Amanda Alker

Rocks on a piece of driftwood with charcoal drawings of microbes

On a small beach in rural Rhode Island, I unplugged for just one moment and considered the small things 🧬🦠🧫🧪
@stcmicrobeblog.bsky.social

Congratulations @doudna-lab.bsky.social !! History will position her name alongside the likes of Darwin, Einstein, and Hodgkin.

A to do list from the article in Nature

From bench to big boss: mitigating the widening gap between PI and lab

Laboratory dynamics can change as the age and experience of the principal investigator increase. But there are ways to combat this.

Read our piece in Nature, with @sprekeler.bsky.social

www.nature.com/articles/d41...

Recurrent acquisition of nuclease-protease pairs in antiviral immunity Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

Excited to finally share this work!
We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts.
tinyurl.com/2uwwy4ty

🚨 Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes.

Check it out: doi.org/10.1093/isme...

graphical abstract of the article the extended mobility of plasmids

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Controlled colonization of the human gut with a genetically engineered microbial therapeutic Precision microbiome programming for therapeutic applications is limited by challenges in achieving reproducible colonic colonization. Previously, we created an exclusive niche that we used to engraft...

Engineering the gut microbiome in people with hyperoxaluria to avoid kidney stones
science.org/doi/10.1126/...
@science.org

This is figure 3, which is FIB-SIMS imaging shows intracellular bioaccumulation of PFAS by E. coli ∆tolC.

The findings of a study in Nature Microbiology show the high bioaccumulation capacity of gut bacteria for PFAS, commonly known as forever chemicals. go.nature.com/4le7Svk #microbiome #medsky 🧪

This perspective highlights why federal research opportunities (e.g. NSF REU internships, NSF GRFP fellowships and grant-supported technician positions) were fundamental for me to advance in the academic research ranks. Without them, I wouldn’t have been able to afford to become a scientist
#saveNSF

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice - Nature Microbiology InducTn-seq, a method for inducible mutagenesis followed by transposon insertion site sequencing, enables temporal control of transposition to bypass population bottlenecks and enable the quantificati...

OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice

#microsky 🧪

www.nature.com/articles/s41...

Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases - Nature Biotechnology Click editing uses DNA polymerases, HUH endonucleases and oligonucleotide templates for genome modification.

Click editing uses DNA polymerases, HUH endonucleases and oligonucleotide templates for genome modification go.nature.com/3zPEIjp
rdcu.be/erfhL

#microsky #synbiosky

It's NSF CAREER season! I've been fortunate to review dozens of CAREER grants and received one in 2022. Here are the most common mistakes I see and actionable tips to strengthen your proposal.

Antagonism as a foraging strategy in microbial communities In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependen...

🄰🅆🄴🅂🄾🄼🄴
Stubbusch et al 𝘚𝘊𝘐𝘌𝘕𝘊𝘌

Bacteria 🦠 repurpose Type VI Secretion Systems based on environmental cues:

Nutrient-rich environments ➜ kill competitors

Under starvation ➜ lyse neighbors to scavenge their nutrients

Even “non-pathogens” shift from competition to predation as a survival strategy

Microbial Interactions – an alternative taxonomy Is it mostly Darwin or Marx: ‘survival of the fittest’ vs ‘socialist cooperation’

Think Like a Microbe is back!!
🧪🧫 #philsci
open.substack.com/pub/thinkmic...

MPS budget

Presidential budget is out. Here's NSF. Biggest cut, by amount, is $1 billion, or 66.8%, from MPS (Physics & Math directorate). nsf-gov-resources.nsf.gov/files/00-NSF...

Scientists, reach out to your local communities about the importance of funding science! Write an op-ed to your local newspaper as part of the #McClintockLetters.

Please spread the word and sign up! DM me if you're interested and need help getting started. I'm trained as a writer and happy to help.

