Antibiotics alter microbiota composition and increase infection susceptibility. However, the
generalizable effects of antibiotics on and the contribution of environmental variables to gut …

Methanogenic archaea are major contributors to the global carbon cycle and were long
thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis …

Efforts to probe the role of the gut microbiota in disease would benefit from a system in
which patient-derived bacterial communities can be studied at scale. We addressed this by …

From bacteria to humans, individual cells within isogenic populations can show significant
variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this…

10.7554/eLife.26580.001 Metagenomics and single-cell genomics have enabled genome
discovery from unknown branches of life. However, extracting novel genomes from complex …

Due to limitations on high-resolution strain tracking, selection dynamics during gut
microbiota colonization and transmission between hosts remain mostly mysterious. Here, we …

Background Cyanobacteria are important agents in global carbon and nitrogen cycling and
hold great promise for biotechnological applications. Model organisms such as …

Gut microbiota metabolism of dietary compounds generates a vast array of microbiome-dependent
metabolites (MDMs), which are highly variable between individuals. The uremic …

Humans constantly encounter new microbes, but few become long-term residents of the
adult gut microbiome. Classical theories predict that colonization is determined by the …

Background Ordered transposon-insertion collections, in which specific transposon-insertion
mutants are stored as monocultures in a genome-scale collection, represent a promising …