Cultivarium is hiring for a diverse set of roles to work on non-model organisms across the tree of life! Check us out on LinkedIn or cultivarium.org www.linkedin.com/posts/we-can...

We can now design proteins. But Nature's most remarkable capabilities still can't be studied or engineered. The biggest breakthroughs hide in the unlikeliest places, so we're building th...

We can now design proteins. But Nature's most remarkable capabilities still can't be studied or engineered. The biggest breakthroughs hide in the unlikeliest places, so we're building the tools to c...

linkedin.com

Do you study non-model bacteria? Cultivarium has you covered with their JEROBA (Jumping Element libRaries with Broad hOst rAnge) Toolkit. Use this kit to screen different transposon configurations and find the optimal constructs for your unique bacteria 🦠 https://twp.ai/4ixKCP

If you're a senior PhD student or recent graduate interested in doing work at the intersection of AI and microbial genomics and/or microbiomes, please feel free to reach out to discuss the possibility of applying together for an MIT Novo Nordisk Fellowship engineering.mit.edu/novo-nordisk

Novo Nordisk Fellowship

Potential areas of focus for postdoctoral fellows participating in the MIT-Novo Nordisk Postdoc Program include, but are not limited to, the following: Your complete application should include: In the...

engineering.mit.edu

Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 7mo ago

High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1

All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social · 8mo ago

A scalable transposon mutagenesis system for non-model bacteria https://www.biorxiv.org/content/10.64898/2025.12.22.696024v1

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...

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...

biorxiv.org

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Intracellular competition shapes plasmid population dynamics

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

science.org

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 9mo ago

Functional genomics in a microbe that degrades and metabolizes PET plastic https://www.biorxiv.org/content/10.1101/2025.11.11.687616v1

New preprint! Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠 Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare! An epic effort by Rosanna Wright www.biorxiv.org/content/10.1...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

biorxiv.org

Such a delight to share our work on the evolution of a cheese rind fungus in @currentbiology.bsky.social. This is the fantastic PhD work of @nicolasleonlouw.bsky.social and resulted from amazing collaborations, a wedding proposal(!), an undergrad course, & more! 🧵 www.cell.com/current-biol...

Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation

Using a unique longitudinal sampling approach, Louw et al. demonstrate how a cheese-associated Penicillium population has adapted in an artisan cheese production facility in Vermont, USA. Adaptation i...

cell.com

Open postdoc position in in my lab in Berlin @mpiib-berlin.mpg.de. Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions. www.mpiib-berlin.mpg.de/2193291/job_...

Postdoctoral position (m/f/d) | Evolutionary Genetics

We are offering a Postdoctoral position in Evolutionary Genetics (m/f/d)

mpiib-berlin.mpg.de

Max Planck Institute for Infection Biology@mpiib-berlin.mpg.de · 11mo ago

#Job opportunity The Key Lab @keyfm.bsky.social is looking for a #postdoc in evolutionary genetics - join a young team in the heart of #Berlin to investigate the evolution of ancient microbial pathogens. ⏰ Deadline: October 17 📌 More info and how to apply: www.mpiib-berlin.mpg.de/2193291/job_...

#Newresearch This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice. #MicroSky www.nature.com/articles/s41...

Learning ecosystem-scale dynamics from microbiome data with MDSINE2 - Nature Microbiology

This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.

nature.com

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome. We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated. Funded by a new grant from MIT-HEALS.

A new study by @mancusosci.bsky.social and @contaminatedsci.bsky.social shows that intraspecies microbial conflict can block new strains from settling in. If we want long-lasting probiotics, we must account for battles within species, not just between them. www.nature.com/articles/s41...

Excited to see our work out in Nature Micro today! Big thanks to everyone involved in seeing it over the finish line!

Tami Lieberman@contaminatedsci.bsky.social · last yr.

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...

Our work on the facial skin microbiome of non-human primates is out in mSystems! We show there is no close relative of Cutibacterium on the faces of gorillas and chimps at the Lincoln Park Zoo, furthering the mysterious origin of the dominant human skin colonizer. journals.asm.org/doi/10.1128/...

The microbiome of the human facial skin is unique compared to that of other hominids | mSystems

Understanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts disti...

journals.asm.org

#Bacteria use weapons to outcompete rivals, but what happens if they're transferred? @prokaryota.bsky.social @jdpal.bsky.social &co show that HGT of toxin #plasmids is rare but recipients can thrive under relaxed nutrient competition, reshaping bacterial warfare @plosbiology.org 🧪 plos.io/43vC3X7

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

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...

nature.com

🧪 The NSF director is lying to you. Let’s fact check 7 claims from yesterday’s letter to the community, while pointing out 3 critical omissions. 🧵

Edited for brevity: I expect the professional society that I have supported with national & regional membership dues, conference fees for myself and mentees, journal publication fees, & my time as an editor and reviewer, to support widely held values & to advocate on behalf of ALL microbiologists, 🧵

My letter to ASM leaders that I sent is too long to be posted here, so I'm going to post highlights in case anyone else needs information for their letter. 🧵

Dr. Kat Napaaqtuk❄️@napaaqtuk.bsky.social · 2y ago

@asm.org this better not be anticipatory obedience. I have 5 lab members planning on going to ASM microbe this year. I will absolutely pivot to another meeting if ASM gives in to anti-DEI efforts.

The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology: www.annualreviews.org/content/jour...

Out in Nature Microbiology, we predicted phage-bacteria interactions in E. coli species using only genomic information. Adsorption, not defense systems, is the main driver at this scale (relevant for a phage therapy context), leading to tailored cocktails! www.nature.com/articles/s41... 🧵👇

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information - Nature Microbiology

Phage–host interactions are computationally predicted using only genomic information, highlighting future research directions and enabling generation of custom phage cocktails.

nature.com

We used in-vitro laboratory evolution to "stress test" the next generation class of antibiotics based on antisense oligos ("asobiotics"). Head over to our new preprint to find out more! www.biorxiv.org/content/10.1...

Want to make beautiful scientific figures? Easy! The NIH released a library of 2000+ free scientific illustrations called *BioArt*. Check it out! bioart.niaid.nih.gov #AcademicSky #PsychSciSky 🧠🟦 🧪

Dear mail-in voters, If your state's return deadline is Election Day (Nov. 5), the U.S. Postal Service recommends that you mail your ballot by Tuesday (Oct. 29). Sincerely, The reporter who wrote this: www.npr.org/2024/09/20/n...

Voters are advised to return their ballots early because of mail delay concerns

Election officials are raising concerns about the U.S. Postal Service's ability to handle this fall’s expected influx of election mail. But USPS say it’s ready to deliver the country’s ballots.

npr.org

Given the recent X-odus, I'll reintroduce my postdoc research: Commensal skin bacteria not only attack pathogens, but also fight among themselves! This intraspecies (& interspecies) warfare not only limits which strains can coexist on each person, it also makes cool-looking petri dishes 😎

Being a postdoc is strange. One day you're writing a faculty applications highlighting your unique and valuable skillset, the next you're making 2L of 8x concentrated artificial sweat...

We are on the look out for postdocs to join the Lieberman Lab at MIT. Areas include: -Connecting bacterial warfare to strain dynamics in vivo -Evolution and transmission of microbes in humans -Revisiting role of microbes in acne vulgaris Take a look at our recent preprints and reach out!