@RyanCookAMR

Viral ecologist with @EvelienAdri at @TheQuadram | All things phage (but mostly viromes) | Formerly at @UniofNottingham with @milja001 | All opinions my own.

 Norwich, England
Joined May 2019
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New #MicrobiomeDigest is OUT microbiomedigest.com/2026/09…  • cattle virome / @RyanCookAMR • mothers-adult daughters vaginal microbiome / @SarahLebeer • microbiome biomarker recovery in CRC / André Salgado  See you next week at the Seerave & #MVIF!

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…

microbiomedigest.com
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Happy to see the last parts of my PhD with @milja001 now published in @MicrobiomeJ (many thanks to all involved!) link.springer.com/article/10…

Distinct gut viral communities across life stages in dairy cattle

Microbiome - Ruminant gut microbial communities influence host health, productivity, and methane emissions, yet viral communities across life stages remain uncharacterized. Whilst bacteriophages...

link.springer.com
Ryan Cook@RyanCookAMR25 May 2025
🧬🐄 NEW PREPRINT: Really happy to finally share the last big piece of work from my PhD! Spoiler: Cows are great and so are their viromes 🧵1/13 biorxiv.org/content/10.1101/…

Life-Stage Transitions Drive Distinct Gut Viral Communities in Dairy Cattle

Ruminant gut microbial communities profoundly influence host health and environmental impacts, yet their viral components remain poorly characterised across developmental transitions. Here, we...

biorxiv.org
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Ryan Cook retweeted
Andrew millard@milja001Aug 19
with @RyanCookAMR and many others we have been working on INPHARED to incorporate more QC data and predictions, make it scale with increased data, and some basic visualisation of the data. Files will be linked from here phagebank.uk/inphared2/ in the future
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Delighted to see our work featured as a Research Highlight in @NatureEcoEvo 🧬 Ancient strep throat 🦠 nature.com/articles/s41559-0… 😷 Strep throat is nothing new – a 700-year-old mummy proves it 🙌@msabrysarhan @RyanCookAMR #Archaeology #aDNA #Genomics #StrepThroat #ScienceNews
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Happy to have played a small role in this cool piece of work led by @Teag4Phage in the lab of Evelien Adriaenssens. She looked at the impacts of using a phage cocktail in a batch-culture fermentation colon model 🦠 #phages microbiologyresearch.org/con…

The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon...

microbiologyresearch.org
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Been really fun to re-visit this with Branko Rihtman, @APonsero , @SMichniewski , @telatin , @TSPKU , Evelien Adriaenssens and @milja001 biorxiv.org/content/10.64898…

Bacteriophage genomics: What has five years of INPHARED taught us?

Bacteriophages are key drivers of microbial ecology and evolution, and the rapid expansion of phage sequencing has created sustained demand for curated reference genome databases. We released the...

biorxiv.org
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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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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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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 @NobregaFL lab)- maybe phages are similar for their anti-defence repertoires?
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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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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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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
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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!
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During my PhD, @milja001 and I started counting phage genomes, and tried to make them available in useful formats with useful metadata. We also described the extent of sequenced phage genomes at the time. Five years on, we've had a look at what's changed biorxiv.org/content/10.64898…

Bacteriophage genomics: What has five years of INPHARED taught us?

Bacteriophages are key drivers of microbial ecology and evolution, and the rapid expansion of phage sequencing has created sustained demand for curated reference genome databases. We released the...

biorxiv.org
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Really happy to have played a small part in this cool piece of work led by @GuidoValverde_ & @msabrysarhan. We characterised S. pyogenes in a pre-Columbian Bolivian mummy (suggesting circulation before European contact) #VivaBolivianMummies nature.com/articles/s41467-0…

An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy

Nature Communications - Streptococcus pyogenes is a human pathogen responsible for a range of diseases. Here, the authors reconstruct an ancient S. pyogenes genome from a pre-Columbian Bolivian...

nature.com
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Salmonella Genomic Markers for Risk to Food Safety biorxiv.org/content/10.64898… #biorxiv_genomic
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Really enjoyed writing a piece for @ConversationUK - trying to write for a general audience, you suddenly realise how much jargon is deeply embedded in your brain #Phages #Microbiome #SciComm theconversation.com/a-virus-…

A virus hiding inside bacteria may help explain colorectal cancer

Scientists found an unexpected viral hitchhiker lurking inside a common gut bacterium – and it was twice as prevalent in people with colorectal cancer.

theconversation.com
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Happy to say this has now been published in @CellReports 🫁🦠 #Phages #Viromics cell.com/cell-reports/fullte…

Bacteriophage diversity declines with COPD severity in the respiratory microbiome

Cook et al. reveal bacteriophage diversity progressively declines with COPD severity. Frequent exacerbators uniquely show decoupled viral-bacterial relationships. Virulence-encoding phages associate...

cell.com
Ryan Cook@RyanCookAMR17 Jun 2025
New pre-print alert! 🚨🫁 COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9 biorxiv.org/content/10.1101/…
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🚨 We’re hiring! 🚨 The Integrative Viromics Lab @UCalgary is looking for a Lab Technician to join us starting November 2025. 🔬 Phage isolation & culture 🧫 Anaerobic chamber work 📦 Lab management & student mentoring Apply now & help us explore the virosphere!
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Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation
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