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Chris Mancuso

@mancusosci.bsky.social
430 followers 353 following 24 posts

Engineering non-model microbes @ Cultivarium | soft spot for microbiomes and DIY tech | he/him

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Chris Mancuso @mancusosci.bsky.social · 13/07/2026
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...
linkedin.com
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...
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Addgene @addgene.bsky.social · 19/03/2026
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 🦠 twp.ai/4ixKCP
New at Addgene!
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Tami Lieberman @contaminatedsci.bsky.social · 18/03/2026
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
engineering.mit.edu
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...
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Tami Lieberman @contaminatedsci.bsky.social · 05/01/2026
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!!
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Alex Crits-Christoph @acritschristoph.bsky.social · 24/12/2025
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)
Figure 2. Himar1 transposon variant screen on a cohort of 92 bacterial species.
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Chris Mancuso @mancusosci.bsky.social · 08/12/2025
Read the preprint to get everything from plasmid ORIs to inducible promoters to TnSeq. But here's my favorite photo from the work, targeted KO of biocementation genes (right) clearly impacts biocement structure relative to WT cells (left).
Left: intact biocement bricks made with sand and bacteria
Right: malformed biocement bricks made by mutant bacteria
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Chris Mancuso @mancusosci.bsky.social · 08/12/2025
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...
biorxiv.org
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...
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Michael Baym @baym.lol · 20/11/2025
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/...
science.org
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...
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Alex Crits-Christoph @acritschristoph.bsky.social · 12/11/2025
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.
Figure 2. PET screen results and RB-TnSeq gene fitness results
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Michael Brockhurst @brockhurstlab.bsky.social · 06/10/2025
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...
biorxiv.org
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...
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Benjamin Wolfe @benwolfe.bsky.social · 16/09/2025
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...
cell.com
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...
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Felix M Key @keyfm.bsky.social · 15/09/2025
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_...
mpiib-berlin.mpg.de
Postdoctoral position (m/f/d) | Evolutionary Genetics
We are offering a Postdoctoral position in Evolutionary Genetics (m/f/d)
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Nature Microbiology @natmicrobiol.nature.com · 12/09/2025
#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...
nature.com
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.
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Tami Lieberman @contaminatedsci.bsky.social · 12/09/2025
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.
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MIT CEE @mitcee.bsky.social · 02/07/2025
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...
Image generated from ChatGPT.
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Chris Mancuso @mancusosci.bsky.social · 30/06/2025
Excited to see our work out in Nature Micro today! Big thanks to everyone involved in seeing it over the finish line!
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Tami Lieberman @contaminatedsci.bsky.social · 30/05/2025
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/...
journals.asm.org
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...
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PLOS Biology @plosbiology.org · 22/05/2025
#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
 Modeling predicts that metabolic diversity increases the ecological impacts of weapon gene transfer. Modeling scenarios for each column are shown across the top row. Bottom row: Example dynamics of the strains (attacker, target, transconjugant) during a contest using parameters that correspond to the cross (X) shown in the parameter sweeps directly below.
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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025
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]
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Daria Van Tyne @dariavantyne.bsky.social · 21/03/2025
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
nature.com
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...
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Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · 12/03/2025
🧪 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. 🧵
Long letter from NSF Director Sethuraman Panchanathan, available here: https://nsf-gov-resources.nsf.gov/files/Letter-to-the-Community.pdf
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 03/02/2025
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, 🧵
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 03/02/2025
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. 🧵
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Michael Baym @baym.lol · 21/11/2024
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...
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Aude Bernheim @audeber.bsky.social · 05/11/2024
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... 🧵👇
nature.com
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.
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Marco Galardini @mgalactus.bsky.social · 30/10/2024
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...
Panel A from figure 1 of the preprint showing the strains and asobiotics used, as well as the in-vitro laboratory evolution assay
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Matthias Nau @matthiasnau.bsky.social · 30/10/2024
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 🧠🟦 🧪
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Hansi Lo Wang (he/him) @hansilowang.bsky.social · 28/10/2024
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...
npr.org
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.
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Chris Mancuso @mancusosci.bsky.social · 21/10/2024
see preprint for more: doi.org/10.1101/2024...
doi.org
Intraspecies warfare restricts strain coexistence in human skin microbiomes
