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Enea Maffei

@phagemuffin.bsky.social
242 followers 305 following 24 posts

Post-doc at D-HEST, ETH Zurich. PhD in microbiology at Biozentrum, Basel. Phagehunter. Hiker. Scout. Music and food enthusiast. Per aspera ad astra orcid.org/0000-0002-0751-9572

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Reposted by Enea Maffei
Dorentina Humolli @humollidorentina.bsky.social · 25/09/2026
Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com! Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems. www.nature.com/articles/s41...
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Alexander Harms @aharms485.bsky.social · 25/09/2026
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4
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STCmicrobeblog @stcmicrobeblog.bsky.social · 20/09/2026
*all* microbiologists take note👇 𝗕𝗮𝗰𝘁𝗲𝗿𝗶𝗮𝗹 𝗴𝗿𝗼𝘄𝘁𝗵 𝗶𝘀 𝘀𝘁𝗿𝗮𝗶𝗴𝗵𝘁𝗳𝗼𝗿𝘄𝗮𝗿𝗱 𝘁𝗼 𝗺𝗲𝗮𝘀𝘂𝗿𝗲, 𝗰𝗼𝗺𝗽𝗹𝗲𝘅 𝗶𝗻 𝗼𝗿𝗶𝗴𝗶𝗻 𝗮𝗻𝗱 𝗲𝘅𝗾𝘂𝗶𝘀𝗶𝘁𝗲𝗹𝘆 𝘀𝗲𝗻𝘀𝗶𝘁𝗶𝘃𝗲 𝘁𝗼 𝗲𝗻𝘃𝗶𝗿𝗼𝗻𝗺𝗲𝗻𝘁𝗮𝗹 𝗮𝗻𝗱 𝗴𝗲𝗻𝗲𝘁𝗶𝗰 𝗽𝗲𝗿𝘁𝘂𝗿𝗯𝗮𝘁𝗶𝗼𝗻𝘀. a first sentence like the opening chords of beethoven's fifth... 😉
beethoven, 5th symphony opening

https://www.omifacsimiles.com/brochures/bee5.html
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Enea Maffei @phagemuffin.bsky.social · 10/09/2026
Rich in life because I get to work with the best students
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Alexander Harms @aharms485.bsky.social · 17/08/2026
Summer trip with the group and local colleagues across Lake Zürich - great fun together on the boats and in the water! ☀️🏖🌊
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Zamin Iqbal @zaminiqbal.bsky.social · 13/08/2026
you are (I am) never too old to make a reverse complement error
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 29/06/2026
Competition against the intestinal microbiota selects for pathoadaptive traits in ESBL E. coli www.biorxiv.org/content/10.64898/20…
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Emma Slack @mucosalimmunology.bsky.social · 01/07/2026
We are recruiting a lab manager for my group in Oxford. This is a lovely team doing great things, and you could be an important part of it! See here: www.path.ox.ac.uk/vacancy/lab-... Please spread the word!
path.ox.ac.uk
Lab Manager - Molecular Immunology - Dunn School
Laboratory Manager/Senior Scientist position in the Molecular Mucosal Immunology group at Oxford
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Itai Yanai @itaiyanai.bsky.social · 24/06/2026
🔥 Published today, and just in time for summer conferences, here are your guidelines for presenting badly www.nature.com/articles/s41... rdcu.be/fqa92
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Enea Maffei @phagemuffin.bsky.social · 18/06/2026
Phage hunting never gets boring 😁
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Alexander Harms @aharms485.bsky.social · 09/06/2026
The "Research Day" at our department D-HEST is always caleidoscope of exciting science from food over health to medicine. Phage biotechnology was well represented with Dorentina @humollidorentina.bsky.social and Enea @phagemuffin.bsky.social from our group and the lab of Martin Loessner. 🧫🧬🍻
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Chenxin Li, PhD @chenxinli2.bsky.social · 20/05/2026
Writing a manuscript is like making a documentary. Instead of a film, it’s in writing and figures. Writing a proposal is like writing evidence based science fiction.
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Vivek Mutalik @vivekmutalik.bsky.social · 20/05/2026
🎊 New Preprint from phagefoundry.org ! Super excited to share our latest work on generating systematic phage-MDR P. aeruginosa interaction dataset & use of ML to predict phage susceptibility & phage cocktails from target genome sequences alone, w validations www.biorxiv.org/cgi/content/...
Systematic lytic host range characterization of 99 multidrug resistant Pseudomonas aeruginosa strains against 95 diverse double strand DNA phages, and AI/ML workflow to predict phage susceptibility and cocktail formulation based on genomic sequence alone.
