A short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...

The Pangenome Is Not a Parts List

The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.

open.substack.com

This is actually shaping up to be a really aesthetically pleasing plasmid editor. Amazing what you can do without leaving the terminal. Love seeing the github say 100% Python. Looks like I'll be able to make the May 24th deadline after all!

Looking for a #postdoc outside the US, focusing on gut microbiome, AMR dynamics & phage-bacteria interactions. Bridging wet lab and computational approaches🦠👩‍💻. Hartmann Lab, Northwestern University, defending late 2026. Boosts appreciated 🙏🧫🧪 #microbiome #metagenomics #MicroSky

Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/ Best of all, the data never leaves your computer! #phage #phagesky

🤯🤯🤯 Prime editing + Gibson assembly =Prime Assembly at decent efficiency. Genome engineering technology is advancing so fast. Very exciting! Congratulations to all!

Erik Sontheimer 🇺🇸💙🇺🇦@eriksontheimer.bsky.social · 3mo ago

Site-specific, multi-kilobase insertions and over-writes in mammalian cells, without DSBs, HDR, recombinases, integrases, transposases, or active cell cycling? Using fully or predominantly single-stranded DNA donors? 1/15

Porter and coworkers present a new set of tools and workflow to transfer large genetic loci, such as PULs, into genetically tractable Bacteroides strains. Read more: journals.asm.org/doi/10.1128/... #PULs #Bacteroides #Polysaccharides #Loci #GeneTransfer

Out now in Nature Biotechnology! Alejandro González-Delgado and a fantastic team of collaborators worked across nine labs to get retron recombineering up-and-running in fifteen bacterial species. Molecular parts on addgene: www.addgene.org/browse/artic... Happy editing!

Nature Biotechnology@natbiotech.nature.com · 3mo ago

Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering - @seth-shipman.bsky.social @gladstoneinst.bsky.social go.nature.com/4tZluOU

Out now: Variations in plasmid transfer in Acinetobacter baumannii: insights from epigenetics, strain properties, and experimental conditions | Microbiology Spectrum journals.asm.org/doi/10.1128/...

Variations in plasmid transfer in Acinetobacter baumannii: insights from epigenetics, strain properties, and experimental conditions | Microbiology Spectrum

Plasmid-mediated gene transfer is one of the major drivers of antibiotic resistance in Acinetobacter baumannii; however, plasmid transfer protocols remain inconsistent and strain-dependent. By assessi...

journals.asm.org

JB Editor's Choice: Khuntia, Nandicoori et al. describe a toolkit for the molecular analysis of mycobacteria. They created 32 modular integrative & 8 episomal E. coli-mycobacterium shuttle vectors, including tools to make tagged proteins. journals.asm.org/doi/10.1128/... @asm.org #JBacteriology

Calling all bacterial geneticists 🧫 Anyone done allelic exchange with sacB counter-selection in Pseudomonas aeruginosa? I'm hitting a wall and would love to connect with people who've been through this. #MicroSky #Pseudomonas #bacterialgenetics #microbiology

🛠️New tool from the lab! #SHARK🦈: a new strain to support complex cloning of transient R6K expression plasmids – perfect for genome engineering. Work led by the talented Shivang Joshi and all strains and strain assembly tools enroute to Addgene. #synbio doi.org/10.1101/2025...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut. Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals. doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

doi.org

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

Autocycler: long-read consensus assembly for bacterial genomes

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

doi.org

And for those interested in creating figures - you can also feed zol results into cgcg to create network-graph visuals: bsky.app/profile/rauf...

Rauf Salamzade@raufs.bsky.social · 2y ago

Check out this 1 min video on using zol + cgcg for scalable visualization of evo info across 1000s of homologous gene cluster instances (e.g. BGCs, phages, plasmids, defense islands, etc.) as network graphs. Github: github.com/Kalan-Lab/zol Docs: github.com/Kalan-Lab/zo... #secmet #phage #genomics

Exclusion systems, far from slowing down plasmid spread, are in fact essential to preserve host cell viability and thereby ensure the successful dissemination of conjugative plasmids and antibiotic resistance genes. @nfrk92.bsky.social @narjournal.bsky.social academic.oup.com/nar/article/...

Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes

Abstract. Plasmid conjugation is a major driver of antibiotic resistance dissemination in bacteria. In addition to genes required for transfer and maintena

academic.oup.com

Can CRISPR-Cas systems target any phage? Yes, no, it depends? What does it depend on? The second paper from my PhD came out today in a special issue of Phil Trans B on the ecology and evolution of bacterial immune systems doi.org/10.1098/rstb...

Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent | Philosophical Transactions of the Royal Society B: Biological Sciences

CRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts against invading genetic material such as phages. It is clear that the importance of acquiring CRISPR-Cas immunit...

doi.org

There's still time to get your abstracts in for this year's International Conference on Microbiome Engineering conference in Antwerp! We extended the deadline to September 15th. #microsky #microbiomesky

Plasmids can be lost from a bacterial community even under positive environmental selection: doi.org/10.1101/2025...

Species interactions determine plasmid persistence in a 3-member bacterial community

Microbial communities are shaped by complex forces, including interspecies interactions and the effects of mobile genetic elements such as plasmids. How these forces interact to affect community respo...

doi.org

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection

Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...

biorxiv.org

Our new paper is online in Genome Biology: "Plasmids, prophages, and defense systems are depleted from plant microbiota genomes" genomebiology.biomedcentral.com/articles/10....

Plasmids, prophages, and defense systems are depleted from plant microbiota genomes - Genome Biology

Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. He...

genomebiology.biomedcentral.com

SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies. #StructuralVariants #SVs #Visualization #WholeGenome #Assemblies #Bioinformmatics academic.oup.com/bioinformati...

www.biorxiv.org/content/10.1... Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use) github.com/rrwick/Autoc...

Autocycler: long-read consensus assembly for bacterial genomes

Motivation: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using ...

biorxiv.org

🚨 New publication: We describe a novel, cultivated #Archaea species from the human microbiome: #Methanobrevibacter intestini sp. nov. ! www.microbiologyresearch.org/content/jour... #Microbiome #GutMicrobiota #NewSpecies #archaeasky #microbiomesky

Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii ‘GRAZ-2’ from human faeces

Two mesophilic, hydrogenotrophic methanogens, WWM1085 and M. smithii GRAZ-2, were isolated from human faecal samples. WWM1085 was isolated from an individual in the United States and represents a nove...

microbiologyresearch.org

OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice #microsky 🧪 www.nature.com/articles/s41...

Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice - Nature Microbiology

InducTn-seq, a method for inducible mutagenesis followed by transposon insertion site sequencing, enables temporal control of transposition to bypass population bottlenecks and enable the quantificati...

nature.com

Happy to share our genetic toolkit designed to make your gene editing (life) easier, faster and very efficient! Also suitable to build saturated chromosomal variant libraries using oligo-recombineering with extra short homology arms! www.biorxiv.org/content/10.1...

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

EASY-CRISPR: a toolbox for high-throughput single-step custom genetic editing in bacteria https://www.biorxiv.org/content/10.1101/2025.03.20.644322v1

I've been waiting for someone to do this: Phase variation via DNA methylation enables gut bacteria to adapt to environmental changes by regulating gene expression and enhancing phenotypic diversity. #microbiome www.biorxiv.org/content/10.1...

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase va...

biorxiv.org

(Part 4 of 5) Available PhD projects in Biology! Start your career in ground-breaking research with Gal Ofir & Christian Rödelsperger from the MPI Biology Tübingen. Apply by: 27 Jan. www.phd.tuebingen.mp... #imprs #graduateprogram #maxplanck #phd #phdlife #phdposition #phdpositiongermany #biology

Thanks to great colleagues including @jweir.bsky.social at the @maxplanckcampus.bsky.social 🦠🧫

Prof. Ruth Ley FRS@microbiome.bsky.social · 2y ago

Here we delve deeper into what makes a flagellin “silent” - see Michael Bell’s cryo-EM structure of a silent flagellin from the flagellum of Roseburia hominis- it has a different charge distribution compared to FliC and it dissociates rapidly from TLR5 www.biorxiv.org/content/10.1...

In a great collaboration with @typaslab.bsky.social, @lisamaierlab.bsky.social and @biocs.bsky.social found that 24% of the tested human-targeted drugs inhibit the growth of gut commensal bacteria. "Extensive impact of non-antibiotic drugs on human gut bacteria" (2018) www.nature.com/artic...

Extensive impact of non-antibiotic drugs on human gut bacteria

Nature - Some non-antibiotic drugs have been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Athanasios Typas and colleagues screened more than...

nature.com

I'm recruiting! I'm looking for a motivated postdoctoral scientist to join my new team at SCELSE in Singapore. The role will explore various aspects of how #eDNA is produced and utilised in #Pseudomonas aeruginosa biofilms. #Microsky #phagesky #Science ntu.wd3.myworkdayjobs.com/Careers/job/...

Research Fellow (eDNA in Biofilms)

The Singapore Centre for Environmental Life Sciences Engineering (SCELSE) is a unique interdisciplinary Research Centre of Excellence (RCE), funded by National Research Foundation, Ministry of Educati...

ntu.wd3.myworkdayjobs.com