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#bacteriophage

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We have a new preprint describing a method for phylogenetics and comparative genomics.

Maybe useful for those interested in all the amazing out there and their bizarre mosaic genomes

Towards a unifying phylogenomic framework for tailed phages

biorxiv.org/content/10.1101/20

bioRxiv · Towards a unifying phylogenomic framework for tailed phagesBackground Classifying viruses systematically has remained a key challenge of virology due to the absence of universal genes and vast genetic diversity of viruses. In particular, the most dominant and diverse group of viruses, the tailed double-stranded DNA viruses of prokaryotes belonging to the class Caudoviricetes, lack sufficient homology in the genetic machinery that unifies them to reconstruct inclusive, stable phylogenies of these genes. While previous approaches to organize tailed phage diversity have managed to distinguish various taxonomic levels, these methods are limited in scalability and reproducibility, and they do not include modes of evolution, like gene gains and losses. Results Here, we present a novel, comprehensive and reproducible framework for examining evolutionary relationships of tailed phages. In this framework, we compare phage genomes based on presences and absences of a fixed set of gene families which is used as binary trait data that is input into maximum likelihood models, which include heterogeneous rates of trait losses and gains. Our resulting phylogeny stably recovers known taxonomic families of tailed phages, with and without the inclusion of metagenomic phages. We also quantify the mosaicism of replication and structural genes among known families. Our results suggest that these exchanges likely underpin the emergence of new families. Additionally, we apply this framework to large phages (>100 kilobases) to map emergences of traits associated with genome expansion. Conclusion Taken together, this evolutionary framework for charting and organizing tailed phage diversity improves the systemization of phage taxonomy, which can unify phage studies and advance our understanding of their evolution. ### Competing Interest Statement The authors have declared no competing interest. * VOG : Virus Orthologous Group Caudo : all complete Caudoviricetes genomes used in this study inCaudo : INPHARED Caudo genomes metaCaudo : metagenome-assembled Caudo genomes cpVOG : Caudoviricetes phylogenetic VOG HMM : Hidden Markov Model APIS : anti-prokaryotic immune system

"The number of viruses that we found is absolutely wild. We found many viruses that we know very little about and many others that we have never seen before. It's amazing how much untapped biodiversity is all around us. And you don't even have to go far to find it; it's right under our noses," said Dr Erica M. Hartmann.

#microbiology #bacteriophage #biology #research #science #nature

labroots.com/trending/microbio

LabrootsA World of Mysterious Microbes on... Your Toothbrush? | MicrobiologyThe world is full of microorganisms, many of which are still a complete mystery to us. Scientists have been working to learn more about some of the ... | Microbiology

i did a Summer internship studying homing introns in college. big advance!

"This work demonstrates how a homing endonuclease can be deployed in interference competition among viruses and provide a relative fitness advantage. Given the ubiquity of homing endonucleases, this selective advantage likely has widespread evolutionary implications in diverse plasmid and viral competition as well as virus-host interactions."

#homing #endonuclease #phage #bacteriophage #virus

science.org/doi/10.1126/scienc

My new story for the Medical Post/Canadian Healthcare Network.
#Doctors and #pharmacists in Canada can log on for free. Here are a few paragraphs.

Could a century old treatment be an answer to antibiotic resistance?
In a first in Canada, a patient with an #antibiotic resistant artificial joint infection has received treatment with phage therapy and is showing promising early responses.

“This is cutting edge stuff, and a potentially new technology,” said Dr. Marisa Azad, the infectious diseases physician who treated the patient. She is also an assistant professor of medicine at the University of Ottawa.

The patient presented with severe periprosthetic joint infection (PJI) in the summer of 2023. She had already undergone multiple surgeries and had experienced several relapses and infections with the same persistent bacteria.

“She’d been on multiple very prolonged courses of antibiotics and had a severe drug allergy to two major drug classes of antibiotics. I was extremely limited in what I could use to treat her,” Dr. Azad told the Medical Post in an interview.

That’s when the idea arose of trying an experimental treatment course with phage therapy. The team got approval for doing the experimental treatment from Health Canada, and worked with Winnipeg-based Cytophage, which supplied the phages.

“We developed a protocol and gave her therapy over two weeks while she was admitted to hospital. She’s completed her therapy. Now we’re monitoring her closely and giving her adjunctive antibiotics,” she said.

The idea didn’t come out of the blue. In the medical literature, a study from just last year in Clinical #Infectious Diseases provided a review of 33 previously published cases of patients with end-stage, refractory bone and joint infections (BJI) who underwent treatment with phage therapy. The authors found that from those case reports, “29 (87%) achieved microbiological or clinical success, two (5.9%) relapsed with the same organisms, and two (5.9%) with a different organism” with no serious adverse events.

The conclusions of that paper stated there were “important advantages, disadvantages, and barriers to the implementation of phage therapy for BJIs.” Yet, at the same time, the authors added they, “believe that if phage therapy were to be used earlier in the clinical course, fewer cumulative antibiotics may be needed in an individual treatment course.”

The word phage is short for #bacteriophage, a word coined in 1917—literally meaning bacteria-eater. They are viruses whose lifecycle depends on certain types of bacteria.

“They latch on to specific types of bacteria and inject their genetic material into the bacterial cell." Dr. Azad explained. "They take over the bacterial cells’ machinery to produce more little viruses inside and explode or burst open the bacteria,” releasing viral particles that can go and infect other cells of the same type of bacteria.

Intriguingly, each #phage targets a specific type of #bacteria...
The story of phages started over 100 years ago. They were independently discovered, first in 1915 by a British pathologist, Frederick Twort, and then again in 1917 by French-Canadian microbiologist Felix d’Herelle. And...

#MedMastodon #IDmastodon #microbiology @medmastodon
canadianhealthcarenetwork.ca/c

A team led by #BioEGSB staff scientist Vivek Mutalik demonstrated for the first time that they can, on a genome-wide scale, identify #bacteriophage genes that are essential (or not) to infecting bacteria. They can then replace non-essential DNA with distinctive barcode tags. These barcodes could enable investigators and clinicians to quickly identify and track different phages in diverse settings, similar to how product barcodes are used in supermarkets.
biosciences.lbl.gov/2024/01/18