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Ryan Cook

@ryancook94.bsky.social
382 followers 269 following 64 posts

Viral ecologist with Evelien Adriaenssens at The Quadram | All things phage (but mostly viromes) | Formerly at Uni of Nottingham with Andy Millard | All opinions my own.

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Reposted by Ryan Cook
Hannah Trivett @hannahtriv.bsky.social · 08/10/2026
Delighted to share our new paper in Genome Medicine! We used long-read #metagenomics to uncover striking changes in the gut #microbiome with advanced #LiverDisease, including E. faecium dominance and #AMR @halllab.bsky.social #Genomics #ECR #Resistome #Cirrhosis link.springer.com/article/10.1...
link.springer.com
Decoding the microbiome and resistome of advanced chronic liver disease through long-read metagenomics - Genome Medicine
Background Patients with advanced chronic liver disease (ACLD) and underlying cirrhosis frequently require repeated courses of antimicrobial therapy, with both the frequency and spectrum of antimicrob...
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Craig MacLean @craigmaclean.bsky.social · 30/09/2026
Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...
jobs.ac.uk
Postdoctoral Research Associate at University of Oxford
Explore an exciting academic career as a Postdoctoral Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
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Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 11/09/2026
New #MicrobiomeDigest is OUT microbiomedigest.com/2026/09/11/s... • cattle virome / @ryancook94.bsky.social • mothers-adult daughters vaginal microbiome / @sarahlebeer.bsky.social • microbiome biomarker recovery in CRC / André Salgado See you next week at the Seerave & #MVIF Symposium!
microbiomedigest.com
September 11, 2026
See you at the Seerave & MVIF Symposium next week! General Integrating multi-omics technologies to decipher microbiome functions – Tim Van Den Bossche – Nature Communications Phylogenetic measu…
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Rafal Mostowy @rafalmostowy.bsky.social · 04/09/2026
🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...
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Ryan Cook @ryancook94.bsky.social · 27/08/2026
Happy to see the last parts of my PhD with @milja001.bsky.social now published in @microbiomej.bsky.social (many thanks to all involved!) link.springer.com/article/10.1...
link.springer.com
Distinct gut viral communities across life stages in dairy cattle - Microbiome
Background Ruminant gut microbial communities influence host health, productivity, and methane emissions, yet viral communities across life stages remain uncharacterized. Whilst bacteriophages shape m...
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Evelien Adriaenssens @evelienadri.bsky.social · 27/08/2026
Dear eukaryotic, archaeal and bacterial virologists, I don't know how most of you feel about taxonomy, but it has an impact on all of our working lives. I am curious to hear from you about your opinion on subspecies classification based on this survey: www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Virus community views on the possible extension of virus taxonomic assignments to a below-species rank
The International Committee on Taxonomy of Viruses (ICTV) is considering a proposal submitted in July 2025 to create an optional additional taxonomic rank below the level of species. This was designed...
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
I am excited to share that our manuscript titled 'Defining the ESKAPE pathogen prophage repertoire with PHORAGER' is now available online as a preprint in BioRxiv! 🤩 (doi.org/10.64898/202...) Here we present PHORAGER, a Nextflow pipeline for the identification and quality assessment of prophages 🧬
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Falk Hildebrand @bioinf.bsky.social · 07/08/2026
After a very long time, I'm very proud that we have now Joachim "magnus opum" on www.biorxiv.org/content/10.6... Protal is a ultra fast metagenomic species profiler. More precise than other profiled software, faster than most (not sylph though), but generates strain resolution instead.
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George Bouras @gbouras13.bsky.social · 07/08/2026
If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!
phage-annotation.org
Phage Annotation Server -- phage genome annotation
Free automated phage genome annotation -- pharokka, phold and phynteny in one pipeline.
