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Tomas Hessler

@tomas-hessler.bsky.social
155 followers 176 following 3 posts

Postdoc at UC Berkeley Metagenomics | Microbial ecology | Phage | Bioprocess engineering 🇿🇦 views are my own

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Reposted by Tomas Hessler
Vivek Mutalik @vivekmutalik.bsky.social · 29/09/2026
In our brand new 🥳 review, @hemaa-selvakumar.bsky.social & team pull a scattered literature in phage biology into a coherent framework for scaling up to engineering complex communities. We poured our hearts into this to share challenges & future opportunities for the nextGen!
Next generation application space with systematic characterization of phage-host interaction landscapes.
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Ashish Malik @ashish-malik.bsky.social · 24/09/2026
📢 New preprint led by former postdoc in my group Lisa Cole. We asked: are microbially-mediated carbon transformations governed principally by the composition of the microbial community or by the soil microenvironment? lnkd.in/ez9TniYP
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Maria Hondele @mariahondele.bsky.social · 18/09/2026
Now on bioRxiv 👇 www.biorxiv.org/content/10.6...
biorxiv.org
A bacterial nucleolus for cold adaptation
Compartmentalisation enables cells to spatially organise essential biochemical processes. This is exemplified by the eukaryotic nucleolus, which concentrates the machinery for ribosome biogenesis. Bac...
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Innovative Genomics Institute @innovativegenomics.bsky.social · 17/09/2026
Before #CRISPR, there was VIPR — a tool viruses used to battle each other with a never-before-seen genetic coding system, uncovered by researchers in the Doudna Lab. Read more here: ow.ly/KblS50ZOxwQ #AI #LanguageModel #RNA
Terry Zhang, Peter Yoon, Kenneth Loi (left to right) wanted to make sure to include Trevor Docter (on the phone from Harvard).
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 23/07/2026
Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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alex jaffe @alexjaf.bsky.social · 21/07/2026
my first 'data descriptor'! hoping this one will be useful for folks interested in tracing the distribution of genomes/genes/proteins over physicochemical gradients in the (deep) marine water column.
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Nature Microbiology @natmicrobiol.nature.com · 17/07/2026
Out Now! Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress #MicroSky
go.nature.com
Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress
Nature Microbiology, Published online: 17 July 2026; doi:10.1038/s41564-026-02422-3Environmental stress shifts microbial composition towards species with high growth rates, providing community-wide protection.
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Jason Hickel @jasonhickel.bsky.social · 05/07/2026
I predicted that even if their AI found ways to improve efficiency, Google's energy use would go up, not down. Seven years later and this is where we're at:
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 27/06/2026
www.science.org/doi/10.1126/... 🦠💫💫💫
science.org
Antibiotics stimulate protein transfer to persister cells
The exchange of biological matter between bacterial cells drives adaptation and evolution. However, whether bacteria can exchange functional proteins remains unclear. In this work, we found that antib...
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Vivek Mutalik @vivekmutalik.bsky.social · 27/06/2026
New preprint!! 🎉 A cool collaborative work with @copabio.bsky.social and Chase Beisel teams on the phage editing technology. @sarshad.bsky.social led the work from our side to validate & characterize the lib. #phage #phagesky www.biorxiv.org/content/10.6... Work supported by: phagefoundry.org
biorxiv.org
Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes
Genetic manipulation of bacteriophages is essential for interrogating phage biology and advancing antimicrobial therapies. However, current genome editing approaches can be inefficient, require multip...
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Bill Lukens @paleosol.bsky.social · 26/06/2026
Um, WTF? "NSF will fund the X-Labs through a rarely used mechanism that .... allows NSF to fund nontraditional recipients such as a limited partnership or a venture capital firm, some of which might have been created solely to receive the NSF award." 🧪⚒️ #AcademicSky www.science.org/content/arti...
science.org
Exclusive: NSF slashes research programs to support new tech initiative, insiders say
Unexpected shift in funds has meant sharp drop in grants this fiscal year
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Masaru Nobu @masarunobu.bsky.social · 23/06/2026
Parasitic bacteria feeding on their hosts’ RNA!? New cultures and Patescibacteriota/Minisyncoccota/CPR continue to surprise us… www.biorxiv.org/content/10.6...
biorxiv.org
A representative of a ubiquitous bacterial lineage parasitically feeds on host RNA
Cellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of red...
