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Duerkop Lab

@duerkoplab.bsky.social
968 followers 435 following 7 posts

Phages and other mobile genetic elements of bacteria | Microbiome and pathobionts | Associate Professor CU-Anschutz | www.duerkoplab.org

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Vivek Mutalik @vivekmutalik.bsky.social · 29/09/2026
Happy to share that @averynoonan.bsky.social paper “Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning” is now published in @natmicrobiol.nature.com 🎉🎊 👉🏽 rdcu.be/nR2NizD7H5va
Machine learning workflow for GenoPHI platform
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Duerkop Lab @duerkoplab.bsky.social · 23/09/2026
Better late than never. Congrats to former PhD trainee Shelby Andersen on the publication of RADS. RADS identifies antiphage defense systems connected to small serine recombinases. The question remains, why are defense systems often placed in this context? 🤔 journals.plos.org/plosbiology/...
journals.plos.org
Small serine recombinases are markers for antiphage defense system discovery
Identifying antiphage defense systems is challenging for bacterial species where such systems are understudied. This study describes a bioinformatic pipeline that uses a small serine recombinase as a ...
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Daria Van Tyne @dariavantyne.bsky.social · 22/09/2026
My lab at Pitt is looking for a Laboratory Technician to help our research and phage therapy efforts. Please share and apply! cfopitt.taleo.net/careersectio...
cfopitt.taleo.net
Laboratory Technician
Click the link provided to see the complete job description.
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Duerkop Lab @duerkoplab.bsky.social · 16/09/2026
SAVE THE DATE! We are excited to announce that the 7th International Conference on Enterococci will be held 25-28 August, 2027 in Munich!! Registration and other details to come soon.
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Manuel Kleiner @manuelkleiner.bsky.social · 10/07/2026
The type and amount of bacterial DNA carried by virus-like particles in the gut microbiome is simply mind-boggling. Amazing work by PhD candidate Jessie Maier in my group and collaborators @duerkoplab.bsky.social and Ben Callahan www.biorxiv.org/content/10.6...
biorxiv.org
Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome
Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of...
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 23/06/2026
Our Dept of Microbiology & Immunology @Geisel School of Medicine @Dartmouth has an opening for an Assistant Professor. Looking for programs bridging multiple areas in Micro & Immuno. A great place to be! Programs: www.M2P2.org www.dartmouthbiofilm.org Job ad: apply.interfolio.com/187637
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Kimberly Kline 🏔 @kimingeneva.bsky.social · 27/01/2026
Lactic acid lover? Check out @ronni.bsky.social 's new work in @cp-cellhostmicrobe.bsky.social showing how Enterococcus faecalis-derived LA suppresses macrophage activation, in turn promoting bacterial persistence and polymicrobial wound infection in vivo. www.sciencedirect.com/science/arti...
sciencedirect.com
Enterococcus faecalis-derived lactic acid suppresses macrophage activation to facilitate persistent and polymicrobial wound infections
Macrophage activation is essential for innate immunity and antimicrobial defense. We show that Enterococcus faecalis suppresses macrophage activation …
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Peter Dougherty @peterdoug.bsky.social · 29/12/2025
Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated! Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking. Thanks to all co-authors for such a great collaboration!
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Ákos T Kovács @evolvedbiofilm.bsky.social · 09/11/2025
The hitchhiker’s guide to cross-species DNA delivery @cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez www.cell.com/trends/micro...
cell.com
The hitchhiker’s guide to cross-species DNA delivery
Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski, et al. reveal how phage satellites assemble chimeric infective particles that deliver DNA across species bound...
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Willem van Schaik @wvschaik.bsky.social · 08/11/2025
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews academic.oup.com/femsre/advan... (accepted manuscript version) TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com
Resistance to last-resort antibiotics in enterococci
Abstract. The genus Enterococcus comprises a diverse group of species, many of which are commensal members of the gut microbiota of humans and animals. The
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Emmanuele Severi @emmseveri.bsky.social · 22/10/2025
www.pnas.org/doi/10.1073/... #microsky
pnas.org
Proteolytically activated antibacterial toxins inhibit the growth of diverse gram-positive bacteria | PNAS
Many species of bacteria produce small-molecule antibiotics that enter and kill a wide range of competitor microbes. However, diffusible antibacter...
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Duerkop Lab @duerkoplab.bsky.social · 20/10/2025
Excited to share some new work from the lab, led by @shelbyeandersen.bsky.social where we developed a method and computational pipeline to identify antiphage defenses across diverse bacterial phyla.
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José R Penadés @jrpenades.bsky.social · 14/10/2025
Our latest work reveals that arbitrium phages cross-communicate across species! These tiny viruses “listen” to signals from others, coordinating lysis-lysogeny decisions across species. Original idea from @albertomarina.bsky.social and, as usual, he was right. www.biorxiv.org/content/10.1...
biorxiv.org
Phages communicate across species to shape microbial ecosystems
Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...
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Haider Manzer @haidermanzer.bsky.social · 09/07/2025
I’m extremely honored to be included with this amazing group of scientists as a recipient of the 2025 BWF PDEP award!
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Prof Peter Hotez MD PhD DSc(hon) @peterhotezmdphd.bsky.social · 13/04/2025
My latest in @plosbiology.org Look I get it, it seems really dark, but there are opportunities. My paper explores some ideas and tries to guide ways of thinking through the anticipated challenges. An emphasis on America’s “biohubs” and entrepreneurship journals.plos.org/plosbiology/...
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Joshua Weitz @joshuasweitz.bsky.social · 31/05/2025
