Amanda Alker

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.

Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...

Fig. 1: Reversal of HFCS-induced metabolic dysfunctions by inulin supplementation.

A study in Nature Metabolism shows that the dietary fiber inulin modifies the gut #microbiome to better process fructose, helping prevent metabolic dysfunctions and emphasizing the role of dietary fiber. go.nature.com/4gKCvHe 🧪

‘Completely shattered.’ Changes to NSF’s graduate student fellowship spur outcry The announcement comes months later than usual, leaving many would-be applicants stranded

Today was a hard day for Ph.D. students who found out that they can no longer apply for NSF's prestigious Graduate Research Fellowship Program. "Devastating“ was how one student described it to me. #GradSchool #NSFGRFP

www.science.org/content/arti...

It’s also pretty great when you see your PhD advisor and your symbiosis role model together. The symbiosis gods smiled a little brighter today because of it!

OPEN INVITATION to the One Health Microbiome Symposium, May 13-14, 2026!! This is not your typical siloed topic conference. It unifies diverse research fields in microbiome science across Ag, Envtl, and Human Health. 1/n

www.eventbrite.com/e/2026-one-h...

We’re looking for highly motivated prospective students interested in interrogating genetic mechanisms driving marine host-bacteria interactions. Reach out to discuss research ideas and language for agency priorities

👀 Very cool - can’t wait to try these!

Check out my colleague’s feature in #mattersmicrobial! @symbiosisrox.bsky.social @urigso.bsky.social
@universityofri.bsky.social

#GoRhody!

Phosphite as an engineered niche for Pseudomonas veronii in a synthetic soil bacterial community | mSystems Bioaugmentation is a promising solution to soil contamination, but its practical application is limited due to poor inoculant establishment in the native soil community. This can often be attributed t...

Phosphite as an engineered niche for Pseudomonas veronii in a synthetic soil bacterial community

#mSystems by Clara Bailey et al with Jan Roelof van der Meer @dmf-unil.bsky.social

journals.asm.org/doi/10.1128/...

A division of labor controls the degradation of fucoidans in the ocean Fucoidans, complex polysaccharides produced by brown algae and diatoms, contribute to long-term carbon sequestration due to their resistance to microbial degradation1,2. While individual microbes can ...

Check out our latest preprint where we show synergistic interactions between bacteria for the degradation of complex polysaccharides 🌊🦠🔺
@envsysmicro.at @akshitg.bsky.social
#MicroSky
www.biorxiv.org/content/10.1...

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