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Alexander Harms @aharms485.bsky.social · 20/05/2026
Some phages are named after gods or rivers, this one was named by journalist Thilo Mischke @thilomischke.bsky.social after his grandma ("Oma Karin") while filming in our lab. It's a cool phage that should be temperate but became virulent due to a transposon at its lysogeny control! ⛓️‍💥💪🏼
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New Concepts in Prokaryotic Virus-Host Interaction @spp2330.bsky.social · 18/05/2026
📢 Registration for our International Symposium on “New Concepts in Prokaryotic Virus-Host Interactions” is now open! 🗓️ 5–7 October 2026 📍 Harnack House, Berlin, Germany ➡️ Information and registration: spp2330.de/symposium-20...
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Alexander Harms @aharms485.bsky.social · 18/05/2026
Small fun story from the lab about a slightly crazy rabbit hole or "guess what's living in your agar?" - all the details in the thread by Enea @phagemuffin.bsky.social 👇🏼🔥
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Enea Maffei @phagemuffin.bsky.social · 18/05/2026
1/6 👻 Something strange in your liquid agar? Who you gonna call? Thermophile hunters. Our new @asm.org #MRA paper reports the complete genome sequence of Geobacillus stearothermophilus strain CS7089 isolated from a commercial agar preparation.
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Tobias Warnecke @tobiaswarnecke.bsky.social · 08/04/2026
academic.oup.com/genetics/adv... Also thanks to Lyndall & @psarkies.bsky.social, @ahocher.bsky.social, and members of the lab for their comments and Francis Barr @oxfordbiochemistry.bsky.social for encouraging me to write down my thoughts. 2/2
academic.oup.com
Actually, what is a gain-of-function mutation?
Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Rob Edwards @linsalrob.bsky.social · 05/04/2026
Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky
biorxiv.org
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European Centre for Disease Prevention and Control @ecdc.europa.eu · 01/04/2026
Did you know? 🧵 1/3
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Alexander Harms @aharms485.bsky.social · 13/03/2026
Fantastic snow excursion of the lab together with our friends in Martin Loessner's group 🏔😁☀️
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Aritz Roa-Eguiara @aritz-roa.bsky.social · 07/03/2026
🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process. www.biorxiv.org/content/10.6...
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Amanda Moehring @flybehaviour.bsky.social · 13/02/2026
Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself. www.science.org/doi/10.1126/...
science.org
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
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Simon van Vliet @simonvanvliet.bsky.social · 11/02/2026
Excited to share first preprint from our lab! @giubotti.bsky.social found that antibiotic tolerance in multispecies biofilms follows a surprising spatial pattern: cells survive only at intermediate distances from a partner species. 🦠 Preprint: doi.org/10.64898/202...
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Alexander Harms @aharms485.bsky.social · 03/02/2026
It seems that NCBI GenBank is currently not active beyond the repository itself and has also been unresponsive to requests for a while already. Do you think this may be a transient inconvenience or a sign that we should explore alternatives such as ENA at EMBL-EBI?
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Vaughn Cooper @vscooper.micropopbio.org · 20/01/2026
What could mirror bacteria do in nature if created? A story of these prospects and a plan to prevent them. Titles aside, I hope you'll read it (the tech is NOT close). Thanks to Tom Freeman for writing help & @jfischman.bsky.social for ace editing! www.scientificamerican.com/article/life...
scientificamerican.com
Life’s evil twins, called mirror cells, could wipe us out if scientists don’t stop them
Researchers are close to making “reversed” cells that may wipe us off the planet
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George Bouras @gbouras13.bsky.social · 14/01/2026
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
academic.oup.com
Protein structure-informed bacteriophage genome annotation with Phold
Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.
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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026
We've got ISSUES. Literally. We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do? arxiv.org/abs/2601.07563 A 🧵 1/n
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Nature Microbiology @natmicrobiol.nature.com · 19/12/2025
As the year ends, we decided to select our favorite papers of 2025 Turns out, it is impossible as we love them all! So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology. Here is a glimpse into #EditorPicks of 2025 #MicroSky 🦠
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The Struggling Scientists @thestrugglings4.bsky.social · 17/12/2025
Do you relate to this as well?
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Our World in Data @ourworldindata.org · 17/12/2025
During the Cold War, US President Reagan put nuclear war in clear words: “A nuclear war cannot be won and must never be fought. The only value in our two nations possessing nuclear weapons is to make sure they will never be used. But then would it not be better to do away with them entirely?”
Line chart showing the nuclear arsenals of Russia and the United States, plus all other nuclear powers, from 1945 to 2024. After a large build-up during the Cold War, nuclear arsenals in the US and Russia have decreased in the last decades. But both still have thousands of warheads. The data source is the federation of American Scientists (2024). The chart is licensed CC BY to Our World in Data.
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Vaughn Cooper @vscooper.micropopbio.org · 02/12/2025
ICYMI, this new preprint is just awesome. "Here, we show that O-antigen–dependent trade-offs between pathogenicity and interbacterial competition have persisted for over two centuries in natural P. viridiflava populations." www.biorxiv.org/content/10.1...
biorxiv.org
Persistent trade-offs balance competition and colonization across centuries
Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments...