One Health microbiome sciences. (a) An expanded One Health microbiome sciences framework that incorporates the ecology of all microbes, beyond disease-causing pathogens, and grows to focus on ecosystem wellness and resilience. This One Health framework will help unify the microbiome sciences and advance core disciplinary theories and principles with cross-system validation and comparative studies, including a few examples highlighted in this article: (b) phylosymbiosis, host-associated microbiome relationships reflect the host’s evolutionary history; (c) Anna Karenina principle, unhealthy microbiomes fail in many different ways, resulting in more heterogeneity; (d) mutualism breakdown, beneficial relations collapse under stress; (e) stress gradient hypothesis, mutualistic interactions are more common in stressful environments; and (f) legacy effects, past events or conditions impact future community responses and traits.

In #mBio, researchers argue that the One Health framework, traditionally focused on microbial threats, needs a bold expansion to include the full breadth of microbial diversity—from pathogenic to beneficial—within its ecological and evolutionary context. asm.social/2qj

FEBS Press The lag phase is crucial for resuming bacterial growth and can be shortened by fueling the methionine cycle with methyl groups from DMSP or other methylated compounds. While DmdA is the primary DMSP ....

DmdA-independent lag phase shortening in Phaeobacter inhibens bacteria under stress conditions febs.onlinelibrary.wiley.com/doi/10.1111/...

1/10 Today in @science.org in collaboration with
the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...

BONCAT-Live for isolation and cultivation of active environmental bacteria In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological...

BONCAT-Live for isolation and cultivation of active environmental bacteria www.biorxiv.org/content/10.1... #jcampubs

Junior faculty job alert in Germany - Marine Evolutionary Genomics @geomarkiel.bsky.social / University of Kiel www.geomar.de/en/karriere/... Marine study system of your choice (no microbes, sorry…), excellent infrastructure and ship access, moderate teaching requirements, closing date 6 June

#MicroSky: In vitro enzyme cascades for synthesis of complex molecules face scale-up challenges. Elias et al boosted cascade efficiency by colocalizing enzymes on synthetic scaffolds via cohesin–dockerin tags. This proximity raised product yield at low enzyme doses. doi.org/10.1111/1751...

That graphical abstract and overall visualization is 🔥 Congrats!

Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research - Nature Biotechnology Overcoming key hurdles for the development of next-generation anaerobic cultivation methods could have major impacts on microbial community research and applications.

Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research www.nature.com/articles/s41... #jcampubs

The president is recommending a 40% cut to next year’s NIH budget. This would be disastrous for our nation’s health and economy. Please contact your representatives, especially if they are Republicans, and tell them why this cannot happen. An easy option: 5calls.org

I’ve been looking into a couple of these. The Cytena B.Sight and the IsolationBio Prospector. Each a little different in features and user friendliness. Unfortunately I haven’t used either yet to have strong opinions

Rapid Response Bridge Funding Program In the face of recent abrupt shifts in federal funding for education research, including large-scale terminations of National Science Foundation (NSF) research grant awards, we have developed a rap...

FYI: The Spencer Foundation, Kapor Foundation, The William T. Grant Foundation, and the Alfred P. Sloan Foundation have collaborated to offer $25K rapid response grants.

"This rapid response bridge funding opportunity is for scholars and teams whose grants have recently been cancelled by NSF."

Left: Group of three T3SS localizing in the same zone of the bacteria surface. T3SS n°1 and 2 contact, deform, and perforate the vacuole membrane at the same spot. T3SS n°1 needle (83 nm) is long and seems to deviate from basal body axis showing that strong constraints between T3SS and the vacuole at are play. The locally relaxed vacuole to bacteria space (~50–55 nm) potentially limits additional damage by the T3SS n°3 needle (56 nm) that only slightly deforms the membrane. Right: Model of initial vacuolar membrane breaching by T3SS-induced mechanoporation. Shigella actively enters host cells in a specialized endomembrane compartment, the vacuole, that is rapidly injured and ruptured for cytosolic access. After host cell entry, the vacuole membrane is intact and tightly juxtaposed to the surface of Shigella, permitting contact between T3SSs and the endomembrane. In the authors’ proposed model, vacuole membrane injury is supported both by the vacuole tightness and the length of individual T3SSs.

How do intracellular #bacteria breach vacuoles to enter the host cytosol? @leaswistak.bsky.social @matthijnvos.bsky.social @enningalab.bsky.social &co show that #Shigella uses its T3SS system to damage endomembranes via mechanoporation to initiate cytosolic access @plosbiology.org 🧪 plos.io/4jXrr9Z