banner
atp-alker.bsky.social
Amanda Alker
@atp-alker.bsky.social
1.8K followers 890 following 39 posts
Marine microbiologist | Assistant professor at the University of Rhode Island | Postdoc - Rubin & Doudna Labs UC Berkeley | Symbiosis, bacterial genetics and microbiome editing Alkerlab.weebly.com
Posts Media Videos Starter Packs
Pinned
atp-alker.bsky.social
Amanda Alker @atp-alker.bsky.social · Nov 30
🚨 The Alker Lab is starting at the University of Rhode Island in early 2025 and we will be hiring! 🚨

If you are interested in marine microbiology, bacterial genetics and/or symbiosis, please consider reaching out! Repost to help spread the word 🪸🧪🧬🌊
The Alker lab at the University of Rhode Island is hiring (students, postdocs and lab staff)! We use cutting edge tools in microbiology to investigate marine animal symbioses. Email or DM for further inquiries
7 51 94
Reposted by Amanda Alker
benadler.bsky.social
Ben Adler @benadler.bsky.social · 7d
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...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
3 54 110
Reposted by Amanda Alker
natureportfolio.nature.com
Nature Portfolio @natureportfolio.nature.com · 11d
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 🧪
Fig. 1: Reversal of HFCS-induced metabolic dysfunctions by inulin supplementation.
1 16 45
Reposted by Amanda Alker
klangin.bsky.social
Katie Langin @klangin.bsky.social · 12d
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...
‘Completely shattered.’ Changes to NSF’s graduate student fellowship spur outcry
The announcement comes months later than usual, leaving many would-be applicants stranded
www.science.org
4 95 160
atp-alker.bsky.social
Amanda Alker @atp-alker.bsky.social · 19d
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!
1 2
Reposted by Amanda Alker
symbionticism.bsky.social
Seth Bordenstein @symbionticism.bsky.social · 23d
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...
2026 One Health Microbiome Symposium
The 2026 One Health Microbiome Symposium will be hosted at Penn State University. Abstract submissions will open early 2026.
www.eventbrite.com
1 15 26
atp-alker.bsky.social
Amanda Alker @atp-alker.bsky.social · Sep 9
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
ecoevolab.bsky.social
Casey terHorst @ecoevolab.bsky.social · Sep 8
The GRFP lives!! (due end of October)
www.nsf.gov/funding/oppo...
NSF Graduate Research Fellowship Program (GRFP)
www.nsf.gov
1 4
atp-alker.bsky.social
Amanda Alker @atp-alker.bsky.social · Sep 2
👀 Very cool - can’t wait to try these!
soreklab.bsky.social
Sorek Lab @soreklab.bsky.social · Sep 2
Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
3
atp-alker.bsky.social
Amanda Alker @atp-alker.bsky.social · Aug 30
Check out my colleague’s feature in #mattersmicrobial! @symbiosisrox.bsky.social @urigso.bsky.social
@universityofri.bsky.social

#GoRhody!
markowenmartin.bsky.social
Mark O. Martin @markowenmartin.bsky.social · Aug 29
New week-new episode of the #MattersMicrobial podcast!! Dr. Roxanne Beinart of the University of Rhode Island joins the #QualityQuorum to chat about the work her group does on deep sea chemoautrophic communities & symbioses! Please spread the #GoodMicrobialWord?