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PLOS Biology @plosbiology.org · 28/11/2025
Capsule diversity limits #phage host range by affecting receptor-binding protein (RBP) interactions in capsulated #bacteria. @pilardomingoc.bsky.social &co show that generalist phages evolve host range via RBP mutation & recombination, but specialists remain stable @plosbiology.org 🧪 plos.io/48nvOqY
Graphic representation of the recombination events in the Sugarlandvirus I and J variants. Top left: Representation of the variants isolates in the different strains in the three lines. Genome fragments of each parent are represented in a different color. Regions with the most abundant recombination events are marked and associated with a schematic representation of the functional annotation and intergenomic similarity between the two parental phages. Bottom left: 3D folding of the RBPγ. The consensus recombinant region, which is associated with the infection of the K-type 47, is represented in light orange. Variable positions detected in the protein sequence alignment of the variants are represented as hot pink spheres. The table indicates the percentage of identity of the parental protein sequences in three protein regions limited by the amino acids indicated. Right: Transmission electron microscopy (TEM) image of Klebsiella myoviruses artificially coloured, showing their characteristic contractile tails and icosahedral capsids. Image acquired by the Environmental and Biomedical Virology group (Institute for Integrative Systems Biology, Universitat de València-CSIC).
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Klebsiella Phage Collection @klebphacol.bsky.social · 22/11/2025
KlebPhaCol paper is now out! Go check it out and see all that we offer. And when ready, visit our website for more: www.klebphacol.org
klebphacol.org
KlebPhaCol
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Science Magazine @science.org · 25/11/2025
Some archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science. The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. scim.ag/4omApQ7
scim.ag
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
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Sullivan Lab at OSU @sullivan-lab.bsky.social · 21/11/2025
🚨NEW paper: Benchmarking Hi-C for virus–host inference journals.plos.org/plosbiology/... A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages. Key results: 👇
journals.plos.org
Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking
Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...
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Dorentina Humolli @humollidorentina.bsky.social · 20/11/2025
In bacteria, TnSeq revolutionized genetics by linking genes to phenotypes at scale. But for phages nothing equivalent exists. So we built HIDEN-SEQ, the first TnSeq approach for phages, enabled by a hide-and-seek interplay between the host CRISPR-Cas13a and a phage anti-CRISPR protein.
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Alexander Harms @aharms485.bsky.social · 20/11/2025
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8
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Dorentina Humolli @humollidorentina.bsky.social · 20/11/2025
🚀New preprint from our lab! I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡 Continue reading (🧵)
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Erik Bakkeren @erikbakkeren.bsky.social · 07/11/2025
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...
nature.com
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.
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 01/11/2025
Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine www.biorxiv.org/content/10.1101/202…
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Meade Krosby @meadekrosby.bsky.social · 07/11/2025
Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).
science.org
Rosalind Franklin and the damage of gender harassment
Spurred by a recent report on sexual harassment in academia, our columnist revisits a historical case and reflects on what has changed—and what hasn’t
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Ricardo León-Sampedro @rleonsampedro.bsky.social · 07/11/2025
🚨 Excited to share our new paper is out! 🎉 We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut. Now published in @natcomms.nature.com rdcu.be/eOf63
rdcu.be
Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes
Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...
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Alexander Harms @aharms485.bsky.social · 05/11/2025
Bacterial Halloween mask crafted by uniquely talented MSc student Dominic Spichtig - the team of Enea @phagemuffin.bsky.social is setting new standards in the lab! 🎃🔥🧬
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Enea Maffei @phagemuffin.bsky.social · 27/10/2025
Happy to see this hit the public! A story worth checking out that started back during my days as master student 🧑‍🔬🧬🦠
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Ellie Jameson @elliejameson.bsky.social · 22/10/2025
Day 22, GOAT. The most iconic (if not the greatest phage of all time) in terms of looks are myovirus like phages. They look like a lunar lander and are instantly recognisable as a virus. #Drawtober #SciArt #PhageSky
Black and white ink drawing of a myovirus, with polyhedral capsid, collar, tail and long articulated tail fibres
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Jeremy Barr @jeremyjbarr.bsky.social · 15/10/2025
Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
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Evelien Adriaenssens @evelienadri.bsky.social · 10/10/2025
For those of you working on tailed #phages, this is the virus realm for you! #Duplodnaviria #virus #taxonomy The Profile in #JGenVirol provides the citable reference. More details in the chapter on the ICTV website: ictv.global/report/chapt...
ictv.global
Duplodnaviria | ICTV
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Ellie Jameson @elliejameson.bsky.social · 04/10/2025
Day 4, Claw. Phages don't really have claws, but they do have tail fibres that recognise receptors on host cells and clamp on, allowing phage particles to infect their hosts. #drawtober #SciArt #Phagesky
Black and white ink drawing of a bacteriophage with an icosahedral capsid short tail and crab claws instead of tail fibres. The ink drawing has a thick black outline and minimal shading
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