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Preprint 🦠🚨: We are diving deeper into #T6SS effectors, and now in #Pantoea. We describe the largest, most diverse effector arsenal associated with a single T6SS, and it's in a plant pathogen that forms galls on beet roots. Sweet! 1/8 www.biorxiv.org/content/10.6...

Pantoea agglomerans T6SS effectors reside in hotspots with combinatorial offensive and defensive arsenalsGram-negative bacteria deploy type VI secretion systems (T6SSs) to mediate interbacterial competition. Although numerous T6SS effectors have been identified, their pan-genomic repertoires and evolutio...www.biorxiv.org

🚀 Thrilled to share our first metaSPLiT preprint from @annabiosys.bsky.social's lab in collaboration with @gibbological.bsky.social! Explore hidden bacterial phenotypic heterogeneity in the human gut microbiome and discover the concept of "physiological guilds": www.biorxiv.org/content/10.6...

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomicsMost of our knowledge about bacterial functional roles in microbiomes comes from bulk measurements. Yet microbial communities are complex ecosystems in which functionally distinct bacterial subpopulat...www.biorxiv.org

We’re so excited to share our new paper, where we tackle the wealth of structural and functional diversity of anti-phage sensors across bacteria (1/6)

Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences | Nature Microbiology

Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences - Nature MicrobiologyThe phage-encoded protein PptA enables its DNA to masquerade as the host and evade cleavage, providing a potential foundation for engineering therapeutic phages that could bypass this widespread defence system.www.nature.com

New Preprint 🥳 Here we wondered how phages that have been extensively studied in laboratory E. coli strains actually behave when they encounter a real pathogen such as O157:H7 strain...one with a far more complex cell surface & one of the most consequential foodborne pathogens in the United States.

Animated E. coli Bacteria DrawingAlt: Animated E. coli Bacteria Drawingstatic.klipy.com

Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15

Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...

A family of lanthipeptides with anti-phage functionBacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…www.sciencedirect.com

Check out this fun collaboration on phages and Polyamines with the Marshall Lab! #microsky #phagesky 🧪🧫🧬🔬

Gabija restricts phage circularization & DNA replication Gabija prevents phage genome circularization & replication w/out impacting bacterial host. Exposed DNA ends & phage end-binding proteins license DNA targeting while RecBCD protects host from Gabija www.cell.com/cell-host-mi...

Gabija restricts phage circularization and DNA replicationGabija acts early during phage infection, preventing phage genome circularization and replication. Phage DNA end-binding proteins prevent RecBCD loading onto linear DNA, and the absence of RecBCD lice...www.cell.com

#phagesky #microsky #phage www.cell.com/cell-reports...

A receptor-centered approach identifies Lom as a LamB-bound superinfection exclusion factor in bacteriophage λGe et al. develop a receptor-centered strategy to identify phage proteins that target host receptors during infection and discover the λ outer-membrane protein Lom. Lom binds and occludes LamB, blocki...www.cell.com

A DNA-scaffolded Retron Ring Mediates Antiphage Immunity https://www.biorxiv.org/content/10.64898/2026.07.14.737667v1

Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️

Bacteria sense virus-induced genome degradation via methylated mononucleotidesPhages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...www.science.org

High-quality phage assembly from metagenomes with PALACE | Nature Biotechnology

High-quality phage assembly from metagenomes with PALACE - Nature BiotechnologyPALACE combines homology features and deep learning to improve phage assembly from metagenomics.www.nature.com

Widespread immune systems protect bacteria against conjugative plasmids https://www.biorxiv.org/content/10.64898/2026.07.06.735840v1

Bacterial and human exonucleases mediate interkingdom antiviral immunity https://www.biorxiv.org/content/10.64898/2026.06.30.735675v1

Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptase | bioRxiv

Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptaseDefense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection. We previously showed that DRT10, a tripartite system comprising an RT, a noncoding RNA (ncRNA), and a SLATT effector protein, catalyzes protein-primed, tandem-repeat DNA synthesis in a mechanism strikingly analogous to eukaryotic telomerase. However, the structural basis by which the RT-ncRNA complex directs repeat addition processivity and controls repeat length remains unknown. Here we present cryo-EM reconstructions of two evolutionarily diverse DRT10 RT-ncRNA systems that reveal an unanticipated 2:1 architecture, wherein two RT monomers bind opposite sides of a single, pseudo-symmetric ncRNA. Biochemical experiments demonstrate that each RT monomer reverse transcribes the template encoded on its respective side of the ncRNA, but only one generates the long repetitive product, with the template sequence defined by the distance between two flanking stem-loop anchors. Together with earlier studies of DRT2, DRT3, and DRT9, our findings identify a conserved mechanistic logic underlying ncRNA-templated tandem-repeat synthesis across Class 2 UG antiviral systems, despite vastly different architectural solutions. ### Competing Interest Statement Columbia University has filed a patent application related to this work. S.H.S. is a co-founder and scientific advisor to Dahlia Biosciences, a scientific advisor to CrisprBits and Prime Medicine, and an equity holder in Dahlia Biosciences and CrisprBits. The remaining authors declare no competing interests.www.biorxiv.org

I am thrilled to share our paper out in @cp-cell.bsky.social : "Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways." (1/4) www.cell.com/cell/fulltex...

Systematic discovery of pathogen effector functions across human pathogens and pathwaysThe eORFeome, a large-scale collection of open reading frames encoding viral proteins and secreted bacterial and parasite effectors, enables functional genomics across diverse pathways and pathogens. ...www.cell.com

Cool new preprint of a new defence family! Antimicrobial-resistance plasmids encode Evangelion, a widespread DUF4062 anti-phage defence family www.biorxiv.org/content/10.6...

Antimicrobial-resistance plasmids encode Evangelion, a widespread DUF4062 anti-phage defence familyMany bacterial anti-phage defence systems are encoded by mobile genetic elements, yet much of this antiviral repertoire remains undiscovered. Antimicrobial-resistance plasmids are well known for disse...www.biorxiv.org

New preprint!! 🎉 A cool collaborative work with @copabio.bsky.social and Chase Beisel teams on the phage editing technology. @sarshad.bsky.social led the work from our side to validate & characterize the lib. #phage #phagesky www.biorxiv.org/content/10.6... Work supported by: phagefoundry.org

Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomesGenetic manipulation of bacteriophages is essential for interrogating phage biology and advancing antimicrobial therapies. However, current genome editing approaches can be inefficient, require multip...www.biorxiv.org

Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity @natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino www.nature.com/articles/s41...

Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity - Nature MicrobiologyThe activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...www.nature.com