Chris Mancuso

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!!

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)

Left: intact biocement bricks made with sand and bacteria Right: malformed biocement bricks made by mutant bacteria

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).

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...

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...

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...

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/...

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.

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...

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...

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...

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...

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_...

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.

#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...

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.

Image generated from ChatGPT.

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!

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...

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/...

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.

#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]

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...

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

Long letter from NSF Director Sethuraman Panchanathan, available here: https://nsf-gov-resources.nsf.gov/files/Letter-to-the-Community.pdf

🧪 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. 🧵

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...

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.

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...
🧵👇

Panel A from figure 1 of the preprint showing the strains and asobiotics used, as well as the in-vitro laboratory evolution assay

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 🧠🟦 🧪

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.

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...

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...

see preprint for more: doi.org/10.1101/2024...

Petri plate photo which shows an array of bacteria inhibiting eachother's growth

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 😎

2 liters of sweat solution in a large beaker in a laboratory.

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!

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"