James Marsh
@jmarsh.bsky.social
Group Leader navigating microbiome genetics & engineering @ Max Planck in Tübingen, Germany. Rarely late.
☕️🎧🇦🇺🎥
☕️🎧🇦🇺🎥
Reposted by 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...
October 7, 2025 at 8:31 AM
🛠️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...
Reposted by James Marsh
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...
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
October 1, 2025 at 4:44 PM
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...
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...
Reposted by James Marsh
And for those interested in creating figures - you can also feed zol results into cgcg to create network-graph visuals:
bsky.app/profile/rauf...
bsky.app/profile/rauf...
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
Github: github.com/Kalan-Lab/zol
Docs: github.com/Kalan-Lab/zo...
#secmet #phage #genomics
September 29, 2025 at 4:36 AM
And for those interested in creating figures - you can also feed zol results into cgcg to create network-graph visuals:
bsky.app/profile/rauf...
bsky.app/profile/rauf...
Reposted by James Marsh
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/...
@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
September 17, 2025 at 10:17 AM
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/...
@nfrk92.bsky.social
@narjournal.bsky.social
academic.oup.com/nar/article/...
Reposted by James Marsh
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...
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
September 4, 2025 at 11:32 AM
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...
doi.org/10.1098/rstb...
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
#microsky #microbiomesky
September 4, 2025 at 9:41 AM
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
#microsky #microbiomesky
Reposted by James Marsh
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
September 3, 2025 at 7:21 PM
Plasmids can be lost from a bacterial community even under positive environmental selection: doi.org/10.1101/2025...
Reposted by James Marsh
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
🧵
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
September 2, 2025 at 10:48 AM
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
🧵
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
🧵
Reposted by James Marsh
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"
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
June 11, 2025 at 1:43 PM
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"
genomebiology.biomedcentral.com/articles/10....
Reposted by James Marsh
SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies. #StructuralVariants #SVs #Visualization #WholeGenome #Assemblies #Bioinformmatics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
June 11, 2025 at 10:31 AM
SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies. #StructuralVariants #SVs #Visualization #WholeGenome #Assemblies #Bioinformmatics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by James Marsh
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, 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
May 16, 2025 at 12:22 AM
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, 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...
Reposted by James Marsh
🚨 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
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
April 17, 2025 at 8:01 AM
🚨 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
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
Reposted by James Marsh
OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice
#microsky 🧪
www.nature.com/articles/s41...
#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
March 27, 2025 at 4:35 PM
OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice
#microsky 🧪
www.nature.com/articles/s41...
#microsky 🧪
www.nature.com/articles/s41...
Reposted by James Marsh
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...
Also suitable to build saturated chromosomal variant libraries using oligo-recombineering with extra short homology arms!
www.biorxiv.org/content/10.1...
March 21, 2025 at 7:06 AM
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...
Also suitable to build saturated chromosomal variant libraries using oligo-recombineering with extra short homology arms!
www.biorxiv.org/content/10.1...
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...
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
January 13, 2025 at 9:35 AM
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...
www.biorxiv.org/content/10.1...
Reposted by James Marsh
(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
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
December 12, 2024 at 8:42 AM
(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
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
Reposted by James Marsh
Thanks to great colleagues including @jweir.bsky.social at the @maxplanckcampus.bsky.social 🦠🧫
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
December 10, 2024 at 2:54 PM
Thanks to great colleagues including @jweir.bsky.social at the @maxplanckcampus.bsky.social 🦠🧫
Reposted by James Marsh
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" (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
December 3, 2024 at 2:00 PM
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" (2018) www.nature.com/artic...
Reposted by James Marsh
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/...
#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
December 2, 2024 at 6:49 AM
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/...
#Microsky #phagesky #Science
ntu.wd3.myworkdayjobs.com/Careers/job/...
Reposted by James Marsh
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
🔁 Please RT & ❤️ this post so we can gather all the microbiome enthusiasts and scientists in one place. #MicrobiomeScience #Networking
November 30, 2024 at 11:26 AM
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
🔁 Please RT & ❤️ this post so we can gather all the microbiome enthusiasts and scientists in one place. #MicrobiomeScience #Networking
Reposted by James Marsh
🚨 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 🪸🧪🧬🌊
If you are interested in marine microbiology, bacterial genetics and/or symbiosis, please consider reaching out! Repost to help spread the word 🪸🧪🧬🌊
November 30, 2024 at 12:14 AM
🚨 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 🪸🧪🧬🌊
If you are interested in marine microbiology, bacterial genetics and/or symbiosis, please consider reaching out! Repost to help spread the word 🪸🧪🧬🌊
Reposted by James Marsh
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
November 29, 2024 at 9:05 AM
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...
Reposted by James Marsh
#Methanogens dominate #methanotrophs and act as a #methane source in aquaculture pond sediments doi.org/10.1016/j.ec...
November 29, 2024 at 8:31 AM
#Methanogens dominate #methanotrophs and act as a #methane source in aquaculture pond sediments doi.org/10.1016/j.ec...
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...
www.nature.com/articles/s41...
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...
www.nature.com
November 28, 2024 at 3:00 PM
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...
www.nature.com/articles/s41...