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Amanda Alker

@atp-alker.bsky.social
1.9K followers 975 following 53 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

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Reposted by Amanda Alker
ISME - International Society for Microbial Ecology @isme-microbes.bsky.social · 15/10/2026
🦠 Meet ISME Host Microbe, ISME’s new fully open access journal! In the launch editorial, discover why an ecological perspective on host–microbe interactions matters, from microbiomes and health to ecosystem function. academic.oup.com/ismehm/artic... #MicrobialEcology @nabroderick.bsky.social
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Mónica Medina @momedinamunoz.bsky.social · 14/10/2026
This just dropped! A fun conversation about the coral holobiont with @markowenmartin.bsky.social in his podcast #MattersMicrobial Thank you so much for the invite! youtu.be/sO_TPJAHfWM?...
youtu.be
Matters Microbial #140: Out of Many, One — Coral and Jellyfish Holobionts
YouTube video by MicrobeTV
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Tami Lieberman @contaminatedsci.bsky.social · 11/10/2026
When is on-person evolution dominated by neutral vs adaptive forces? If you're looking for a postdoc position and this is a question that interests you, please see my lab website and reach out! [More info in next posts]
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Tominaga K. (tomiken) @pacyc184.bsky.social · 10/10/2026
De novo design of miniprotein inhibitors of bacterial adhesins | Nature Communications
nature.com
De novo design of miniprotein inhibitors of bacterial adhesins - Nature Communications
Here, the authors show that protein design is a generalizable strategy to generate new antimicrobials by neutralizing the function of bacterial adhesins to combat two causative agents of urinary tract infections, E. coli and A. baumannii.
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Reposted by Amanda Alker
Tomas Hessler @tomas-hessler.bsky.social · 08/10/2026
I’m happy to share our study out in Microbiome! link.springer.com/article/10.1... Knowing that coculture interactions often disappear in larger communities, we used cocktails of phages to study vitamin exchange interactions within enrichment cultures.
link.springer.com
Phage-based depletion of Variovorax reveals interactions within intact microbiomes - Microbiome
Background Testing microbial interaction hypotheses, including metabolite cross-feeding, remains a major challenge in microbiome research. Phages have the potential to probe organism-organism interact...
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Reposted by Amanda Alker
Tung Le @tunglejic.bsky.social · 08/10/2026
🚨PhD opportunity alert!!! Come work with us on this new cool NERC DTP PhD project Investigate How Bacterial Hosts Control Domesticated Viral Machines to Drive Horizontal Gene Transfer in Marine Environments. Retweet = nice. Thank you!!! aries-dtp.ac.uk/studentships...
aries-dtp.ac.uk
Investigate How Bacterial Hosts Control Domesticated Viral Machines to Drive Horizontal Gene Transfer in Marine Environments? | Aries
Professor Tung Le, John Innes Centre – contact me Professor Jonathan Todd, Quadram Institute & UEA Dr Ngat Tran, John Innes Centre Horizontal gene transfer (HGT) is a major driver of bacterial…
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Reposted by Amanda Alker
Pavel Payne @pavelpayne.bsky.social · 07/10/2026
Finally, my paper is out! It shows how bacteria can utilize their CRISPR immunity against transducing phages to turn them into "pollinators". This way bacteria can speed up their own adaptation through recombination by two orders of magnitude compared to mutations, and they do so when starving!
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Reposted by Amanda Alker
Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 07/10/2026
My session, now in YouTube 👉🏻 youtu.be/j4DvfXN1ldY?...
youtu.be
Synthetic Biology at the Intersection of Science, Ethics and Policy 2
YouTube video by BakerInstitute
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Reposted by Amanda Alker
Vincent Burrus 🇨🇦💙💛 @vincentburrus.bsky.social · 05/10/2026
#plasmidbiology #plasmid Just out! 🚀 Thrilled by our discovery: the function of the C-terminal domain of MOBH1 relaxases! We uncovered this thanks to a fertility inhibitor encoded by a parasitic mobile genetic element. Congrats to Florence on a great piece of work! 👏 academic.oup.com/nar/article/...
academic.oup.com
Conjugative transfer inhibition of IncA and IncC plasmids by SGI1-like elements via relaxosome assembly interference
Abstract. Broad-host-range IncA and IncC (A/C) conjugative plasmids propagate multidrug resistance in bacteria and mobilize chromosomal resistance islands,
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Asaf Levy @asaflevylab.bsky.social · 29/09/2026
Our new preprint is out. www.biorxiv.org/content/10.6... We applied an XGBoost algorithm with genomic and biochemical features to detect all T6SS effectors in bacterial genomes. Next, we validated 3 novel effectors that serve as antibacterial or anti-euk toxins. One of the effectors, from
biorxiv.org
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 24/09/2026
ProFinder: Candidate constitutive promoter prediction across the bacterial tree for genetic tool development in non-model species www.biorxiv.org/content/10.64898/20…
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Willem van Schaik @wvschaik.bsky.social · 20/09/2026
Brilliant paper by the labs of @epcrocha.bsky.social @jrpenades.bsky.social 'Mobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance' www.nature.com/articles/s41...
nature.com
Mobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance - Nature Communications
Plasmids drive bacterial adaptation, but how their diversity arises has remained unclear. Here, they show that in Staphylococcus aureus, mobile genetic elements repeatedly fuse and delete plasmids, re...
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Snorre Sulheim @sulheim.bsky.social · 18/09/2026
Finally online! Cross-feeding enables robust coexistence between four bacterial species | PNAS www.pnas.org/doi/10.1073/... #microsky
pnas.org
Cross-feeding enables robust coexistence between four bacterial species | PNAS
Resource supply is generally considered a dominant driver of microbial diversity. Here, using a four-species bacterial consortium, we asked whether...
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Doudna Lab @doudna-lab.bsky.social · 19/09/2026
Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
science.org
A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas
CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...
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JL Weissman @jlw-ecoevo.bsky.social · 10/09/2026
My lab is hiring two(!) postdocs interested in (1) building trait prediction models capable of resolving complex microbial traits from genomes and metagenomes, and/or (2) building mathematical models of microbial community dynamics www.microbialgamut.com/mGAMUT_postd...
microbialgamut.com
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 09/09/2026
The Institute for Systems Biology in Seattle (@isbscience.org) is recruiting faculty across all ranks. Are you a systems-level thinker who is interested in tackling ambitious problems in biomedical research? Come and join us! isbscience.bamboohr.com/careers/71
isbscience.bamboohr.com
Faculty (Assistant, Associate, or Full Professor)
The Institute for Systems Biology (ISB) seeks a highly motivated andtalented Assistant, Associate, or Full Professor to join our faculty and leadtransformative efforts in AI, machine learning, and com...
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Reposted by Amanda Alker
Phillip Cleves @pcleves.bsky.social · 02/07/2026
Our work on the symbiont-containing organelle that supports coral reefs is published today. Also, new genetic tools to study symbiosis in both corals and Aiptasia. Great work by Shumpei Maruyama, Cat Henderson, and the rest of the fantastic team. #SymbioSky www.cell.com/cell/abstrac...
cell.com
Co-option of lysosomal machinery shapes the evolution of the intracellular photosymbiosis supporting coral reefs
Corals harbor intracellular algal symbionts in specialized organelles that enable them to build diverse reef ecosystems. Corals and other cnidarians have repeatedly evolved this symbiosis through the ...
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Richard Lenski @relenski.bsky.social · 19/08/2026
If Zachary Blount had one dollar for every cell he plated in his dissertation looking for new Cit+ mutations, he could single handedly pay off the US debt of $40,000,000,000,000. www.npr.org/2026/08/19/n...
Zachary Blount with giant stacks of petri dishes used in his research on historical contingency and the evolution of citrate use in the LTEE.
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Savitski Lab @savitski-lab.bsky.social · 20/08/2026
1/5 How much phosphorylation can a single kinase deposit? In our new study with @typaslab.bsky.social out in @nature.com, phage T7's kinase (T7K) modifies almost all the E. coli proteome + more densely than all ~500 kinases do our own proteomes 🤯 www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
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Ursula Hofer @hoferu.bsky.social · 19/08/2026
If you need some inspiration. Bad graphical abstracts can be hilarious. tocrofl.tumblr.com
tocrofl.tumblr.com
TOC ROFL
funny table-of-contents images from scientific journal articles. inspired by crazy TOC images and...
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Cameron Thrash @jcamthrash.bsky.social · 18/08/2026
As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles journals.asm.org/doi/full/10.... #jcampubs
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STCmicrobeblog @stcmicrobeblog.bsky.social · 19/08/2026
#MicroSky maybe we should update this post?
smallthingsconsidered.blog
A two-part res­ur­rec­tion tale (1|2)
by Christoph — Besides a resurrection tale that I'll re­late to in the se­cond part, this post will be about an­ti-de­fense sys­tems of plas­mids as an in­trin­sic part of the seem­ing­ly end­less…
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Reposted by Amanda Alker
Anna Allen @akallen10.bsky.social · 17/08/2026
New NSF BIO solicitation is live.... this replaces the previous IOS, MCB, DEB solicitation www.nsf.gov/funding/oppo...
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Kaçar Lab at UW-Madison @kacarlab.bsky.social · 06/08/2026
🚨 Job alert! 🚨 Join the faculty at UW–Madison Bacteriology! We have two faculty searches: • Asst Prof (Microbial Communities & Bioeconomy) • Asst / Assoc / Full Prof (Systems & Synthetic Biology) Check out the open positions and apply👇 #FacultyJobs #SynBio #Microbiology #Astrobiology #Evolution
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Steven Robbins @stevenjrobbins.bsky.social · 22/07/2026
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...
nature.com
The planktonic microbiome of the Great Barrier Reef - Nature
The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...
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Chuliang Song @clsong.com · 16/06/2026
Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!
drive.google.com
physics_for_biologists.pdf
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Waggoner Lab @labwaggoner.bsky.social · 25/06/2026
Cell-to-cell cooperation through membrane vesicles enhances antibiotic persistence @science.org @bcmfromthelabs.bsky.social www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...
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Vivek Mutalik @vivekmutalik.bsky.social · 21/06/2026
www.sciencedirect.com/science/arti... #microbiomesky #microsky
sciencedirect.com
In situ genetic modification of gut bacteria
The crucial role of the gut microbiome in human health has driven a need to understand bacterial function within their complex native ecosystem. Howev…
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Reposted by Amanda Alker
Antoine Hocher @ahocher.bsky.social · 16/06/2026
Very cool! www.biorxiv.org/content/10.6...
biorxiv.org
A plasmid-encoded H-NS protein selectively binds its own plasmid
H-NS is an abundant nucleoid-associated protein found in Enterobacterales species. Some conjugative plasmids encode H-NS homologues, which are thought to facilitate plasmid maintenance and reduce the ...
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 16/06/2026
Join experts Alexandra Worden, Christian Voolstra & Jennifer Bowen for the webinar Marine microbiology in a changing climate. @northeasterncos.bsky.social @mblscience.bsky.social dlvr.it/TT44v1
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Michael Baym @baym.lol · 28/05/2026
This is very cool: a simple statistical test of dysbiosis, or really any microbiome composition data relative to a reference. Outperforms Bray-Curtis and every other metric, while simultaneously being very simple to compute. Probably would work on RNAseq data too.
Three ROC curves showing RPD outperforming BCD for each dataset
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Amanda Alker @atp-alker.bsky.social · 28/05/2026
So excited for you! I want to be like you when I grow up
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ISME - International Society for Microbial Ecology @isme-microbes.bsky.social · 26/05/2026
What is the scope of ISME Host Microbe, ISME's newest journal? Effects of antimicrobial agents, human activities, immunity and environment on AND ecological studies, cross-kingdom studies, microbiome studies of host-microbiome/microbe interactions academic.oup.com/ismehm/pages... #MicrobialEcology
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Tami Lieberman @contaminatedsci.bsky.social · 22/05/2026
Missed this very cool protocol for amplicon sequencing using nanopore
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Mark Mandel @markjmandel.bsky.social · 14/05/2026
event.fourwaves.com/vibrio2026/p...
event.fourwaves.com
Vibrio2026: The International Meeting on the Biology of Vibrios
Join Vibrio2026: The International Meeting on the Biology of Vibrios, September 13-16, 2026. Learn more on Fourwaves.
