterium for microbially-induced calcium carbonate precipitation (MICP), a process of intense interest for materials and construction applications. D...
www.biorxiv.org
December 8, 2025 at 2:24 PM
The #1 organism used to make biocement has never been engineered... until now! Excited to share our work on Sporosarcina pasteurii! Esp. since it's the first project I've contributed to here at Cultivarium :)
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Tami Lieberman
Pretty cool!
Interkingdom sensing of fungal tyrosol promotes Yersinia pseudotuberculosis antifungal T6SS activity in the murine gut. The effector acts as a chitinase.
Tyrosol acts as a quorum sensing molecule in species like Candida albicans,
From Xihui Shen's lab.
www.nature.com/articles/s41...
Interkingdom sensing of fungal tyrosol promotes Yersinia pseudotuberculosis antifungal T6SS activity in the murine gut. The effector acts as a chitinase.
Tyrosol acts as a quorum sensing molecule in species like Candida albicans,
From Xihui Shen's lab.
www.nature.com/articles/s41...
Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut - Nature Microbiology
Yersinia pseudotuberculosis senses fungal tyrosol signalling through EnvZ–OmpR which triggers T6SS activation and antifungal effector release to reduce fungal competitors in the mouse gut.
www.nature.com
December 8, 2025 at 2:42 PM
Pretty cool!
Interkingdom sensing of fungal tyrosol promotes Yersinia pseudotuberculosis antifungal T6SS activity in the murine gut. The effector acts as a chitinase.
Tyrosol acts as a quorum sensing molecule in species like Candida albicans,
From Xihui Shen's lab.
www.nature.com/articles/s41...
Interkingdom sensing of fungal tyrosol promotes Yersinia pseudotuberculosis antifungal T6SS activity in the murine gut. The effector acts as a chitinase.
Tyrosol acts as a quorum sensing molecule in species like Candida albicans,
From Xihui Shen's lab.
www.nature.com/articles/s41...
Reposted by Tami Lieberman
The @ragoninstitute.bsky.social is launching a new faculty search for a computational immunologist! Applications are open now and reviewed on a rolling basis. Please share broadly with your networks! #immunosky
www.nature.com/naturecareer...
www.nature.com/naturecareer...
Computational Immunologist - Boston, Massachusetts (US) job with Ragon Institute of MGH, MIT, & Harvard | 12849577
The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard in Cambridge MA, together with the Departmen
www.nature.com
December 7, 2025 at 4:32 PM
The @ragoninstitute.bsky.social is launching a new faculty search for a computational immunologist! Applications are open now and reviewed on a rolling basis. Please share broadly with your networks! #immunosky
www.nature.com/naturecareer...
www.nature.com/naturecareer...