Recently, we’ve been vibe coding bioinformatics projects and vibe analysing bioinformatics data. Have we reached the singularity yet?

Free automated phage genome annotation -- pharokka, phold and phynteny in one pipeline.

In a survey of > 1600 specimens across all mammalian orders, we found that most species present dental calculus. We found calculus production to be strongly associated with herbivory, and we provide ...

Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02405-4Prophage FRφ rewires the flagellar apparatus of its Enterobacter sp. host through RNA-guided repression of native flagellin, favouring its own phage-encoded isoform. This enhances host motility and reduces immune recognition, boosting bacterial fitness in mice.

A pipeline for the analysis of sedimentary ancient mtDNA. - mpieva/quicksand

A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.

The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...

Migration of microbial communities is poorly understood. Here, the authors use a meso-tube assay to show that hundreds of microbial species co-migrate over metre scales via chemotaxis, which restructu...

Prophages are pervasive in the human gut yet largely overlooked in microbiome research, despite substantial functional potential. Emerging evidence indicates that prophages regulate bacterial fitness,...

Gut bacteriophages defy simple classification as beneficial or harmful, instead shifting between roles that stabilize or destabilize microbial communities depending on phage lifestyle dynamics, host i...

Abstract. Microbial population genetic studies often involve the use of a dated phylogeny to show how the genomes are related over a relevant timescale. Ma

Comprehensive assessment of the host range of phages is a prerequisite for their safe and effective use in multiple applications but is rarely undertaken. This Review outlines the molecular and ecolog...

Nature Microbiology, Published online: 17 April 2026; doi:10.1038/s41564-026-02326-2Phosphoribosyl pyrophosphate synthetase from Faecalibacterium prausnitzii inhibits PD-L1 trafficking to boost anti-tumour immunity and potentiate anti-PD-1 immune checkpoint inhibitor therapy during colorectal cancer.

FAMSA2 accurately aligns millions of protein sequences at high speed.

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

Abstract. Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interact

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

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...

Human host-associated cellular products may act as induction agents for bacteriophages.

Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats...

The microbial composition of metagenomes is identified in seconds by profiling against large databases.

Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

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...

Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...