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
Thank you so much to all of my co-authors, I couldn't have done it without you! ❤️ Alise Ponsero, James Docherty, Andrea Telatin (@telatin.bsky.social), Emmanuelle Crost, Nathalie Juge (@jugelab.bsky.social), Ryan Cook (@ryancook94.bsky.social), and Evelien Adriaenssens! (@evelienadri.bsky.social)
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
Finally, PHORAGER is freely available as open-source software (github.com/aponsero/PHO...) and the ESKAPE prophage collection generated in this study is available online as a reusable resource for further investigations (zenodo.org/records/1832...) Happy PHORAGING! 🦠🧬🧺
github.com
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
We also investigated anti-phage defence systems and found that 23.6% of prophages encoded at least 1 system 🛡️ Additionally, we observed that bacterial defence carriage is negatively correlated with prophage carriage among the ESKAPE pathogens 📉
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
We screened the recovered prophages for AMR genes (ARGs) and virulence factors, and found that putative ARGs were detected at very low frequencies, with only 0.48% of prophages encoding an ARG 💊 Putative virulence factor genes were found to be more common, particularly in S. aureus prophages⚡
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
In total 23,132 putative prophages were identified, 99.9% belonging to the class Caudoviricetes, and exhibiting a high degree of host-specificity 🦠 Further taxonomic analysis classified the prophages into 115 viral families and 2,250 viral genera, the majority representing putatively novel taxa!
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
To validate PHORAGER, we tested it on a dataset of 30,824 publicly available ESKAPE pathogen genomes. PHORAGER recovered more high-quality prophages than individual mining tools alone, and through extensive quality assessments removed a substantial number of false-positive predictions ✅
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
PHORAGER incorporates robust bacterial genome pre-processing steps 🦠, methods to de-replicate predictions generated by multiple prophage mining tools 🧬, and advanced quality assessments to reduce the number of false positives identified ✅
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Ryan Cook @ryancook94.bsky.social · 06/08/2026
The first first-author research paper from Xena's fantastic PhD. Great piece of work and of interest to anybody who likes prophages, pathogens and bioinformatics 🍄 #MicroSky #Phages
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Ryan Cook @ryancook94.bsky.social · 04/08/2026
Nice to see this perspective piece out that synthesises ~10 years of work from the NERC EVAL-FARMS consortium. Also love that the thumbnail for the link is a cat. Please be advised that the work is on AMR in dairy (cow) farms, not cat farms 🐄 doi.org/10.3389/fvet...
doi.org
Frontiers | Interdisciplinary insights on selection, surveillance and mitigations of antimicrobial resistance dynamics on a UK dairy farm with relevance to other one health sectors
Antibiotic use in agriculture is a global driver for antimicrobial resistance (AMR). Dairy farming, one of the largest producers of agricultural waste, repre...
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RevathyKrishnamurthy @revathykri.bsky.social · 09/07/2026
#Vom2026: Had a fantastic opportunity to share my work on Maternal influence in shaping up the infants' virome at this year's VoM in front of 900 researchers. Thank you all for the wonderful feedback so far, and I will be happy to talk more about it. @evelienadri.bsky.social @ryancook94.bsky.social
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Anita Tarasenko @anitatarasenko.bsky.social · 09/07/2026
Excited to share my PhD work at #VoM2026 exploring what drives phage infectivity in cystic fibrosis-associated Achromobacter. Across 105 phage–host interactions, we found host identity plays a major role, with defence systems and phage tail architecture adding further complexity.
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Evelien Adriaenssens @evelienadri.bsky.social · 09/07/2026
In our final poster at #VoM2026, @rapher97.bsky.social explores the gut virome in healthy ageing. Visit his poster to find out what to expect when you get older…
Man standing in front of science poster titled Ecological structure and individuality of the gut virome during healthy aging.
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Evelien Adriaenssens @evelienadri.bsky.social · 09/07/2026
If you work with Klebsiella phages, you would probably like to know what genes are involved in resistance. Check out @deuskamya.bsky.social’s poster at #VoM2026 featuring lots of mutants.
