Tomas Hessler

Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch

Teaser: Increased proline in ΔputP
#microsky #MEvoSky

Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...

Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

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

@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social

Bacteriophage genome-wide transposon mutagenesis Bacteriophages have genomes that span a wide size range, are densely packed with coding sequences, and frequently encode genes of unknown function. Classical forward genetics has defined essential gen...

#microsky #phagesky

Transposon mutagenesis of jumbo #phage using an anti-CRISPR factor as selectable marker

www.biorxiv.org/content/10.1...

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...

Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria - Microbiome Background Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. Ho...

We are thrilled to announce our latest publication in the Microbiome journal in collaboration with
@thehesslab.bsky.social
Supplementation with red seaweed in cows reduces methane and induces previously uncharacterized hydrogenotropic bacteria.
microbiomejournal.biomedcentral.com/articles/10....

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.

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...

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
🦠🧫

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...

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

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

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

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

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...

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

📢 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...

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...

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...

🧵

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.

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...

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...

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...

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...

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...

AlphaFold model of the complex formed between HK2 and the SOX10 5′UTR (189–204 nts). The predicted RNA structure is shown in cyan, and HK2 protein is shown in green. HK2 residues and SOX10 mRNA nucleotides at the interaction interface are highlighted in red. Inset: schematic representation of the secondary structure of the SOX10 5′UTR (189–204 nts) predicted by Mfold, with the putative HK2-binding region (194–198 nts) marked in red.

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

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...

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6

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.

Nature research paper: Programmable antisense oligomers for phage functional genomics

go.nature.com/46b1XAQ

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...

Quantifying phage infectivity from characteristics of bacterial population dynamics www.pnas.org/doi/abs/10.1... #jcampubs

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

Our paper on model cyanobacterial communities by @andrejakust.bsky.social is finally typeset and looks beautiful, check it out:

academic.oup.com/ismej/articl...

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.🧵

Widespread purine bias in bacterial genes driven by runaway transcription www.biorxiv.org/content/10.1... #jcampubs

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)

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...

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...

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...

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...

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...

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

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...

‼️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!