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Reposted by James Marsh

Thomas Gorochowski @chofski.bsky.social · 3d

🛠️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...

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Reposted by James Marsh

Dan Portik @dportik.bsky.social · 9d

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

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Reposted by James Marsh

Ryan Wick @rrwick.bsky.social · 12d

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

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Reposted by James Marsh

Rauf Salamzade @raufs.bsky.social · 12d

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 · Dec 6

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

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Reposted by James Marsh

Agathe couturier @agathe-couturier.bsky.social · 23d

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

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Reposted by James Marsh

Josie Elliott @josie-e.bsky.social · Sep 4

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

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James Marsh @jmarsh.bsky.social · Sep 4

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

Conference flyer for the 2025 International Conference on Microbiome Engineering. Lists the session topics and organizing committee.

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Reposted by James Marsh

Kaitlin Schaal @evokait.bsky.social · Sep 3

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

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Reposted by James Marsh

Sorek Lab @soreklab.bsky.social · Sep 2

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...

www.biorxiv.org

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Reposted by James Marsh

Asaf Levy @asaflevylab.bsky.social · Jun 11

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

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Reposted by James Marsh

Javier Santoyo @jsantoyo.bsky.social · Jun 11

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

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Reposted by James Marsh

George Bouras @gbouras13.bsky.social · May 16

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 ...

www.biorxiv.org

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Reposted by James Marsh

Christine Moissl-Eichinger @chmoei.bsky.social · Apr 17

🚨 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...

www.microbiologyresearch.org

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Reposted by James Marsh

Nature Microbiology @natmicrobiol.nature.com · Mar 27

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...

www.nature.com

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Reposted by James Marsh

Maxence Lejars @mlejars.bsky.social · Mar 21

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...

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James Marsh @jmarsh.bsky.social · Jan 13

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...

www.biorxiv.org

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Reposted by James Marsh

MPI for Biology Tübingen & Friedrich Miescher Laboratory @mpi-bio-fml.bsky.social · Dec 12

(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

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Reposted by James Marsh

RuthLeyMicro @microbiome.bsky.social · Dec 10

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

RuthLeyMicro @microbiome.bsky.social · Dec 10

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...

Kinetic and structure-based comparisons of silent and stimulatory flagellin interactions with TLR5

The bacterial protein flagellin is the sole ligand of the innate immune receptor Toll-like receptor 5 (TLR5). Flagellins with strong agonism bind TLR5 at their D1 and D0 domains, while poor agonist si...

www.biorxiv.org

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Reposted by James Marsh

Bork Group at EMBL Heidelberg @borklab.bsky.social · Dec 3

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...

www.nature.com

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Reposted by James Marsh

Prof Cynthia Whitchurch FAA🏳️‍🌈 @cwhitch.bsky.social · Dec 2

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

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Reposted by James Marsh

Patrick Veiga @patrickveiga.bsky.social · Nov 30

Just landed here from Twitter/X! 🚀 Time to rebuild my followers/following list. If u’re into microbiome science like me, let’s connect and grow a refreshed community!
🔁 Please RT & ❤️ this post so we can gather all the microbiome enthusiasts and scientists in one place. #MicrobiomeScience #Networking

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James Marsh @jmarsh.bsky.social · Nov 30

Fingers crossed!

James Marsh @jmarsh.bsky.social · Nov 30

Impressive! My cat failed miserably at this (or maybe I was too impatient..) It usually ended with me cleaning up cat poo from the bathtub - he decided that was the better option. Looks like you’ll pull it off - good luck!

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Reposted by James Marsh

Amanda Alker @atp-alker.bsky.social · Nov 30

🚨 The Alker Lab is starting at the University of Rhode Island in early 2025 and we will be hiring! 🚨

If you are interested in marine microbiology, bacterial genetics and/or symbiosis, please consider reaching out! Repost to help spread the word 🪸🧪🧬🌊

The Alker lab at the University of Rhode Island is hiring (students, postdocs and lab staff)! We use cutting edge tools in microbiology to investigate marine animal symbioses. Email or DM for further inquiries

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Reposted by James Marsh

Lizbeth Sayavedra @lizsayavedra.bsky.social · Nov 29

Our brand-new paper in #GutMicrobes reveals how Bilophila wadsworthia and Bacteroides thetaiotaomicron interact in the gut, driving H₂S production & metabolic shifts with potential links to inflammation & disease. #GutHealth Check it out: doi.org/10.1080/1949...

Bacteroides thetaiotaomicron enhances H2S production in Bilophila wadsworthia

Sulfate- and sulfite-reducing bacteria (SRB) are a group of strict anaerobes found within the human gut. Bilophila wadsworthia, a sulfite-reducing bacterium which produces hydrogen sulfide (H2S) fr...

doi.org

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