Studying within-species variation has traditionally been limited to culturable bacterial
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …

Escherichia coli is the most researched microbial organism in the world. Its varied impact on
human health, consisting of commensalism, gastrointestinal disease, or extraintestinal …

Microbial taxonomy is increasingly influenced by genome-based computational methods.
Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS …

A perfect bacterial genome assembly is one where the assembled sequence is an exact
match for the organism's genome—each replicon sequence is complete and contains no …

The immense diversity of soil bacterial communities has stymied efforts to characterize
individual taxa and document their global distributions. We analyzed soils from 237 …

Microbiome research has grown rapidly over the past decade, with a proliferation of new
methods that seek to make sense of large, complex data sets. Here, we survey two of the …

Background: Data sets from long-read sequencing platforms (Oxford Nanopore
Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely …

Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient
populations in hospitals around the world. Intensive care unit (ICU) patients are particularly …

Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an
enzymatic core that is encapsulated by a selectively permeable protein shell. The potential …

Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home
to an unimaginable diversity of microorganisms. This review explores key drivers for …