How bad will it be? Catastrophic. Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come. But, this is the WH's *proposed* budget. Speak up now before it is too late. (inflation adjusted $-s below)
NSF, NASA and NIH budgets per year, inflation adjusted from 2000-2025 along with the proposed cuts. NSF includes research component only. Massive cuts across all sectors, well below support spanning 25 years.
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Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · 31/05/2025
10/ And to reiterate a key point: CONGRESS 👏 SETS 👏 BUDGET 👏 LEVELS Today's update is called a **request** for a reason. And Congress should reject it. History provides optimism:
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Andreas Bäumler @abaumler.bsky.social · 12/05/2025
Great meeting coming up next May www.keystonesymposia.org/conferences/...
keystonesymposia.org
Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection | Keystone Symposia
Join us at the Keystone Symposia on Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection, May 2026, in Breckenridge, with field leaders!
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Carl T. Bergstrom @carlbergstrom.com · 30/05/2025
Gold standard science
nytimes.com
White House Health Report Included Fake Citations
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Andrea Love, PhD | Biomedical Scientist @drandrealove.bsky.social · 29/05/2025
RFK Jr’s COVID vaccine rollback will kill people—including kids. Read my latest: news.immunologic.org/p/rfk-jrs-co... Unlike RFK Jr., my citations are not only real, they are relevant and rigorous data.
news.immunologic.org
RFK Jr's COVID-19 vaccine rollback will kill people — including kids.
Revoking vaccine guidance is a public health failure with deadly, costly, and avoidable consequences.
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Drug Monkey @drugmonkey.bsky.social · 21/05/2025
You are not alone in this NIH grant game drugmonkey.wordpress.com/2025/05/21/y...
drugmonkey.wordpress.com
You are not alone in this NIH grant game
Many years ago I started blogging about the NIH system of extramural grant award because of my own frustrations with the system, as it appeared to be to me. Over time, I realized that there were a …
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Vivek Mutalik @vivekmutalik.bsky.social · 14/05/2025
😢 No words. ☹️
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Vivek Mutalik @vivekmutalik.bsky.social · 09/05/2025
#phage #phagesky
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Joshua Weitz @joshuasweitz.bsky.social · 24/04/2025
Whoa... This resignation should alarm scientists, leaders, and elected officials across the aisles. For over 70 years, NSF has promoted science, advanced an innovation economy, and supported the national defense. America's future depends on federal investment in NSF, NIH + beyond.
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Mark O. Martin @markowenmartin.bsky.social · 11/04/2025
I had a nice time recording a podcast session with @manuelkleiner.bsky.social today for next week's #MattersMicrobial. I learned so much about how the microbiome responds to dietary changes. Plus thoughts about mucus farming by microbiota... Such fun! Heard about VIM @nicoledubilier.bsky.social!
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Mike Lee @astrobiomike.org · 05/04/2025
Biology is so cool - P. syringae produces syringafactin, which is deacylated by amoebae - Deacylated syringafactin binds to CraR, triggering amoebicidal pyrofactin synthesis - Cra allows P. syringae to infect Arabidopsis thaliana in the presence of amoebae #MicroSky
cell.com
A chemical radar allows bacteria to detect and kill predators
Pseudomonas syringae can detect and kill microbial predators via a chemical radar (Cra), which also allows the bacterium to infect plants despite predation pressure.
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Nanami Kubota @nanamikubota.bsky.social · 02/04/2025
Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons @shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
biorxiv.org
Filamentous cheater phages drive bacterial and phage populations to lower fitness
Many bacteria carry phage genome(s) in their chromosome (i.e., prophage), and this intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages ...
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Gemma C. Atkinson @gemmaatkinson.bsky.social · 19/03/2025
Please spread the word! We have an opening in the Atkinson lab for a post-doc with a focus on the molecular mechanisms of microbial immune systems. Can be a fully computational or experimental or hybrid project. Read more and apply here: lu.varbi.com/en/what:job/... #phage #bioinformatics
lu.varbi.com
Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions
Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b
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Michael Baym @baym.lol · 21/02/2025
Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!
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Vaughn Cooper @vscooper.micropopbio.org · 21/02/2025
Fascinating paper about the potential of phage for local drug delivery by Brian Hsu (Va Tech) and colleagues. (also nice acknowledgment for SeqCoast Genomics @seqcoast.bsky.social!) www.nature.com/articles/s41...
nature.com
Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage - Nature Biotechnology
Biologics are delivered to the gut using phage that infects resident commensal bacteria.
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Dr. Michael D. L. Johnson @copperbae.bsky.social · 23/01/2025
We must have an unprecedented amount of grace, collaboration, and support for our colleagues and trainees right now. We will get out of this mile one. It won’t make the run easier, but we will settle in and we will finish. I wrote this because I needed to hear it. I hope it was helpful to you.
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Eduardo Rocha @epcrocha.bsky.social · 01/01/2025
To start the year on the good path. Our preprint on plasmid-chromosome cross-talk and how it may favour MDR bacteria, is now out. Work led by @sanmillan.bsky.social Laura Toribio-Celestino et al.
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Atif Khan @atifmicro.bsky.social · 19/11/2024
A complete list of 150 bacteriophage researchers. go.bsky.app/Lkm6xoN
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Kimberly Kline 🏔 @kimingeneva.bsky.social · 20/11/2024
Hey Enterococcus lovers: go.bsky.app/T24bCrJ. Who are we missing here?
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