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The Banfield Lab @banfieldlab.bsky.social · 15/06/2026
🌲🔥🧬 New pre-print from Elliot Weiss in the Banfield Lab! We tested whether inoculating burned forest soils with native microbes could aid recovery. A single inoculation accelerated the return of symbiotic fungi and nitrogen cycling! www.biorxiv.org/content/10.6...
biorxiv.org
Microbial inoculation accelerates post-fire soil recovery in a mixed conifer forest
High-severity wildfires of increasing size and frequency result in release of carbon dioxide and loss of timber resources, reduction in biodiversity, loss of soil, diminished water quality, and reduce...
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Ling-Dong Shi @lingdong-shi.bsky.social · 24/05/2026
Super excited to share the final project of my postdoc career! We found that Borgs and mini-Borgs are widespread across diverse ecosystems. They don't just exist in Banfield Lab — they are everywhere! 🌎
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 17/05/2026
Codon degeneracy contributes to divergent fitness effects of rare tRNAs with A-starting anticodons www.biorxiv.org/content/10.6... => why are tRNAs with adenine at the wobble position (tRNA_ANN) are almost universally absent in nature ? mistranslation-related fitness costs... 🦠
biorxiv.org
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Tomas Hessler @tomas-hessler.bsky.social · 14/05/2026
Amazing work! "In E coli, we achieved 142 kb insertions at >90% efficiency, megabase-scale inversions (2.3 Mb), and pathway-scale 50 kb excisions. With a single ortholog and bridge RNA (bRNA), we edited bacterial isolates spanning five phyla and diverse members of two human gut communities."
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Cameron Thrash @jcamthrash.bsky.social · 23/04/2026
Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering www.nature.com/articles/s41... #jcampubs
nature.com
Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering - Nature Biotechnology
Retron-based systems for genome editing are functional across bacterial species.
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Christian Kost @kostchristian.bsky.social · 10/04/2026
Planetary microbiome structure and generalist-driven gene flow across disparate habitats: Cell www.cell.com/cell/fulltex...
cell.com
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological boundaries to mediate gene flow across disparate habitats, including the dissemination of antimicrobial resistance.
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Shuai Wang @wshuai.bsky.social · 30/03/2026
Studying DNA modification in microbes shouldn't be limited by methodology. 🧬 We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...
biorxiv.org
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Nature Portfolio @natureportfolio.nature.com · 11/03/2026
A paper published in Nature presents Evo 2: an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and provides a rich generative model for researchers in biology. 🧪
go.nature.com
Genome modelling and design across all domains of life with Evo 2 - Nature
Evo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and provides a rich generative model for researchers in biology.
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Chang Liu @chang-c-liu.bsky.social · 03/03/2026
Very happy to see this work from Fabian Rehm, Jason Chin, and team on the development of a high error-rate orthogonal DNA replication system in E. coli, thus supporting continuous hypermutation and evolution of target genes in vivo. www.nature.com/articles/s41...
nature.com
Highly mutagenic continuous evolution in E. coli using a Φ29-based orthogonal replication system - Nature Biotechnology
Mutational rates of bacterial evolution are increased using an error-prone orthogonal system.
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Vivek Mutalik @vivekmutalik.bsky.social · 18/02/2026
📣new preprint from the phagefoundry.org team 🎉 Jessica Trinh and Catherine Mageeney (Sandia National Laboratories)!! Systematic analysis of prophages from ~1000 Acinetobacter baumannii isolates, induction & screening. We found this 😎 looking phage with bunch of 💍💍
Bacterial viruses image
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Phil Holliger @philholliger.bsky.social · 13/02/2026
New paper from my group in @science.org : "A small polymerase ribozyme that can synthesise itself and its complementary strand" www.science.org/doi/10.1126/... Outstanding work by @edogia.bsky.social
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 09/02/2026
Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex... See the quoted post below for a thread on the preprint!
cell.com
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...
