Dipped into the bird site for work for 5 mins and wow boiling frogs

I *should* be writing my dissertation...

Instead I just released gcplyr v1.3.0 on github

gcplyr is an #RStats package that makes it easy to wrangle and do model-free analyses of #microbial growth curve data

v1.3.0 includes:
- new methods to calculate lag time and doubling time
- improved warnings for common situations
- improved documentation

https://mikeblazanin.github.io/gcplyr/

#microbiology #MicrobialEcology #MicrobialEvolution #ggplot2 #tidyverse #dplyr #data

Today's mood

#Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut #microbiota: iScience

https://www.cell.com/iscience/fulltext/S2589-0042(23)00084-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004223000846%3Fshowall%3Dtrue

Exciting new paper in @PLOSBiology — we show that plasmids use translational global regulators to rewire host cells including expression of key ecological traits, like metabolism and motility, whilst also boosting horizontal transmission of the plasmid

This was a big collaborative effort with colleagues at John Innes Centre, Birmingham, Sheffield & Liverpool

#plasmid #HGT #MobileGeneticElements

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001988

lol

Happy to say I'll be at the Weizmann Institute symposium on the Immune System of Bacteria, with a poster on some of my very first bits of data from my current fellowship! "Exploring the evolution of phage resistance in A. baumannii" in all it's shiny and confusing wonder ✨

The coordination of #anti-phage #immunity mechanisms in #bacterial cells |
#phage

https://www.nature.com/articles/s41467-022-35203-7

🎬 🧫🦠 This amazing time-lapse video shows bacteria-phage coevolution occurring on agar plates over ~6d. Mesmerising visuals, enhanced even more when you read the paper for a glimpse at the underlying evolutionary genetics 😍 #microbiology #journalclub #microbialevolution #phage https://www.nature.com/articles/s41467-022-35351-w

Super interesting paper that analayzes one of the #LTEE populations that evolved stably coexisting #ecotypes from Joao Ascensao, Kelly Wetmore, Ben Good, Adam Arkin & Oskar Hallatschek. https://www.nature.com/articles/s41467-022-35677-5
#Microbiology #Evolution #ExperimentalEvolution #EcoEvo #popgen #PopulationDynamics #Genomics

What Lies Beneath? Taking the Plunge into the Murky Waters of Phage Biology

@mSystemsJ MiniReview by @MirjamZuend et al from @KatrineWhiteson

https://journals.asm.org/doi/10.1128/msystems.00807-22

What the world of molecular biology feels like to an ecology and evolution person 🦠

Happy to see this collaborative work with Jenny Wachter, Margie Kinnersley, Patti Rosa, & team in print @NatureComms!

Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete

Borrelia phages are so cool!

https://www.nature.com/articles/s41467-023-35897-3

Adaptive laboratory evolution of #antimicrobial resistance in bacteria for #genetic and #phenotypic analyses - #amr

https://www.sciencedirect.com/science/article/pii/S2666166722008851

I love microbial ecology its so cool yall

Response to reviewer:
Didn't I do it for you?

#Microbial population dynamics decouple growth response from environmental nutrient concentration | PNAS
#microbiology

https://www.pnas.org/doi/10.1073/pnas.2207295120

Couple of Microbial Genomics editors picks this week

A fascinating study showing no genomic differences between an obligate endosymbiont and its cultivable twin. Shows that small non-genomic factors determine endosymbiosis initiation

https://microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000909?emailalert=true

A few years ago we showed that restriction-modification systems shape gene flow within species. Now we show how plasmids cope with these systems to spread across bacterial populations. Small plasmids avoid restriction sites, large plasmids recruit counter-defenses (methylases). And the plasmids most avoiding restriction sites have the broadest host ranges. Great collaboration in a project led by Liam Shaw and Craig MacLean. https://www.biorxiv.org/content/10.1101/2022.12.15.520556v1

In a new #preprint we report that recently discovered anti-phages systems (Mokosh, Eleos, Lamassu…) have eukaryotic homologs.

We harnessed this conservation to discover novel defense mechanisms in humans.

@jeanrjc @emordret

https://www.biorxiv.org/content/10.1101/2022.12.12.520048v1