Emmanuele Severi

A brand-new Gordon Conference on Microbiomes!🦠 The opening session (Jan 2026) dives into microbiome editing - how fundamental research and new technologies can advance human health and environmental sustainability. Super looking forward!🧪 #microsky #microbiomesky #grc
www.grc.org/microbiome-e...

Engineered orthogonal translation systems from metagenomic libraries expand the genetic code Genetic code expansion with non-canonical amino acids (ncAAs) opens new opportunities for the function and design of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation...

#microsky #synbio

www.biorxiv.org/content/10.1...

All the world’s a phage | PNAS A renewed interest in bacteriophages has emerged from the explosive discovery of the complex pan-immune bacterial defense system and a revival of t...

#microsky #phagesky
Mycobacterium #phage review by Graham Hatfull covering the state of the art

www.pnas.org/doi/10.1073/...

Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases Bacteria are frequently attacked by viruses, known as phages, and rely on diverse defence systems like restriction endonucleases and CRISPR-Cas to survive. While phages can evade these defences by cov...

#phagesky #phage defence #microsky

www.biorxiv.org/content/10.1...

A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights The oral microbiome is increasingly linked to human health. To further examine this microbial community, we present the human reference oral microbiom…

#microsky oral #microbiome goes supersize

www.sciencedirect.com/science/arti...

Jumbo phage–mediated transduction of genomic islands | PNAS Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

#phagesky jumbo #phage -mediated HGT

www.pnas.org/doi/10.1073/...

Anoxia activates CRISPR–Cas immunity in the mouse intestine - Nature Microbiology The Citrobacter rodentium CRISPR–Cas system is activated by the oxygen-responsive transcriptional regulator Fnr in the anoxic environment of the mouse gut.

#phagesky #microsky #phage defence #microbiome

CRISPR-cas activated by anoxia and regulated by Fnr in Citrobacter rodentium

www.nature.com/articles/s41...

Antimicrobial resistance: a concise update Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately 5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted and cohesive...

#microsky review on #AMR

www.thelancet.com/journals/lan...

Directed evolution of compact RNA-guided nucleases for homology-directed repair in mammalian cells RNA-guided nucleases enable DNA editing and offer promise for treating genetic diseases, particularly when used for precise sequence replacement. However, many of the most effective enzymes, such as S...

#microsky #synbio “miniCas9” 🤗

www.biorxiv.org/content/10.1...

Seems amazing that one of the most intensively studied organisms on earth can still yield new(ish) & exciting antibiotics...
www.genengnews.com/topics/infec...

😲😱

𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘰𝘦𝘭𝘪𝘤𝘰𝘭𝘰𝘳 A3(2) produces a so far unknown antibiotic (because no one has looked closer, that is)
#MicroSky
🙏thx for pointing this out @microbingle.bsky.social

Temperature as a Driver of Phage Ecology and Evolution Bacteriophages (phages) are virtually ubiquitous and play a fundamental role in the ecological and evolutionary dynamics of their bacterial hosts. While phages are found across many thermal environmen...

www.annualreviews.org/content/jour...

#phagesky #phage

One transcript, two functions: the emerging roles of dual-function RNAs Abstract. Bacteria use small regulatory RNAs (sRNAs) and small proteins to change gene expression and modulate cellular processes in response to changing e

One transcript, two functions: the emerging roles of dual-function RNAs

microLIFE review by @lizmarialuke.bsky.social and Kai Papenfort at @uni-jena.de

academic.oup.com/microlife/ad...

A family of endonucleases that block nanotube-mediated plasmid dissemination Small non-conjugative plasmids constitute a substantial portion of the bacterial mobile genome, driving the dissemination of beneficial genes, with their transfer primarily attributed to transformatio...

www.biorxiv.org/content/10.1...

#phagesky #phage #MGE a prophage-encoded endomuclease antagonises plasmid transmission

Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...

New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome

Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky

www.biorxiv.org/content/10.1...

Catalyst optimization through synthetic Darwinian evolution - Nature Catalysis A study demonstrates that fully synthetic molecules can undergo self-replication, mutation and selection — hallmarks of Darwinian evolution — without relying on DNA or proteins.

www.nature.com/articles/s41...

#synbio

DNA extraction free whole genome sequencing of bacteriophage genomes from a single plaque DNA sequencing is at the core of genome characterization, proteomics, and identification of novel organisms. For microorganisms such as bacteriophages, sequencing their DNA can provide key insights in...

www.biorxiv.org/content/10.1...

#phagesky #phage

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

www.nature.com/articles/s41...

#phagesky #phage genomics on host range

Bacterial TIR-based immune systems sense phage capsids to initiate defense - Nature Microbiology After sensing capsids, the Thoeris antiphage defense system triggers a cascade that leads to NAD+ cleavage and cell arrest, which are dynamics that are mirrored in some mammalian immune pathways.

www.nature.com/articles/s41...

#phagesky #phage defence system Thoeris

#MicroSky #CryoEM #CryoET #teamtomo

New retron systems from environmental bacteria identify triggers of anti-phage defense and expand tools for genome editing Bacteria rely on retrons for phage defense, yet most known systems come from clinical or lab strains. This study identifies new and diverse retrons from environmental bacteria, uncovering their phage ...

journals.plos.org/plosbiology/...

#phagesky #phage defence #synbio

The field is awash with cool stuff, but I confess it’s a relief I don’t do anti-phage and don’t have to compete lol

#phagesky #phage

#microsky

Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states - Nature Communications Marín-Arraiza and colleagues report the cryo-EM structures of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states, providing structural insigh...

www.nature.com/articles/s41...

#microsky but kinda #phagesky too

Flexible Motion of T7 bacteriophage Tail Fibers Suggest a Dynamic Viral Infection Mechanism https://www.biorxiv.org/content/10.1101/2025.10.22.683886v1

academic.oup.com/nargab/artic...

#phagesky #phage

Proteolytically activated antibacterial toxins inhibit the growth of diverse gram-positive bacteria | PNAS Many species of bacteria produce small-molecule antibiotics that enter and kill a wide range of competitor microbes. However, diffusible antibacter...

www.pnas.org/doi/10.1073/...

#microsky

Wouldn’t the term “phase variation” apply? Mhmmm…

Phages use contingency loci as a bet-hedging strategy Bacteriophages are estimated to outnumber bacteria by ~10-fold. Here, we show that phage genomes contain contingency loci (CL), hypermutable DNA regions that promote reversible frameshift mutations th...

www.biorxiv.org/content/10.1...

#phagesky #phage really cool genetic trick