youtu.be/mERRJOuEsB4?...
3 11
Reposted by Amanda Alker
evolvedbiofilm.bsky.social
Ákos T Kovács @evolvedbiofilm.bsky.social · Aug 17
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/...
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...
journals.asm.org
2 7
Reposted by Amanda Alker
andisichert.bsky.social
andisichert @andisichert.bsky.social · Aug 14
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...
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 ...
www.biorxiv.org
13 16
atp-alker.bsky.social
Amanda Alker @atp-alker.bsky.social · Aug 12
On a small beach in rural Rhode Island, I unplugged for just one moment and considered the small things 🧬🦠🧫🧪
@stcmicrobeblog.bsky.social
Rocks on a piece of driftwood with charcoal drawings of microbes
2 21
Reposted by Amanda Alker
carolynbertozzi.bskyverified.social
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · Aug 9
Congratulations @doudna-lab.bsky.social !! History will position her name alongside the likes of Darwin, Einstein, and Hodgkin.
cenmag.bsky.social
C&EN (Chemical & Engineering News) @cenmag.bsky.social · Aug 9
Jennifer A. Doudna will receive the 2026 Priestley Medal, the highest honor given out by the American Chemical Society. She helped discover the gene editing technology CRISPR and has made many contributions to our knowledge of RNA chemistry. cen.acs.org/people/award...
Jennifer Doudna is named 2026 Priestley Medalist
The award recognizes the biochemist for discoveries on ribozyme function and CRISPR gene editing, and international science leadership
cen.acs.org
3 27 160
Reposted by Amanda Alker
mrillig.bsky.social
Matthias C. Rillig @mrillig.bsky.social · Aug 3
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...
A to do list from the article in Nature
7 12
Reposted by Amanda Alker
owentuck.bsky.social
Owen Tuck @owentuck.bsky.social · Jul 29
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
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...
tinyurl.com
2 30 58
Reposted by Amanda Alker
andrejakust.bsky.social
Andreja Kust @andrejakust.bsky.social · Jul 11
🚨 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...
3 24 44
Reposted by Amanda Alker
epcrocha.bsky.social
Eduardo Rocha @epcrocha.bsky.social · Jul 23
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/...
graphical abstract of the article the extended mobility of plasmids
4 94 190
Reposted by Amanda Alker
erictopol.bsky.social
Eric Topol @erictopol.bsky.social · Jul 17
Engineering the gut microbiome in people with hyperoxaluria to avoid kidney stones
science.org/doi/10.1126/...
@science.org
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...
science.org
6 25 140
Reposted by Amanda Alker
natureportfolio.nature.com
Nature Portfolio @natureportfolio.nature.com · Jul 11
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 is figure 3, which is FIB-SIMS imaging shows intracellular bioaccumulation of PFAS by E. coli ∆tolC.
8 25
atp-alker.bsky.social
Amanda Alker @atp-alker.bsky.social · Jul 9
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
cyrilpedia.bsky.social
Thiago Carvalho @cyrilpedia.bsky.social · Jul 6
'The myth of meritocracy in science collapses under the financial sacrifices expected at every career stage. From unpaid internships and self-funded conferences to underpaid graduate and postdoctoral positions, the hidden costs of ‘doing science’ are profound.'
journals.plos.org/plosbiology/...
Too poor to science: How wealth determines who succeeds in STEM
From student to researcher, a career in science can come with a high price tag. This Perspective explores how persistent financial barriers limit who can succeed in science, revealing how wealth shape...
journals.plos.org
8 14
Reposted by Amanda Alker
simrouxvirus.bsky.social
Simon Roux @simrouxvirus.bsky.social · Jun 13
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...
doi.org
3 45 92
Reposted by Amanda Alker
natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · Mar 27
OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice

#microsky 🧪

www.nature.com/articles/s41...
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...
www.nature.com
3 50 90
Reposted by Amanda Alker
natbiotech.nature.com
Nature Biotechnology @natbiotech.nature.com · Jun 24
Click editing uses DNA polymerases, HUH endonucleases and oligonucleotide templates for genome modification go.nature.com/3zPEIjp
rdcu.be/erfhL
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.
go.nature.com
1 6 14
Reposted by Amanda Alker
vivekmutalik.bsky.social
Vivek Mutalik @vivekmutalik.bsky.social · Jun 23
#microsky #synbiosky
erictopol.bsky.social
Eric Topol @erictopol.bsky.social · Jun 23
This is wild!
Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
2 13
Reposted by Amanda Alker
uncultured.carinilab.com
Paul Carini @uncultured.carinilab.com · Jun 17
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.
2 18 59