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Peter Dougherty

@peterdoug.bsky.social
73 followers 14 following 11 posts

PhD student at the University of Copenhagen, interested in microbiology and bioinformatics

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Reposted by Peter Dougherty
Ryan Wick @rrwick.bsky.social · 21/01/2026
New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...
rrwick.github.io
P2 Solo announcement and the trade-offs of a more stable ONT
a blog for miscellaneous bioinformatics stuff
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Reposted by Peter Dougherty
Nature Microbiology @natmicrobiol.nature.com · 02/01/2026
#NewResearch The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles. #MicroSky 🦠 @peterdoug.bsky.social @emggroupucph.bsky.social www.nature.com/articles/s41...
nature.com
Persistent virulent phages exist across bacterial isolates - Nature Microbiology
The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles.
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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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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
Finally, this has been a proper collaborative effort, and I’m very proud to have worked with (and learned from) all co-authors. Thank you all!
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
What’s the difference between a persistent virulent phage and a temperate phage? Phenotypically, maybe not so much. We argue that phages exist on a spectrum, with rapid, lytically replicating virulent phages on one side, and stable, non-inducing prophages on the other.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
If these phages are non-temperate, how do they persist in bacterial cultures? Given their diversity, we argue there is not a single explanation. Here we suggest three possible mechanisms for persistence: phase variation, asymmetric phage inheritance, and lysis inhibition.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
In a targeted follow-up search for the three jumbo-phage clusters in bacterial assemblies beyond Escherichia, we found an additional 285 persistent jumbo-phages. The Seoul- and Goslar-like phages encoded chimallin, a protein some phages use to produce a protective phage nucleus.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
We also clustered the persistent phages with all virulent Escherichia phage isolates. Most (27/37) clusters contained persistent phages, demonstrating this is broad phenomenon. However, the three clusters with a highest proportion of persistent phages were all jumbo phages.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
After extensive QC, we found 373 non-temperate phage genomes. These phages were not integrated in the bacterial genome, and do not resemble phage-plasmids.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
We therefore hypothesized that virulent phage genomes in bacterial assemblies represent non-temperate infections, persistent infections. To test this, we first searched 267,092 Escherichia genome assemblies for contigs resembling virulent phage genomes.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
Recently, we sequenced two large jumbo phages. When we ran a BLAST search, we found similar sequences in bacterial genome assemblies. This surprised us, as there are no known temperate phages this big. These phages were also a pain to work with, forming only tiny, faint plaques.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
Usually, phage lifestyles are described as either strictly virulent (lytic cycle) or temperate (lytic or lysogenic cycles). However, some phages don’t fit either label, persisting with their bacterial hosts without crashing the host population or entering classical lysogeny.
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Peter Dougherty @peterdoug.bsky.social · 02/01/2025
Are there virulent phages hiding in your bacterial culture? Here we find hundreds of virulent phage genomes in bacterial genome assemblies. Bioinformatic and experimental evidence indicate these are not contaminations, but represent persistent infections. www.biorxiv.org/content/10.1...
biorxiv.org
Persistent virulent phages exist in bacterial isolates
Despite the immense diversity of tailed bacteriophages, they are traditionally classified as either virulent or temperate, with only the latter thought capable of long-term persistence in bacterial ce...
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