Super cool symposium in Berkeley!!

Simon Roux@simrouxvirus.bsky.social · 2mo ago

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

How can we study life’s deep evolutionary past? By bringing it into the lab! This @asm.org feature highlights our on-going efforts. Read how synthetic biology allows us to reconstruct ancient microbial systems, test hypotheses about early metabolism and explore how life and Earth co-evolved. 🌍

ASM@asm.org · 5d ago

Synthetic biology is advancing how scientists study early microbial life. Their findings could revolutionize how we think about Earth’s earliest residents—and those that exist today. asm.org/articles/202...

Interested in working with the JGI and never led a proposal with us? Now is your chance! We are accepting submissions to our New Investigator call for first-time PIs. Deadline to submit is Sept. 9. jointgeno.me/CSPnewPI @berkeleylab.lbl.gov @biosci.lbl.gov

CSP New Investigator Call | Joint Genome Institute

The CSP New Investigator Call is for investigators and research initiatives new to the JGI. Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previous...

jointgeno.me

West Nile made up 92 percent of reported US arboviral cases in 2024. Powassan hit a record 60 cases. No vaccines or antiviral treatments are available, so prevention matters www.cidrap.umn.edu/west-nile/we...

West Nile accounted for most US arboviral cases in 2024 as Powassan cases hit record high

24K-Production / iStock

cidrap.umn.edu

DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation Out now: how DNA sequencing can transform microbial surveillance in lung disease and what must change for clinical use. journals.asm.org/doi/10.1128/...

DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation | Clinical Microbiology Reviews

SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using m...

journals.asm.org

Reminder: ASM Microbe 2027 session proposals are open until Aug 12 !

Simon Roux@simrouxvirus.bsky.social · 5d ago

Session proposals are now open for ASM Microbe 2027 ! asm.org/events/asm-m... If there is a specific topic or speaker you would like to see in Chicago, this is your chance (until Aug 12) ! This is for Micro Symposia and Hub Sessions, but my DMs are open if you have ideas for bigger AEM sessions

www.nature.com/articles/s41... Such an important (series of) comparison(s) for soil viromics, h/t @jrr-microbio.bsky.social and team !!

Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities - Nature Communications

Profiling soil viral communities is challenging due to the inherent complexity of soil samples. In this study, the authors show that soil sample preparation strongly shapes which DNA and RNA viruses a...

nature.com

From our FY26 Functional Genomics call: Seagrass meadows shelter marine life and stabilize coasts, but seed survival is threatened by Phytophthora. Hanin Alzubaidy uses EcoFABs and multi-omics to reveal how seed bacteria suppress disease. Full portfolio: https://jointgeno.me/FGFY26

Very interesting paper on smallpox sequences from when they were ibtrocuced to South America, capturing the complex evolutionary forces at play in the pathogen city of this virus. www.science.org/doi/10.1126/...

The genomic identity of early smallpox in South America

Smallpox was a major driver of population collapse in the Americas after European contact, yet the genetic identity of the causal strains remains unknown. Here, we report the first ancient smallpox ge...

science.org

Antibiotic Resistomes And Microbial Communities In The 18th-Century Urban Settlement And Slaughterhouse Environment https://www.biorxiv.org/content/10.64898/2026.07.31.742145v1

Pls share. Assistant Professor of Biological Sciences - Genetics/Genomics at Smith College. apply.interfolio.com/190342

Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes academic.oup.com/ismej/advanc... #jcampubs

Session proposals are now open for ASM Microbe 2027 ! asm.org/events/asm-m... If there is a specific topic or speaker you would like to see in Chicago, this is your chance (until Aug 12) ! This is for Micro Symposia and Hub Sessions, but my DMs are open if you have ideas for bigger AEM sessions

Roberto is great ... the project is great ... the food is great ...

RobertoFeuda@robertofeuda.bsky.social · 6d ago

We're hiring 4 postdocs at @unibo.it to study nervous system evolution. Seeking expertise in single-cell genomics, molecular or developmental biology in ctenophores, cnidarians, echinoderms, flies or human stem cells. 2+2 yrs contract. Deadline: 26 Aug. Please share! bandi.unibo.it/s/apos7/proc...

I am hiring a computational postdoctoral fellow or bioinformatics scientist! Please apply here if interested, or share with anyone who may be. This position will be following up on our work studying the virus-host conflict. Reposts appreciated! aithyra.onlyfy.jobs/en/job/v2gwu...

Postdoctoral Fellow or Bioinformatics Scientist, Nomburg Lab (all genders)

About AITHYRAAITHYRA is a pioneering biomedical research institute in Vienna, Austria, where artificial intelligence meets life sciences to drive the next biological revolution. AITHYRA is an institut

aithyra.onlyfy.jobs

Jason Nomburg@jnoms.bsky.social · 2w ago

Ad forthcoming, but I am hiring for a postdoc or staff scientist to advance related investigations of the virus-host conflict. This position is ~80-100% computational, but with opportunities for experimental work if desired. If interested, shoot me an email with your CV! Reposts appreciated! 15/15

The prestigious Miller Research Postdoctoral Fellowship is open! University of California, Berkeley This is a postdoc fellowship with substantial support and independence to be hosted at a lab at Berkeley, reach out with interests! miller.berkeley.edu/nominate-app...

