James Marsh

🛠️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...

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...

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...

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

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

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

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

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/...

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...

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...

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

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

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...

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

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...

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
🧵

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...

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

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

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/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...

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...

🚨 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

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...

OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice

#microsky 🧪

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

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...

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...

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...

(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 🦠🧫

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...

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...

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...

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/...

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

Fingers crossed!

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!

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

🚨 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 🪸🧪🧬🌊

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...

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...

#Methanogens dominate #methanotrophs and act as a #methane source in aquaculture pond sediments doi.org/10.1016/j.ec...

Gut microbiota strain richness is species specific and affects engraftment - Nature Strain richness of gut microbiota ecosystems is a key characteristic underpinning engraftment in faecal microbiota transplantation, and could improve the design of defined live biotherapeuti...

Interesting look at gut strain-level dynamics: The human gut has low strain variation compared to other environments and has a limited capacity for strain richness. #microbiome

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

Why are some microbes are better (gastrointestinal) commensals?
Join for a Postdoc 19+12 months to investigate bacterial & fungal evolution in the human gut in a novel family cohort, using 3rd gen seq, metagenomics.
Application deadline is 1st Dec: t.co/FE8tyW3Q3K

A very cool app to compare a list of microbes with microbial signatures in BugSigDB and Bugphyzz 🧫 #microbiome

I wanted to share our beautiful synthetic gut community Com20, highlighting my favourites

🧪cutie little R. intestinalis shaped like a banana

🧫big boss C. perfringens needs privacy around its rods

🧪E. ramosum showing it’s spores

@lisamaierlab.bsky.social
#microbiome
#MicrobiomeSky
#microscopy