The RAxML-NG v2.0 preprint is out: www.biorxiv.org/content/10.6... v2.0 features integrated model testing, fast branch support metrics, automatic parallelization, phylogenetic difficulty prediction, genotype evolution models, to name but the most important features. And it is A LOT FASTER of course

RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics

RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...

biorxiv.org

Ten years ago Tami, Roy, and I released a movie we made of antibiotic resistance evolving in real time. I thought maybe a couple thousand people tops would see it. I couldn't have imagined it would be seen millions of times, and be taught from middle school through the graduate level worldwide

What a Friday, finally seeing this published in @cp-trendsmicrobiol.bsky.social! We hope this will be of interest to anyone working in the bacterial immune system field (or microbiology in general), and who wants an evolutionary take on it 🦠🧫 Open Access link: authors.elsevier.com/a/1nllx,L%7E...

Ellinor Alseth@ellinoralseth.bsky.social · 4mo ago

When is an antiphage mechanism an evolved defence adaptation? This question has been on my mind for so long, because despite the field’s rapid progress there is currently no widely agreed framework in place to answer it. So @brownlab.bsky.social and I wrote this, and I'm happy to share the preprint!

Our paper is now out in the @isme-microbes.bsky.social Journal (and selected as editor's choice)! We use an ecological framework to analyze the distribution of small transposable elements in over 30,000 prokaryotic genomes, characterizing their genomic niche doi.org/10.1093/isme...

Characterizing the ecological niche of insertion sequences within prokaryotic genomes

Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious

doi.org

Flora Gaudillière-Jami@fgaudilliere.bsky.social · last yr.

The preprint of my first article is available on bioRxiv! We use a transposon ecology framework to analyze the distribution of insertion sequences within prokaryotic genomes. We characterize their ecological niche and show evidence of niche construction 🧪🧬💻 www.biorxiv.org/content/10.1...

Our new paper is out in @PLOS Biology! 🎉 “Ecological theory sheds light on plasmid diversity and dynamics” 🔗 doi.org/10.1371/jour... More on the main findings in the next posts 👇

Ecological theory sheds light on plasmid diversity and dynamics

Bacterial genomes are remarkably dynamic, shaped by horizontal transfer of plasmids that follow evolutionary trajectories of their own. This study uses eco-evolutionary perspectives to reveal how the ...

doi.org

Now published in @asm.org mSystems! journals.asm.org/doi/10.1128/...

Species-specific prophage induction by ciprofloxacin in human gut metagenomes | mSystems

Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses ...

journals.asm.org

Jesse Shapiro@bjesseshapiro.bsky.social · 6mo ago

In the lab, antibiotics can make integrated viruses (prophages) pop out of bacterial genomes. In this (short!) preprint, we asked a simple question: how much does this happen outside the lab, in the human gut? TLDR: Not much overall, in specific bacterial species. 🧵 www.biorxiv.org/content/10.6...

Hey everyone! Happy to announce the completion of a longstanding project in partnership with @irisirby.bsky.social and @brownlab.bsky.social that I have been really excited about. www.biorxiv.org/content/10.6...

Canonical pathoadaptive cystic fibrosis genes in Pseudomonas aeruginosa are not CF-specific

Research on Pseudomonas aeruginosa adaptation in cystic fibrosis (CF) has historically relied on comparing chronic isolates to laboratory reference strains, or evolving reference strains in environmen...

biorxiv.org

We are excited to share our new preprint, “Canonical pathoadaptive cystic fibrosis genes in Pseudomonas aeruginosa are not CF-specific”! 🦠 Great project with @emehlferber.bsky.social and @brownlab.bsky.social www.biorxiv.org/content/10.6... Thread below 🧵

Canonical pathoadaptive cystic fibrosis genes in Pseudomonas aeruginosa are not CF-specific

Research on Pseudomonas aeruginosa adaptation in cystic fibrosis (CF) has historically relied on comparing chronic isolates to laboratory reference strains, or evolving reference strains in environmen...

biorxiv.org

As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles journals.asm.org/doi/full/10.... #jcampubs

New from the lab--C. diff uses phase variation to initiate infection in a virulent state but that phenotype presents a fitness cost as disease develops. A programmed reset mechanism primes Clostridioides difficile virulence at the onset of infection | Science Advances www.science.org/doi/10.1126/...

A programmed reset mechanism primes Clostridioides difficile virulence at the onset of infection

Clostridioides difficile is a major cause of antibiotic-associated diarrhea. This pathogen produces toxins essential for disease and flagella that promote intestinal colonization. Flagella and toxins ...

science.org

How the social lives of bacteria affect their pangenome: thank you @whelanfj.bsky.social for reviewing how community ecology affects pangenomes, and for a special issue of Essays in Biochemistry on the social lives of bacteria #MicroSky portlandpress.com/essaysbioche...

Thrilled to share my first paper out of grad school. We sequenced dental wastewater (yes, the stuff collected during teeth cleaning) and found previously unknown bacteriophages harbored in the human mouth. #phagesky #microsky 🧵 journals.asm.org/doi/10.1128/...

Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity | Microbiology Spectrum

The human oral cavity contains a diverse microbial community, but the bacteriophages (phages) that infect many oral bacteria remain poorly characterized. This gap limits our understanding of how phage...

journals.asm.org

I am enjoying #SocialViruses2026 in Vancouver, organized by @asherleeks.bsky.social and @sociovirology.bsky.social. Also, we finally got our #GeneticConflict in #Herpesviruses review published in #VirusEvolution, first conceived at the 2024 #SocialViruses meeting in Puerto Rico!

Antagonistic Co-Evolution Throughout the Herpesvirus Life Cycle

Abstract. Herpesviruses are a widespread and diverse family of large double stranded DNA viruses. Narrow host ranges maintained over long evolutionary time

academic.oup.com

If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

Last talk of the day at #SocialViruses26: Iris Irby @irisirby.bsky.social (Georgia Institute of Technology @gtresearch.bsky.social) with "Conflict dynamics: ecological drivers of prophage coexistence and the evolution of viral cheats"

Wow! A fourth class of transmissible cancers. CONTAGIOUS FISH MELANOMA, discovered in Lake Memphremagog (Vermont / Quebec) 🎣 🧬 😷 www.nature.com/articles/s41... @uvmvermont.bsky.social

Brown bullhead catfish melanoma represents a novel transmissible cancer - Nature

Whole-genome sequencing analysis of tumour and matched non-tumour host tissues of the brown bullhead catfish reveals a type of naturally occurring transmissible cancer.

nature.com

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

#microsky #phagesky #phage The secret life of prophages journals.asm.org/doi/10.1128/...

From hijackers to architects: the role of prophages in bacterial genome evolution | Journal of Bacteriology

Bacteriophages (phages) are one of the most important drivers of bacterial evolution, regulating physiology, genetic diversity, population dynamics, and coevolution through complex host-phage interact...

journals.asm.org

The type and amount of bacterial DNA carried by virus-like particles in the gut microbiome is simply mind-boggling. Amazing work by PhD candidate Jessie Maier in my group and collaborators @duerkoplab.bsky.social and Ben Callahan www.biorxiv.org/content/10.6...

Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome

Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of...

biorxiv.org

#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️

Widespread immune systems protect bacteria against conjugative plasmids

Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...

biorxiv.org

Horizontal gene transfer (HGT) in ants - several likely underpinning functional innovations, primarily by mediating immune-system adaptations or facilitating nutritional niche expansions academic.oup.com/gigascience/... #biodiversity #genomics

Comparative analysis of 163 ant genomes reveals recurrent horizontal gene transfer from bacteria to ants

AbstractBackground. Horizontal gene transfer (HGT) from bacteria can drive phenotypic innovation and adaptation in eukaryotes. Ants are likely carriers of

academic.oup.com

We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...

🚨New paper alert 🚨 Here we tried to leverage an (incredible) metagenome time-series to better understand MGE diversity and activity in soil across decade(s). @scbagby.bsky.social has an amazing thread about this work with all the details - bsky.app/profile/scba...

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature Microbiology

An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.

nature.com

Sarah Bagby@scbagby.bsky.social · 3mo ago

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/

SOS-mediated prophage induction constrains resistance evolution to DNA-damaging antibiotics

Most naturally occurring bacteria are lysogens, encoding one or more temperate phages (prophages) integrated into their genome. As prophages are induced by the bacterial SOS response, DNA-damaging ant...

biorxiv.org

Latest work from my lab, in which @amycrobes.bsky.social probes the evolutionary consequences of prophages potentiating death at otherwise sublethal antibiotic doses

Amy Zamora@amycrobes.bsky.social · 3mo ago

We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/

Evolutionary rescue in a phage community! New paper from former PhD student, Sam Greenrod, with brilliant colleague @craigmaclean.bsky.social : academic.oup.com/ismej/advanc...

Rapid adaptation accelerates competitive suppression in a parasite community

Abstract. Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites

academic.oup.com

Review summarises how viruses dominate genetic diversity on Earth and evolve through multiple origins, gene sharing, and host–virus arms races, reshaping the global virosphere and replicator space 🧬🌍🦠 #Virology #Evolution #Metagenomics 📄 doi.org/10.5802/crbi... 👤 EVBC member: Mart Krupovic

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

📣 New Preprint! Here we use bees as a model to study how a temperate phage-bacteria pair interact in the gut and how antibiotics change these interactions. The take home? Phage can play a major role in shaping how gut microbiomes respond to antibiotic perturbation! #microsky #phagesky 🐝 🦠 🧪

It’s a day late, but worth the wait: on this episode of #MattersMicrobial, Dr. Sam Brown chats with the #QualityQuorum about generalists, specialists, and sociomicrobiology. Please spread the #GoodMicrobialWorld. @univpugetsound @ASMicrobiology @microbe.tv youtu.be/K_gEeazaCQM?...