Cyanobacteria are a globally abundant bacterial phylum that make key contributions to primary production and nutrient cycling in aquatic ecosystems. However, some cyanobacteria also cause substantial ...

MetaCAT is a computational framework to assess host–microbiome interaction via a combination of high-accuracy and efficient microbial genome reconstruction and metagenome-wide association studies with...

Bacteria of the genus Gardnerella are associated with bacterial vaginosis. Here, the authors compile and analyse a reference set of high-quality Gardnerella genomes, revealing previously hidden specie...

Abstract. The wide geographic distribution of microorganisms, combined with their vast taxonomic and functional diversity, make them indispensable reservoi

The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02318-2Cayman enables computational analysis of carbohydrate-active enzymes (CAZymes) in microbial community data. It revealed novel mucus-foraging gut microorganisms and differences in gut microbial CAZyme repertoires associated with lifestyle and disease.

Biotic interactions modulate protein abundance, reducing functional redundancy and increasing productivity in complex bacterial communities.

Abstract. When environmental bacteria transition to laboratory conditions, a process termed domestication, the shift from the native habitat to a culture m

Introducing ggsql, a grammar of graphics for SQL that lets you describe visualizations directly inside SQL queries.

Horizontal gene transfer from Microcystis-like cyanobacteria to members of the Methylococcaceae has enabled the latter to become capable of biomineralizing intracellular amorphous calcium carbonate i...

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

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

Scientific Data - Growth dynamics of 3,909 Escherichia coli single-gene knockouts in rich and minimal media

Abstract. Plasmids play a pivotal role in the spread of antibiotic resistance genes. Accurately reconstructing plasmids often requires long-read sequencing