Man standing in front of science poster titled Genetic determinants of phage susceptibility and phage-driven capsule variation in Klebsiella spp identified by TraDIS
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Evelien Adriaenssens @evelienadri.bsky.social · 09/07/2026
Today @ryancook94.bsky.social is presenting his posters on the trials and tribulations of working with phages and organoid models. #VoM2025
Man standing in front of science poster titled Absence of evidence isn’t evidence of absence.
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Evelien Adriaenssens @evelienadri.bsky.social · 09/07/2026
Have you ever wondered about prophages in an important gut bacterium? Check out @xenadyball.bsky.social’s poster at #VoM2026
Woman standing in front of science poster titles Exploring phage-mediated adaptation of Ruminococcus gnavus to the human gut.
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Evelien Adriaenssens @evelienadri.bsky.social · 08/07/2026
Who infects whom? A big question in virome research. If you want to learn more, check out the work from @apedramfar.bsky.social from her PhD. #VoM2026
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Evelien Adriaenssens @evelienadri.bsky.social · 08/07/2026
Earlier today at #VoM2026 @revathykri.bsky.social presented her work on the virus population sharing between mothers and infants. She did a amazing job! Find her during breaks to talk methods, findings and everything virome!
Woman on stage in front of a presentation entitled Preferential sharing of virus populations between mothers and infants in early life
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Evelien Adriaenssens @evelienadri.bsky.social · 07/07/2026
If you’re at the Viruses of Microbes conference, interested in Pseudomonas or phage therapy, check out @hannahvpye.bsky.social ‘s poster no84. #VoM2026
Woman standing in front of science poster
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ISVM @isvm-society.bsky.social · 06/07/2026
#VoM2026 has started! 🎉 We were delighted to hear welcoming remarks from ISVM President Lone Brøndsted as we begin a week of exciting science, collaboration, and new connections. Here's to a fantastic week of science and networking in Prague! #VoM2026 #ISVM #Microbiology #Virology
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Ryan Cook @ryancook94.bsky.social · 02/07/2026
DRC played brilliantly and England were made to struggle but I'm not sure "undeserved" is fair...
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Xena Dyball @xenadyball.bsky.social · 01/07/2026
Last week I had the pleasure of attending and presenting at the 4th Mobile Genetic Elements workshop in York! 🧬 Thanks to the organisers for putting on such a great meeting! 😊 @mgeworkshop.bsky.social
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Quadram Institute @quadraminstitute.bsky.social · 23/06/2026
Dr Hannah Morelli reflects on her journey from studying animal health to launching Quadlytics, a new spinout company developing bacteriophage therapies to tackle Salmonella in livestock. Read more in our blog ➡️ buff.ly/49FFKxa
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Ann Gregory, PhD @gregoryannc.bsky.social · 23/06/2026
The Integrative Viromics Lab at the University of Calgary is recruiting MSc and PhD students to study viruses in lakes, glaciers, permafrost, and other changing environments. Strong computational skills are preferred. Send a CV and cover letter to ann.gregory[at]ucalgary.ca
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Quadram Institute @quadraminstitute.bsky.social · 19/06/2026
🆕 Blog! Dr Hannah Morelli reflects on her journey from studying animal health to launching Quadlytics, a new spinout company developing bacteriophage therapies to tackle Salmonella in livestock 🧪 buff.ly/0wCCXJW
quadram.ac.uk
From phages to pigs: turning research into a spinout company - Quadram Institute
“I’m currently a postdoctoral researcher here at the Quadram Institute. My day-to-day research is looking at bacteriophages, which are viruses that can infect and kill bacteria, and how they can be…
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Quadram Institute @quadraminstitute.bsky.social · 10/06/2026
"I’m interested in what viral communities look like in nature. The overwhelming majority of these are bacteriophages, which are viruses that infect bacteria." 💬 @ryancook94.bsky.social
buff.ly
Understanding viral ecology and diversity to develop future phage therapy - Quadram Institute
Dr Ryan Cook describes viruses and the database he’s developed to help document and understand the diversity of viruses in nature
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Phage Canada @phagecanada.bsky.social · 29/05/2026
Save the date! The 27th Biennial Evergreen International Phage Meeting is coming to Canada for the first time in its history! 🦠 🧬 📅 July 25 - 29, 2027 📍 University of Guelph, Guelph, ON More info to follow...