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Alex Crits-Christoph @acritschristoph.bsky.social · 24/12/2025
All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
Figure 2. Himar1 transposon variant screen on a cohort of 92 bacterial species.
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Ling-Dong Shi @lingdong-shi.bsky.social · 23/01/2026
Excited to share our discovery of archaeal circular, jumbo extrachromosomal elements (up to ~535 kb genomes). One related, 409-kb genome is integrated in CH4-eating Methanoperedens, representing the largest integrative element in Archaea so far! Curious about what they are doing? See the paper
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André Marques @amarques.bsky.social · 27/01/2026
A new extreme of meiotic evolution: ✔️ 𝗻𝗼 crossovers ✔️ 𝗻𝗼 gene conversion ✔️ 𝗻𝗼𝗿𝗺𝗮𝗹 meiosis & fertility Sex mimics clonality without becoming asexual, in the holocentric multicellular eukaryote 𝘙𝘩𝘺𝘯𝘤𝘩𝘰𝘴𝘱𝘰𝘳𝘢 𝘵𝘦𝘯𝘶𝘪𝘴. more about it: www.biorxiv.org/content/10.6...
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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 20/01/2026
A related study from Nandita’s group on gene-specific sweeps - a great idea to compare non-synonymous linkage disequilibrium (LD) vs synonymous LD! Gut microbiome show pervasive selective sweeps in carbohydrate metabolism - diet adaptation! #microsky #microbiomesky 🧪🦠 www.nature.com/articles/s41...
nature.com
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
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Emmanuele Severi @emmseveri.bsky.social · 02/01/2026
#microsky #synbiosky www.science.org/doi/10.1126/...
science.org
Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing
Whole-genome screening reveals strategies to boost CRISPR-associated transposase genome editing efficiency.
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Microbiology Society @microbiologysociety.org · 18/12/2025
Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.
Esther Lederberg in the laboratory in the 1950's. Credit: Estherlederberg.com
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Snorre Sulheim @sulheim.bsky.social · 03/12/2025
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
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The Banfield Lab @banfieldlab.bsky.social · 28/11/2025
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
nature.com
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...
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Emmanuele Severi @emmseveri.bsky.social · 25/11/2025
#microsky #phagesky Transposon mutagenesis of jumbo #phage using an anti-CRISPR factor as selectable marker www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Veronika Kivenson @kivenson.bsky.social · 23/11/2025
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
science.org
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...
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Diamond Lab @diamondlab.bsky.social · 19/11/2025
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....
microbiomejournal.biomedcentral.com
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...
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Alex Crits-Christoph @acritschristoph.bsky.social · 12/11/2025
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.
Figure 2. PET screen results and RB-TnSeq gene fitness results
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Prof. Ruth Ley FRS @microbiome.bsky.social · 28/10/2025
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 🦠🧫
rdcu.be
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...
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 03/11/2025
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
journals.plos.org
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...
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Genetics Society of America @genetics-gsa.bsky.social · 07/10/2025
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
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John Innes Centre @johninnescentre.bsky.social · 03/10/2025
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
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Erin Doherty @erinedoherty.bsky.social · 02/10/2025
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...
nature.com
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
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Allison G @assemblerag.bsky.social · 01/10/2025
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
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Ashish Malik @ashish-malik.bsky.social · 04/08/2025
📢 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...
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Tami Lieberman @contaminatedsci.bsky.social · 22/09/2025
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... 🧵
biorxiv.org
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...
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Martial Marbouty @mmarbout.bsky.social · 19/09/2025
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...
nature.com
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.
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Dan Sloan @sloanevolab.bsky.social · 08/09/2025
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
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...
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Nature Methods @natmethods.nature.com · 18/09/2025
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...
nature.com
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...
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PLOS Biology @plosbiology.org · 17/09/2025
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
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.
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Andrian Gajigan @adi-gajigan.bsky.social · 17/09/2025
Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail nature.com/articles/s41467-025-63463-6
nature.com
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...
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