Determining why only a fraction of encountered or applied bacterial strains engraft in a given person’s microbiome is crucial for understanding and engineering these communities[1][1]. Previous work h...
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Chris Mancuso @mancusosci.bsky.social · 21/10/2024
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 😎
Petri plate photo which shows an array of bacteria inhibiting eachother's growth
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Chris Mancuso @mancusosci.bsky.social · 24/09/2024
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...
2 liters of sweat solution in a large beaker in a laboratory.
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Tami Lieberman @contaminatedsci.bsky.social · 11/07/2024
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!
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Tami Lieberman @contaminatedsci.bsky.social · 07/07/2024
Those of you at SMBE, check out Poster #86 on Tuesday by grad student Evan Qu: "Phylogeny-aware strain profiling limits false positive detections and quantifies divergence time of novel strains"
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Chris Mancuso @mancusosci.bsky.social · 16/06/2024
Lots of amazing EEB sessions at #ASMicrobe, but consider stopping by B312 at 315 to see how ecoevo dynamics and antagonism play out for S epi living on people!
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Tami Lieberman @contaminatedsci.bsky.social · 14/06/2024
Chris Mancuso @mancusosci.bsky.social will be sharing our story in bacterial antagonisms on Sunday at 3:15p in the session on Integrating in silico models in host-microbe biology. Check it out for more antagonism goodness ! #ASMicrobe
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Chris Mancuso @mancusosci.bsky.social · 09/05/2024
This is amazing! I was just brainstorming with a labmate about modeling hgt-environment-antagonism tradeoffs, so glad you tackled it already! Really curious whether your results can help resolve debate re:similarities/differences between host associated bugs (Staphs) and environmental bugs (Vibrios)
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
Thanks for the link, sorry I missed this one! Nice evidence pointing to anti-aureus activity. Love that you examined ZOI size rather than just binary data, feel like these types of data are often underutilized!
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
In addition to Jacob, I want to thank Evan Qu, Delphine Tripp, and Ishaq Balogun for all their help on this project. And of course Tami Lieberman (@contaminatedsci.bsky.social) for guiding us all along the way! 12/12
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
This work would not have been possible without the amazing strain collection and analyses described in Jacob Baker‘s (@microjacob.bsky.social) recent preprint. www.biorxiv.org/content/10.1...
biorxiv.org
Highly-resolved within-species dynamics in the human facial skin microbiome
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
So, as you might have guessed, the culprit may be phage! Mutants were protected from phage at the cost of sensitivity to antimicrobials. This underscores the sheer number of lethal selection pressures that skin microbes must adapt to. 10/12
Cartoon depicting tradeoff between phage and antimicrobials
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
We thought this might be on-person evolution of resistance, but the phylogeny suggested the opposite! So why would strains evolve sensitivity to antimicrobials? We identified parallel mutations in the vraFG complex, which regulates cell surface modifications. 9/12
Bar graph showing mutants are more sensitive to antimicrobials
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
For most S. epidermidis lineages, we saw no variation in production or sensitivity across the lineage. On these subjects however, we found two lineages with differences in sensitivity to antimicrobials. In fact, the exact same pattern of sensitivity… 8/12
Heat map with two samples highlighted that differ from the rest
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
Of course, no rule is without exceptions. We looked into the few adult subjects who appeared to have antagonism between co-existing strains. Turns out, there’s more going on here… 7/12
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
Strains that co-reside on the same person tend not to antagonize each other, suggesting possible exclusion of sensitive strains by antagonists. In fact, MOST people have ZERO on-person warfare, despite living with family members that have antagonistic or sensitive strains. 6/12
Plot of antagonism frequency vs subject. Most samples show zero antagonism
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
There are more details about these weapons in the preprint, but in summary: interactions are 1. driven by diverse peptides/proteins, 2. independent of the relatedness between strains, and 3. consistent with rapid evolution via horizontal gene transfer. 5/12
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
In this giant summary heatmap, intensity encodes the presence of antagonisms. Strains that inhibit many others show up as white horizontal lines. It’s sorted by genomic relatedness, so the lack of clustering is striking! 4/12
Heatmap showing lots of interactions among bacteria
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
To test this, we screened 14,884 Staphylococcus epidermidis intraspecies interactions (plus 6,141 involving other species) in spot-on-lawn assays to detect warfare between isolates. By looking for zones-of-inhibition, we found tons of cases of active antagonism between S. epidermidis isolates. 3/12
Petri dish with bacterial spots showing inhibition
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
In theory, strains currently residing on a person could attack incoming strains in order to protect their niches from invasion. If true, this would help explain why each person’s strain composition is unique. 2/12
Diagram of a network of strains that inhibit each other
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Chris Mancuso @mancusosci.bsky.social · 08/05/2024
Why don’t people who live together have the same strains of microbes? Tami Lieberman (@contaminatedsci.bsky.social) and I put forward one underexplored reason in our new preprint: Intraspecies warfare restricts strain coexistence in human skin microbiomes
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Chris Mancuso @mancusosci.bsky.social · 23/03/2024
It was so great to see the MIT Microbiome Symposium come to life yesterday after months of planning. The rest of the symposium organizing team and I are so grateful to all the speakers, presenters, panelists, judges, support staff, and sponsors for making this event a success!
Audience at the MIT Microbiome Symposium
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