Open position in our lab for a research engineer. The applicant must hold a PhD in life sciences and have demonstrable experience in molecular biology and biochemistry. For more info: emploi.cnrs.fr/Offres/CDD/U...

Institut Jacques Monod@ijmonod.bsky.social · 7d ago

#JobOffer 💼 Research Engineer (M/F) 📆 October 15th 📍Institut Jacques Monod, @sandraduharcourt.bsky.social 🔗 emploi.cnrs.fr/Offres/CDD/U...

journals.asm.org/doi/10.1128/... comprehensive review of bacterial RNA modifications 🦠

Compendium of RNA modifications for bacterial stress adaptation | Microbiology and Molecular Biology Reviews

SUMMARYRNA modifications in the tRNA, rRNA, and mRNA constitute a widespread layer of post-transcriptional gene regulation, commonly known as the epitranscriptome. In bacteria, tRNA and rRNA modifications are well documented and play essential roles in tRNA folding, rRNA maturation, translation, and peptidyl transfer. Although mRNA modifications have been extensively characterized in eukaryotes, their functional implications for mRNA fate in prokaryotes remain uncertain, and their identities and locations are the subject of an emerging field of research. Importantly, RNA modification is a dynamic process, and variation in the presence and abundance of these modifications has significant consequences for bacterial physiology. Here, we discuss current knowledge of modified RNA nucleotides in bacteria, with a particular focus on their roles in bacterial adaptation to environmental stress.

journals.asm.org

Bacteriology-Focused Assistant Professor Position in Microbiology and Immunology at the University of Michigan Application deadline: August 15, 2026 Come be my colleague!

Glad to have this out in the world 🤓 If you want to genetically modify Staphylococcus haemolyticus, you have to dodge its phage defence systems! 🧬🧫 www.microbiologyresearch.org/content/jour...

Genetic engineering of Staphylococcus haemolyticus: overcoming restriction-modification barriers and targeting virulence genes

Staphylococcus haemolyticus is an emerging multidrug-resistant nosocomial pathogen noted for robust biofilm formation and complex restriction-modification (RM) systems that hinder genetic manipulation...

microbiologyresearch.org

Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ

Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature

Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.

go.nature.com

Ran into a frustrating issue with nf-core/pacvar today: it crashed saying the bam file was malformed. Took a minute of digging but pbalign depends on pbbam, which has a hard-coded check for instrument names that hasn't been updated in years. We have Vega data that wasn't included in the check...

New preprint from the lab! "Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential" Nitrogen fixation is scattered right across the prokaryotic tree — but it's heterotrophs, not cyanobacteria, that dominate the potential. 🧵

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last wk.

Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential https://www.biorxiv.org/content/10.64898/2026.07.27.741065v1

We rely on healthy soil microbial communities to support ecosystem functioning and plant growth, but what happens when soils are exposed to multiple environmental stressors simultaneously? Spoiler: it's not good doi.org/10.1093/isme...

Fungicide and warming interact to reduce soil ecosystem functioning

Abstract. Soil microbial communities are essential to the functioning of their ecosystems, providing vital services such as plant growth promotion and bior

academic.oup.com

Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Joanna Masel@joannamasel.bsky.social · 8mo ago

Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10

A fundamental question in disease ecology remains unresolved: How can an acute, immunizing virus persist in nature? Theory says viruses like measles need huge pools of susceptible hosts. Our new preprint offers an answer. www.biorxiv.org/content/10.6...

Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus

Canine distemper\---|a measles-like disease with high mortality and presently without a cure\---|poses a major threat to wild and domestic carnivores globally. Domestic dogs are generally considered t...

biorxiv.org

Reminder, registration for the Viral EcoGenomics & Applications (VEGA) 26 symposium is open ! See jgi.doe.gov/work-with-us... for more information

VEGA Symposium | Joint Genome Institute

Berkeley, CA

jgi.doe.gov

Simon Roux@simrouxvirus.bsky.social · 2mo ago

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

The major phenotype is tolerance, not resistance, but it's broad: a mutation selected by one drug protects against totally different classes, because it isn't targeting the drug, it's targeting the crisis the drug causes. Thanks to Ralph Isberg and lab for many contributions along the way

Andy Nishimoto from the Rosch lab at St. Jude led this massive project to evolve Spn in mice across 10 antibiotics and 3 immune states. Shockingly, classic resistance almost never evolved because it was too costly for fitness in the face of host immunity. www.sciencedirect.com/science/arti...

And here's a second NYU postdoc job ad, where I'm looking for a candidate that is interested in working on the gut-brain axis: apply.interfolio.com/189975 please share 🙏