Shotgun sequencing enables the reconstruction of genomes from complex microbial
communities, but because assembly does not reconstruct entire genomes, it is necessary to bin …

To the Editor—The standardization, portability and reproducibility of analysis pipelines are
key issues within the bioinformatics community. Most bioinformatics pipelines are designed …

Background Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although
the genome is a foundation for understanding the metabolism, ecology and evolution of …

We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample
metagenomes are being generated but strain variation results in fragmentary co-…

Background Prokaryotes dominate the biosphere and regulate biogeochemical processes
essential to all life. Yet, our knowledge about their biology is for the most part limited to the …

The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose
material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We …

Metagenomics enables the reconstruction of microbial genomes in complex microbial
communities without the need for culturing. Since assembly typically results in fragmented …

The deep terrestrial subsurface remains an environment where there is limited understanding
of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is …

The genome encodes the metabolic and functional capabilities of an organism and should
be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted …

Microbial life is widespread in the terrestrial subsurface and present down to several
kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic …