Amanda Alker

illustration of petri dishes growing different microbes

We're excited to help launch the inaugural Gordon research conference on #microbiome editing, coming up in January in Pomona, CA! Learn more and register here: https://ow.ly/a6Am50X9XkE

BarTn7: Optimizing Bacterial Lineage Tracking at Sub-Species Resolution for Population Dynamics in Ecological and Evolutionary Studies Communities of bacteria undergo population bottlenecks which are crucial to their population, ecological, and evolutionary dynamics. However, conventional amplicon sequencing cannot distinguish such d...

Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments.
www.biorxiv.org/content/10.1...

Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis | mSystems Variation among strains of a bacterial species is a powerful factor underlying the intensity of host responses during pathogenic infections. Less is known about the cellular and molecular responses of...

Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis

in #mSystems from Margaret McFall-Ngai

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

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/...

What is the best strategy to win any contest?

Eliminate your opponents of course.

Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.

www.biorxiv.org/content/10.1...

The Lariviere lab at UMiami is recruiting PhD students! Incoming students will join us in studying host-microbe interactions in the honey bee gut, using molecular and genetic approaches. Please see the attached flyer for more details.

#Symbiosis #SymbioSky #MicroSky #PhDOpportunity #AcademicJobs

Figure 3. Conjugation tractability mutant screen results.

We also performed a neat screen where you deliver a plasmid to the RB-TnSeq library, and select to enrich gene mutants with improved transformation efficiency. This is kind of similar to a recent approach by @cresslab.bsky.social and colleagues (www.biorxiv.org/content/10.1...)

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.

Apply and come be my colleague!

Strain displacement in microbiomes via ecological competition - Nature Microbiology Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Bacterial warfare is associated with virulence and antimicrobial resistance - Nature Communications Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...

So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...

Growth-coupled microbial biosynthesis of the animal pigment xanthommatin — Led by Leah Bushin, featuring M. Gracia Alvan, @danielvolke.bsky.social @oscarpuiggene.bsky.social in a fantastic collaboration w/Brad Moore @labnikel.bsky.social @natbiotech.nature.com 🦑
www.nature.com/articles/s41...

Adapting CRISPR-associated transposons for rapid and high-throughput reverse genetics CRISPR-associated transposons (CAST) use guide RNAs to direct their transposition and are being harnessed as tools for programmable genome engineering across diverse bacterial species. However, CAST s...

#mycrosky #synbio

www.biorxiv.org/content/10.1...

Development of a CRISPR/Cas9-induced gene editing system for Pseudoalteromonas fuliginea and its applications in functional genomics journals.asm.org/doi/full/10.... #jcampubs

Bacteriophages of the predominant coral symbiont Endozoicomonas: novel models for coral holobiont interactions https://www.biorxiv.org/content/10.1101/2025.10.29.685362v1

Binary vector copy number engineering improves Agrobacterium-mediated transformation - Nature Biotechnology Agrobacterium-mediated transformation of plants and fungi is enhanced by plasmid copy number variants.

Agrobacterium-mediated transformation of plants and fungi is enhanced by plasmid copy number variants go.nature.com/3CdewQS
rdcu.be/eNaje

Can synthetic biology help save endangered ecosystems?
Our new paper with @vmaull.bsky.social explores how engineered genes can spread through soil microbes.
We model how synthetic gene transfer can support biodiversity. @vdlorenzo.bsky.social @guimaguade.bsky.social www.biorxiv.org/content/10.1...

What an incredible opportunity to meet with my symbiosis superheroes, establish new collaborations and put the Alker Lab on the map.
Thanks @memartino.bsky.social and @raquelpeixoto.bsky.social for organizing and bringing us all together in such a beautiful venue!

Generating gnotobiotic bivalves: a new method on Manila clam (Ruditapes philippinarum) | Microbiology Spectrum The extensive diversity of host-microbe symbioses across ecosystems requires the use of different models to identify conserved and specific processes underlying such relationships. The need for novel models is particularly relevant in the context of the ...

Extending microbiome research across diverse organisms is key to understand the complexity of host–microbe symbioses

In our latest study, we developed a protocol to generate #gnotobioticclams
We hope it will be useful for a wide range of bivalves to test microbial traits in nature and aquaculture

Please share this with anyone who may be interested in a post-doc in Germany:

jobs.awi.de/Vacancies/20...

This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.

We're excited to share with everyone a preprint of our manuscript that resolves the cellular origins of the symbiosome in cnidarian-algal symbiosis through proteomics of the symbiosome, RNAi, and CRISPR/Cas9 experiments. ⬇️
www.biorxiv.org/content/10.1...

Read on below!

1/12 🧵

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

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!