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Guido Valverde @guido-valverde.bsky.social · 29/05/2026
Delighted to see our work featured as a Research Highlight in @natecoevo.nature.com 🧬 Ancient strep throat 🦠 nature.com/articles/s41... 😷 Strep throat is nothing new – a 700-year-old mummy proves it 🙌@msabrysarhan.bsky.social @ryancook94.bsky.social #aDNA #Genomics #StrepThroat #ScienceNews
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Susie Grigson @susiegriggo.bsky.social · 26/05/2026
New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...
biorxiv.org
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Professor Lesley Hoyles @bugsinyourguts.bsky.social · 23/05/2026
Postdoc position available within Malick Gibani’s team at Imperial College London, part of a Wellcome-funded project focused on the microbiota associated with the 2025 CHANTS Salmonella human challenge study. #microbiome #jobs www.imperial.ac.uk/jobs/search-...
imperial.ac.uk
Description
Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...
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Ryan Cook @ryancook94.bsky.social · 22/05/2026
Happy to have played a small role in this cool piece of work led by Teagan Brown in the lab of @evelienadri.bsky.social. She looked at the impacts of using a phage cocktail in a batch-culture fermentation colon model 🦠 #phages www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study
The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacte...
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Aude Bernheim @audeber.bsky.social · 22/05/2026
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
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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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Vivek Mutalik @vivekmutalik.bsky.social · 19/05/2026
Revised story Systematic receptor mapping in acapsular Klebsiella www.biorxiv.org/content/10.6...
biorxiv.org
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
Been really fun to re-visit this with @cyanoney.bsky.social, Alise Ponsero, Slawomir Michniewski, @telatin.bsky.social, Thomas Sicheritz-Pontén, @evelienadri.bsky.social, and @milja001.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
We're also putting out a fully updated pipeline with defence (and anti) predictions, lifestyle predictions and other fun improvements. Community involvement in this project has been great over the last 5 years and I hope this continues!
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
Conversely, anti-defence systems are more common in temperate phages. Likely to protect their host lysogen from invading phages. A small number of phages also carried both defence and anti-defence, highlighting the complex selection pressures they face
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
Anti-defence systems are widespread on (mostly virulent) phages. Some of them co-occur. It's know that defence systems act synergistically and don't co-occur randomly in bacteria (Great work by @fnobrega.bsky.social lab)- maybe phages are similar for their anti-defence repertoires?
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
Genomic properties of sequenced phages are broadly the same in 2026 vs 2021, not necessarily surprising. We predicted lifestyles with PhaTYP- wondering if this is a phage specific field that GenBank entries could allow submitters to add this where known?
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
Massive changes in phage taxonomy. RIP to Myo-, Podo- and Siphoviridae. Hello to genomically defined families. Huge community efforts have re-classified many of these but still many to go (especially former Sipho)
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
A small number of clinically/agriculturally relevant genera dominate as isolation hosts (~50% of phages from only 6 genera). Escherichia has also displaced Mycobacterium as #1. Big jumps up for Vibrio and Klebsiella also. Strep decrease due to removal of satellite phages (cool but not autonomous!)
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Ryan Cook @ryancook94.bsky.social · 08/05/2026
In raw numbers, the number of complete phage genomes from cultured isolates has doubled but the amount of unique genomes has slightly decreased- we're starting to sequence the same phages again. People are also getting better at giving their phages unique names! (Please no more phages named P1)
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