Bacteriocins in archaea and archaeocins in bacteria

Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...

biorxiv.org

Bacteriocins in archaea and archaeocins in bacteria

Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...

biorxiv.org

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies

antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00

biorxiv.org

Emergence of histone-based chromatin complexity in Asgard archaea

The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...

biorxiv.org

A Bactericidal Phospholipase from Archaea

Archaea kill bacteria, at least on occasion. The molecular underpinnings of these lethal interactions are barely understood. Here, we describe cinquedea, an α/β hydrolase secreted by the halophilic ar...

biorxiv.org

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2

Nature Methods - AF2BIND is a logistic regression model trained on AlphaFold2 pair features to predict small-molecule binding-site residues in proteins, without multiple sequence alignments,...

rdcu.be

Bluesky Map

Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

bluesky-map.theo.io

pnas.org

A synthetic bacterium that degrades and assimilates poly(ethylene terephthalate)

Polyethylene terephthalate (PET) is the fourth most commonly used plastic worldwide. Like all plastics, post-consumer PET is poorly managed and accumulates in the environment, posing significant ecolo...

biorxiv.org

Early Microbial Evolution | ASM.org

How did life begin, and why does it matter? Scientists are tracing early microbial life—from LUCA to multicellularity—to unlock insights for biotech, climate science and even space exploration.

asm.org

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

biorxiv.org

Structure of a functional archaellum in Bacteria of the Chloroflexota phylum - Nature Microbiology

Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.

nature.com

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

nature.com

EvoChromo: Evolutionary approaches to research in chromatin

Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…

meetings.embo.org

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...

biorxiv.org

Supervisors and Projects

bioch.ox.ac.uk

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate

Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...

biorxiv.org

Missing the Company of Elio

Paying tribute to Elio Schaechter, former TWiM host, blogger, and microbiologist extraordinaire, and review of the finding that Archaea produce peptidoglycan hydrolases that kill bacteria - a form of ...

asm.org

The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance

The 2024 WHO BPPL is a key tool for prioritising research and development investments and informing global public health policies to combat AMR. Gram-negative bacteria and rifampicin-resistant M tuber...

thelancet.com

The nature of mutation: a legacy of bacterial genetics

Abstract. A central question in the fields of genetics and evolution was the nature and origin of spontaneous mutation. Bacterial genetic experiments throu

doi.org

Protein structure alignment significance is often exaggerated

Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...

biorxiv.org

Archaea produce peptidoglycan hydrolases that kill bacteria

Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

journals.plos.org