Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various
intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes …

Xanthomonas spp. encompass a wide range of plant pathogens that use numerous
virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine …

Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …

The ancient, ongoing coevolutionary battle between bacteria and their viruses,
bacteriophages, has given rise to sophisticated immune systems including restriction …

Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago.
Genome sequencing has put pressure on the classification system and recent years have …

In recent years, there has been an increasing interest in bacteriophages, which has led to
growing numbers of bacteriophage genomic sequences becoming available. Consequently …

Comprehensive, high-quality reference genomes are required for functional characterization
and taxonomic assignment of the human gut microbiota. We present the Unified Human …

Big data abound in microbiology, but the workflows designed to enable researchers to
interpret data can constrain the biological questions that can be asked. Five years after …

Complete and accurate reference genomes and annotations provide fundamental resources
for functional genomics and crop breeding. Here we report a de novo assembly and …

Enteric pathogens are exposed to a dynamic polymicrobial environment in the
gastrointestinal tract. This microbial community has been shown to be important during …