Tomas Hessler
@tomas-hessler.bsky.social
Postdoc at UC Berkeley Metagenomics | Microbial ecology | Phage | Bioprocess engineering 🇿🇦 views are my own
Reposted by Tomas Hessler
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Reposted by Tomas Hessler
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Selection and transmission of the gut microbiome alone can shift mammalian behavior
Nature Communications - Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and...
rdcu.be
October 28, 2025 at 7:51 AM
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Reposted by Tomas Hessler
Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae
Author summary This study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and st...
journals.plos.org
November 3, 2025 at 11:58 PM
Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
Reposted by Tomas Hessler
How do spontaneous mutations arise?
In this latest #GENETICS review, Susan Lovett and @thalia.bsky.social provide a detailed overview of bacterial genetics experiments instrumental in understanding how genomes change. buff.ly/CXJnTqn
In this latest #GENETICS review, Susan Lovett and @thalia.bsky.social provide a detailed overview of bacterial genetics experiments instrumental in understanding how genomes change. buff.ly/CXJnTqn
October 7, 2025 at 6:02 PM
How do spontaneous mutations arise?
In this latest #GENETICS review, Susan Lovett and @thalia.bsky.social provide a detailed overview of bacterial genetics experiments instrumental in understanding how genomes change. buff.ly/CXJnTqn
In this latest #GENETICS review, Susan Lovett and @thalia.bsky.social provide a detailed overview of bacterial genetics experiments instrumental in understanding how genomes change. buff.ly/CXJnTqn
Reposted by Tomas Hessler
VACANCY - Independent research fellowships leading to tenured positions
We’re inviting applications from outstanding researchers who either hold, or wish to apply for, Independent Research Fellowships.
APPLICATION DEADLINE: 10 November 2025
Click here to apply: jic.link/Fellows
We’re inviting applications from outstanding researchers who either hold, or wish to apply for, Independent Research Fellowships.
APPLICATION DEADLINE: 10 November 2025
Click here to apply: jic.link/Fellows
October 3, 2025 at 3:11 PM
VACANCY - Independent research fellowships leading to tenured positions
We’re inviting applications from outstanding researchers who either hold, or wish to apply for, Independent Research Fellowships.
APPLICATION DEADLINE: 10 November 2025
Click here to apply: jic.link/Fellows
We’re inviting applications from outstanding researchers who either hold, or wish to apply for, Independent Research Fellowships.
APPLICATION DEADLINE: 10 November 2025
Click here to apply: jic.link/Fellows
Reposted by Tomas Hessler
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 2, 2025 at 3:01 AM
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Reposted by Tomas Hessler
Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social
Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1
October 1, 2025 at 5:10 AM
Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social
Reposted by Tomas Hessler
📢 New preprint on work by my first PhD student William Pallier.
Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration.
We demonstrate that microbial ecophysiology predictably changes with peatland ecosystem health.
www.biorxiv.org/content/10.1...
Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration.
We demonstrate that microbial ecophysiology predictably changes with peatland ecosystem health.
www.biorxiv.org/content/10.1...
August 4, 2025 at 4:31 PM
📢 New preprint on work by my first PhD student William Pallier.
Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration.
We demonstrate that microbial ecophysiology predictably changes with peatland ecosystem health.
www.biorxiv.org/content/10.1...
Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration.
We demonstrate that microbial ecophysiology predictably changes with peatland ecosystem health.
www.biorxiv.org/content/10.1...
Reposted by Tomas Hessler
How much of selection in human microbiomes is driven by phage?
Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
www.biorxiv.org/content/10.1...
🧵
Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
www.biorxiv.org/content/10.1...
🧵
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one syst...
www.biorxiv.org
September 22, 2025 at 5:57 PM
How much of selection in human microbiomes is driven by phage?
Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
www.biorxiv.org/content/10.1...
🧵
Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
www.biorxiv.org/content/10.1...
🧵
Reposted by Tomas Hessler
You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
Phages with a broad host range are common across ecosystems - Nature Microbiology
Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.
www.nature.com
September 19, 2025 at 9:32 AM
You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
Reposted by Tomas Hessler
The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!
jobs.colostate.edu/postings/165...
jobs.colostate.edu/postings/165...
Assistant Professor Plant-Microbe Interactions
We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...
jobs.colostate.edu
September 8, 2025 at 3:45 PM
The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!
jobs.colostate.edu/postings/165...
jobs.colostate.edu/postings/165...
