Ellinor Alseth

New home office assistant is doing his part to help boost morale

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

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

New family member added! Say hello to Molotov 🔥

Published in Current Biology! P. aeruginosa can use its filamentous phage to inhibit competitors but high phage production is susceptible to cheater miniphage invasion. Subsequent phage tragedy of the commons can lower bacteria and phage fitness. Link: authors.elsevier.com/c/1lt5I3QW8S...

So happy for you! This work is honestly so amazing, congrats 🎉

DYK most P. aeruginosa carry filamentous phage(s) that don't need to kill the cell to reproduce?

We 👉🏻@nanamikubota.bsky.social show that these Pf phages can go ROGUE.

"Filamentous cheater phages drive bacterial and phage populations to lower fitness"

🔗 authors.elsevier.com/c/1lt5I3QW8S...

A teal flyer for a PhD opportunity to investigate how warming may change antimicrobial resistance. The project will use experiments on Klebsiella bacteria to answer questions about how temperature affects their response to antibiotics, plasmid transfer, and fitness costs. The research involves microbiology lab work, bioinformatics, and mathematical modeling. The flyer includes contact details for Dr. Daniel Padfield and the logos of the sponsoring institutions.

I have an MRC-funded PhD project available (www.exeter.ac.uk/study/fundin...) on how warming will change the problem of AMR. Join a small and friendly group (padpadpadpad.netlify.app/about) in (sometimes) sunny Cornwall. 🧪🦠 #microsky

Please share the ad below with anyone who may be interested.

Come and work with me and @ariannebabina.bsky.social on #Streptomyces evolution and antibiotic production

Origins of a tangled bank: Adaptation and evolution in antibiotic-producing Streptomyces

www.gla.ac.uk/postgraduate...

please repost

The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem

#CurrOpinMicrobiol from @lgbacteria.bsky.social

www.sciencedirect.com/science/arti...

A link to the past: classical phage ISP infects the recently described Staphylococcus borealis species - Virology Journal Background Staphylococcal infections, caused by a large variety of species within the Staphylococcus genus, are a threat to human health. Although antibiotics are the current choice of treatment for these infections, bacteriophage (phage) therapy has been used with success against Staphylococcus since the dawn of phage therapy. In 2020 a new coagulase-negative species named Staphylococcus borealis was described in Norway. In this study, we focused on understanding phage infections in S. borealis. Methods: First, we predict the presence of prophages and phage-defence mechanisms in the genomes of a collection of twelve S. borealis strains by bioinformatics. We also attempted to isolate S. borealis-infecting phages from Norwegian samples and tested the host-range of three known staphylococcal phages against a panel of fifty Norwegian staphylococcal strains. Results: The presence of prophages and phage defence systems was verified in all tested S. borealis strains. No local Norwegian phages could be obtained in a phage isolation attempt targeted towards S. borealis. The host range analysis shows that phage ISP, originally isolated in the 1920s and still used for phage therapy to date, can infect S. capitis and the S. borealis Hus23 strain. Phage ISP was shown to limit S. borealis Hus23 growth in liquid cultures and lower the formation of biofilm by the bacterium. The efficiency of plating of phage ISP can be improved by repeated passages in the new S. borealis Hus23 host. Conclusions: here we expand the known host range of the traditional phage ISP by showing that it also infects S. borealis and can be adapted to the new host by serial passages, showcasing the flexibility of phages as an antimicrobial strategy.

Collab with the Norwegian team at UiT – Tromsø : #phage ISP infects #Staphylococcus borealis species and its efficacy was boosted by adaptation to enable #phagetherapy use.

doi.org/10.1186/s129...

#Microbiology #HostRange #Antimicrobials #PhageAdaptation #NewSpecies #AMR

When you swear to never work on phages, but phages still work on you… :)

Very cool story!!!

View from the lab now. Did I mention that we are recruiting faculty microbiologists?

www.linkedin.com/posts/vaughn...

Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!

www.microbiologyresearch.org/content/jour...

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations

royalsocietypublishing.org/doi/epdf/10....

Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska

Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections - Nature Microbiology The Entelli-02 phage product containing five phages has frontline potential to address infections caused by the multidrug-resistant Enterobacter cloacae complex.

Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology.

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

Faculty Professor Associate - Full-Time | Vaughn Cooper We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one syst...

How much of selection in human microbiomes is driven by phage?

Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin

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

🧵

Prestige over merit: An adapted audit of LLM bias in peer review Large language models (LLMs) are playing an increasingly integral, though largely informal, role in scholarly peer review. Yet it remains unclear whether LLMs reproduce the biases observed in human de...

Yet again, machine learning — even gussied up via the transformer architecture — encodes and reinforces societal biases.

This study reveals that LLM-based peer review relies heavily on author institution in its decisions.

arxiv.org/abs/2509.15122

Microbial risks triggered by oral administration of antibiotics in fish aquaculture persist long after the legally mandated antibiotic withdrawal time - Nature Water Florfenicol treatment substantially increased the abundance and mobility of antibiotic resistance genes (ARGs) in the common carp gut microbiome. The resistome and mobilome profiles failed to return t...

🐟💊🦠Our new study in @natwater.nature.com 🐟💊🦠

"Microbial risks triggered by oral administration of antibiotics in fish aquaculture persist long after the legally mandated antibiotic withdrawal time"

www.nature.com/articles/s44...

#microsky #amr
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Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes Abstract. Plasmid conjugation is a major driver of antibiotic resistance dissemination in bacteria. In addition to genes required for transfer and maintena

Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes url: academic.oup.com/nar/article/...

Phage-mediated lysis increases growth rate of surviving bacterial cells Bacterial phage infection and subsequent lysis are traditionally considered mechanisms of bacterial mortality and viral propagation; additionally, emerging evidence indicates that they may also contri...

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

#phagesky #phage
Anecdotally, a few years ago a very trigger-happy temperate had infected a strain of E. coli of mine and caused significant lysis. The release of enzymes in the medium degraded a sugar into a different form which could be used by the other cells.

This promises to be a great read!
“the pathogenicity island was horizontally transferred from Yersinia pestis to E. coli and other Enterobacterales approximatively 4,800 years ago” ⏩️ it then spread to Klebsiella and positively selected over the last 100 yrs ago

A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome Plasmids play a pivotal role in the horizontal gene transfer of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) ca...

Super paper from the mighty Mia Winkler, @genomarit.bsky.social and Iren Lohr.
"We have previously shown that there were relatively few strain-sharing events across ecological niches...plasmid-sharing is considerably more common across niches than strain-sharing. "
www.biorxiv.org/content/10.1...

If there were a collection of E. coli with every combination of a bunch of resistance markers fluorophores on the chromosome, would this be something people would be interested in using?

Congrats!

Population densities and frequencies of protease-deficient mutants over time. Differences in environmental factors associated with inflammation varied the population density (A) and the frequency of evolved protease-deficient mutants, PDMs (B), over time. Box plot tracks the average and overall distribution of population density at each detected time point within each selective environment. Each line shows the tracked population density or PDM frequency along the daily passage in a single population, grouped by selective environments (Casein SCFM or casamino acids, labeled CAA SCFM, and with or without supplemented 2 mM hydrogen peroxide, OS±).

Using experimental evolution in host-mimicking media, researchers show that inflammation-like environments limit the loss of quorum sensing—a common adaptation during chronic infections—in Pseudomonas aeruginosa. Learn more in #mSystems: asm.social/2vd

How do loci for bacterial capsules (Klebsiella) manage to get swapped around despite their outstanding phenotypes? They just plug and play, having little impact on the rest of the genome. Kudos to @julielebris.bsky.social , check her thread below

Programmable antisense oligomers for phage functional genomics - Nature Establishing antisense oligomers as versatile, non-genetic tools to silence phage mRNAs opens applications in basic research and biotechnology, as shown by identifying essential factors for propagatio...

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

#phagesky #phage

A screenshot of Google Maps of Oxbridge, Dorset

My plans to start a new university in Dorset have run into significant economic headwinds, but I am confident that the business case is solid