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Amanda Alker @atp-alker.bsky.social · 11/05/2026
Way to slay @leosong.bsky.social
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Ákos T Kovács @evolvedbiofilm.bsky.social · 11/05/2026
See a brief review summarizing the use of synthetic microbial communities (SynComs) for revealing the ecology of specialized metabolites [my holiday break writing exercise] portlandpress.com/essaysbioche... #MicrobiomeEcology at Institute of Biology Leiden (IBL)
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Martin Polz @polzlab.bsky.social · 06/05/2026
Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...
nature.com
Genome-wide sweeps create ecological units in the human gut microbiome - Nature
Genome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.
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bioRxivpreprint @biorxivpreprint.bsky.social · 01/05/2026
Plasmid-plasmid interactions reshape extracellular vesicle cargo and gene transfer potential www.biorxiv.org/content/10.64898/20…
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Amanda Alker @atp-alker.bsky.social · 01/05/2026
The viruses from Contagion and I am Legend!
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Amanda Alker @atp-alker.bsky.social · 01/05/2026
Way to go @cresslab.bsky.social! So excited to see this out and how much the story progressed — stoked for a new flavor of microbiome editing!
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Cress Lab @cresslab.bsky.social · 30/04/2026
Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.
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Doudna Lab @doudna-lab.bsky.social · 27/04/2026
We present VIPR, a phage-encoded RNA-guided system that recognizes DNA with a noncontiguous code unlike CRISPR. Tiny, programmable, possibly ancestral to CRISPR immunity; VIPR is built around a striking RNA-DNA-DNA triplex.
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Cameron Thrash @jcamthrash.bsky.social · 23/04/2026
Our first collaboration with the Levine lab! Defining metabolic niches for marine microbial heterotrophs www.science.org/doi/full/10.... #jcampubs 🌊
science.org
Defining metabolic niches for marine microbial heterotrophs
Understanding carbon cycling requires simplifying bacterial diversity into functional groups defined by genetic signatures.
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Tyler J. Carrier @tylerjcarrier.bsky.social · 23/04/2026
New paper entitled "Sea urchin eggs contain a plastid-derived structure that contributes to their development" is now out in @plosbiology.org! Here is a summary... journals.plos.org/plosbiology/...
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The Daily Pub @thedailypub.bsky.social · 21/04/2026
Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.
doi.org
Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.
Published in The ISME journal
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Nick Pizzo @nickpizzooceans.bsky.social · 18/04/2026
Our recent paper on using thermal imagery from geostationary satellites to infer surface currents was published! We call the method GOFLOW 🧪🌊 www.nature.com/articles/s41...
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Harmit Singh Malik @harmitmalik.bsky.social · 16/04/2026
@hhmi-science.bsky.social's #FreemanHrabowski Scholars Program offers early career faculty up to $10M over 10 yrs, plus salary & benefits Stable, sustained support can transform your career: Senior Postdoc? This year's competition has a program for you too. Applications open 11/3! bit.ly/4vhC0LA
bit.ly
Early Career Faculty Program | Freeman Hrabowski Scholars | HHMI
The Freeman Hrabowski Scholars Program offers comprehensive support to outstanding early career faculty committed to scientific excellence in their own research, and to fostering labs that expand the ...
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Sophien Kamoun @kamounlab.bsky.social · 13/04/2026
I just published Don’t Perish! A Step-by-Step Guide to Writing a Scientific Paper (2026 edition) Great science deserves to be read—not buried under unclear writing. This is the updated 2026 edition of your favorite guide to writing scientific papers. medium.com/p/dont-peris...
medium.com
Don’t Perish! A Step-by-Step Guide to Writing a Scientific Paper (2026 edition)
Great science deserves to be read — not buried under unclear writing. This is the updated 2026 edition of your favorite guide to writing…
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Scripps Institution of Oceanography @scrippsocean.bsky.social · 13/04/2026
🌊 Scripps Oceanography researchers developed an #AI approach that can spot patterns in satellite thermal imagery of the sea to reveal ocean currents in unprecedented detail. Learn how this advancement increases insights into ocean surface temperatures. ⤵️
today.ucsd.edu
New AI Approach Reveals Ocean Currents in Unprecedented Detail
Scientists have developed a new method to measure ocean surface currents over large areas in greater detail than ever before.
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