Reposted by Tomas Hessler
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 18, 2025 at 8:09 PM
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tomas Hessler
Hexokinase 2 (HK2) is known for its metabolic role in #glycolysis. This study shows that it also functions as an #RNAbindingProtein that regulates mRNA translation, particularly of SOX10, promoting #melanoma cell proliferation independently of glycolysis @plosbiology.org 🧪 plos.io/3ViI1qL
September 17, 2025 at 4:44 PM
Hexokinase 2 (HK2) is known for its metabolic role in #glycolysis. This study shows that it also functions as an #RNAbindingProtein that regulates mRNA translation, particularly of SOX10, promoting #melanoma cell proliferation independently of glycolysis @plosbiology.org 🧪 plos.io/3ViI1qL
Reposted by Tomas Hessler
Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6
nature.com/articles/s41467-025-63463-6
Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail - Nature Communications
Rodrigues and Queiroz et al. report the discovery of Naiavirus, the largest enveloped virus, isolated from a Brazil biome. With an oval capsid and flexible tail, its giant genome holds many novel gene...
nature.com
September 17, 2025 at 3:36 PM
Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6
nature.com/articles/s41467-025-63463-6
Reposted by Tomas Hessler
Nature research paper: Programmable antisense oligomers for phage functional genomics
go.nature.com/46b1XAQ
go.nature.com/46b1XAQ
Programmable antisense oligomers for phage functional genomics - Nature
Establishing antisense oligomers as versatile, non-genetic tools to silence phage mRNAs opens applications in basic research and biotechnology, as shown by identifying essential factors for propagation of the nucleus-forming jumbo phage ΦKZ such as the RNase H-like protein ΦKZ155.
go.nature.com
September 12, 2025 at 8:14 AM
Nature research paper: Programmable antisense oligomers for phage functional genomics
go.nature.com/46b1XAQ
go.nature.com/46b1XAQ
Reposted by Tomas Hessler
Quantifying phage infectivity from characteristics of bacterial population dynamics www.pnas.org/doi/abs/10.1... #jcampubs
Quantifying phage infectivity from characteristics of bacterial population dynamics | PNAS
A frequent goal of phage biology is to quantify how well a phage kills a population
of host bacteria. Unfortunately, traditional methods to quantif...
www.pnas.org
September 9, 2025 at 2:33 PM
Quantifying phage infectivity from characteristics of bacterial population dynamics www.pnas.org/doi/abs/10.1... #jcampubs
Reposted by Tomas Hessler
Our paper on model cyanobacterial communities by @andrejakust.bsky.social is finally typeset and looks beautiful, check it out:
academic.oup.com/ismej/articl...
academic.oup.com/ismej/articl...
Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species
Abstract. Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habita
academic.oup.com
September 2, 2025 at 4:21 PM
Our paper on model cyanobacterial communities by @andrejakust.bsky.social is finally typeset and looks beautiful, check it out:
academic.oup.com/ismej/articl...
academic.oup.com/ismej/articl...
Reposted by Tomas Hessler
I was shocked when I first saw these results from standard climate models used in IPCC reports: for high emissions, the Atlantic overturning circulation #AMOC shuts down in all 9 models that ran past 2100, and is well on the way to shutdown by 2100.
Our paper on that is out today.🧵
Our paper on that is out today.🧵
August 28, 2025 at 3:55 PM
I was shocked when I first saw these results from standard climate models used in IPCC reports: for high emissions, the Atlantic overturning circulation #AMOC shuts down in all 9 models that ran past 2100, and is well on the way to shutdown by 2100.
Our paper on that is out today.🧵
Our paper on that is out today.🧵
Reposted by Tomas Hessler
Widespread purine bias in bacterial genes driven by runaway transcription www.biorxiv.org/content/10.1... #jcampubs
August 26, 2025 at 1:12 PM
Widespread purine bias in bacterial genes driven by runaway transcription www.biorxiv.org/content/10.1... #jcampubs
Reposted by Tomas Hessler
New evidence of AI’s impact on the job market — Stanford economists found that early career employment has weakened in occupations vulnerable to AI automation (eg: software engineers and customer service reps)
August 26, 2025 at 4:51 PM
New evidence of AI’s impact on the job market — Stanford economists found that early career employment has weakened in occupations vulnerable to AI automation (eg: software engineers and customer service reps)
Reposted by Tomas Hessler
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Tomas Hessler
Putting the Global South on the Microbiome research map -
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
August 11, 2025 at 5:24 PM
Putting the Global South on the Microbiome research map -
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
Reposted by Tomas Hessler
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Protein language models reveal evolutionary constraints on synonymous codon choice
Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...
www.biorxiv.org
August 7, 2025 at 8:29 AM
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Reposted by Tomas Hessler
Outcome of soil microbiome transplants is controlled more by selective pressures of recipient soil environment (habitat filtering) than original composition of transplanted community, emphasising habitat’s characteristics, not microbiota origin, determine transplant success👇
doi.org/10.1093/isme...
doi.org/10.1093/isme...
Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil
Abstract. Human activities cause a global loss of soil microbiome diversity and functionality. One way to reverse this trend is through microbiota transpla
doi.org
August 4, 2025 at 4:31 PM
Outcome of soil microbiome transplants is controlled more by selective pressures of recipient soil environment (habitat filtering) than original composition of transplanted community, emphasising habitat’s characteristics, not microbiota origin, determine transplant success👇
doi.org/10.1093/isme...
doi.org/10.1093/isme...
Reposted by Tomas Hessler
‼️Diamond Lab is considering potential a new postdoctoral researcher. If you have strong interests in microbiomes, metagenomics, machine learning, or rumen biology drop us a line and shoot us a CV!
August 1, 2025 at 10:57 PM
‼️Diamond Lab is considering potential a new postdoctoral researcher. If you have strong interests in microbiomes, metagenomics, machine learning, or rumen biology drop us a line and shoot us a CV!