Peter Dougherty

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!

We sequenced 112 Pseudomonas genomes from 2 wheat cultivars, & never expected to find this: 28 biosynthetic gene clusters enriched in one cultivar over the other! Why & how did the 2 cultivars structure their Pseudomonas communities so differently? Ideas? sciencedirect.com/science/articl…

White smoke, we have not only a new pope, but also 16 new anti-phage systems in integrons ! In collaboration with the @amazeld lab, we show in our new paper that cassettes of these large platforms encode known anti-phage defenses and uncovered 16 new ones. science.org/doi/10.1126/sc…

When are rhizosphere Pseudomonads different from other rhizosphere Pseudomonads? When they are isolated from different wheat cultivars! We found surprising intra-genus diversity with implications for secondary metabolite production 👇 sciencedirect.com/science/articl…

Our paper on phages targeting phyllosphere bacteria is out today! Theres some interesting stuff here, including some interesting phages with single-stranded DNA breaks🧬

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!

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.

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.

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.

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.

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. biorxiv.org/content/10.110…

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.

For the past two years, we have been working on a novel approach to identify origins of transfer by conjugation in plasmids from any bacterial species. We are thrilled to see this work now published in @NatureMicrobiol after thorough peer review! nature.com/articles/s4156…

(1/4) Our new preprint: a metagenome binner TaxVAMB that uses taxonomic labels to create better bins. In a nutshell, TaxVAMB is great for small number of samples, incomplete genomes and non-bacterial entities @AiCentreDK @Metabolcenter biorxiv.org/content/10.110…

Lastly, a big thanks to all authors, it's been a pleasure doing research with you all!

Why would phages want nicks in their DNA? We discuss possible functions in our article, but in short we don't know! On the bright side, there never seems to be a shortage of interesting phage biology to study.

Meet phages Hallingskeid, Kaldavass, Rembedalsseter, et. al. in our new pre-print out today! We isolated eight phages against bacterial hosts from the wheat phyllosphere and found some interesting phage biology along the way. biorxiv.org/content/10.110…