Excited to share our work on bacterial immune signaling! Our preprint reveals how RNA-guided Cas13 cleaves host tRNAs to generate small-molecule messengers that activate 2TMβ, linking RNA recognition to membrane damage and phage defense. 1/11
Tomas Hessler
@tomas-hessler.bsky.social
Postdoc at UC Berkeley Metagenomics | Microbial ecology | Phage | Bioprocess engineering 🇿🇦 views are my own
I’m happy to share our study out in Microbiome! link.springer.com/article/10.1... Knowing that coculture interactions often disappear in larger communities, we used cocktails of phages to study vitamin exchange interactions within enrichment cultures.
Phage-based depletion of Variovorax reveals interactions within intact microbiomes - Microbiome
Background Testing microbial interaction hypotheses, including metabolite cross-feeding, remains a major challenge in microbiome research. Phages have the potential to probe organism-organism interact...
link.springer.com
@pavelpayne.bsky.social et al. show that bacterial herd immunity can promote homologous recombination, suggesting bacterial immune systems can shape molecular evolution not only by blocking infection but also by regulating genetic exchange 🔗 academic.oup.com/mbe/article/... #societyjournal #evobio
Herd immunity underlies homologous recombination in stationary phase bacteria
Abstract. Homologous recombination is ubiquitous across evolution, generating variation through genetic reshuffling. Although bacteria lack meiotic recombi
academic.oup.com
Very happy that this work found a good home at @pnas.org Thanks to the reviewers for their constructive comments. www.pnas.org/doi/10.1073/...
Two D-loop resolution systems enable natural genetic transformation in bacteria | PNAS
Natural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds from the capture of extracellular DNA released ...
pnas.org
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!
📢 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
Now on bioRxiv 👇 www.biorxiv.org/content/10.6...
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...
biorxiv.org
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: https://ow.ly/KblS50ZOxwQ #AI #LanguageModel #RNA
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
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 {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
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.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3mo agoDeeply-sequenced metagenomes and over 1000 draft genomes from the epipelagic to bathypelagic Northeast Pacific Ocean https://www.biorxiv.org/content/10.64898/2026.07.18.739368v1
Out Now! Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress #MicroSky
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.
go.nature.com
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:
www.science.org/doi/10.1126/... 🦠💫💫💫
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...
science.org
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
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...
biorxiv.org
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...
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
science.org
Parasitic bacteria feeding on their hosts’ RNA!? New cultures and Patescibacteriota/Minisyncoccota/CPR continue to surprise us… www.biorxiv.org/content/10.6...
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...
biorxiv.org
🌲🔥🧬 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...
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...
biorxiv.org
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! 🌎
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5mo agoThe origin and evolution of archaeal Borg extrachromosomal elements https://www.biorxiv.org/content/10.64898/2026.05.22.727314v1
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
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."
bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social · 6mo agoBridge recombinase enables versatile rewriting of bacterial genomes https://www.biorxiv.org/content/10.64898/2026.04.29.721476v1
Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering www.nature.com/articles/s41... #jcampubs
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.
nature.com
Planetary microbiome structure and generalist-driven gene flow across disparate habitats: Cell www.cell.com/cell/fulltex...
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.
cell.com
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
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. 🧪
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.
go.nature.com
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...
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.
nature.com
📣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 💍💍
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 8mo agoDiscovery, induction, and screening of prophages in clinical Acinetobacter baumannii isolates https://www.biorxiv.org/content/10.64898/2026.02.16.706188v1
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
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!
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 ...
cell.com
Chan Yeong Kim@chanyeong-kim.bsky.social · last yr.Our new preprint is out! www.biorxiv.org/content/10.1... In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide. @podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
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)
bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social · 10mo agoA scalable transposon mutagenesis system for non-model bacteria https://www.biorxiv.org/content/10.64898/2025.12.22.696024v1