The human intestine, colonized by a dense community of resident microbes, is a frequent
target of bacterial pathogens. Undisturbed, this intestinal microbiota provides protection from …

We have created a compendium of single cell transcriptomic data from the model organism
Mus musculus comprising more than 100,000 cells from 20 organs and tissues. These data …

Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption,
and widespread laxative use. Here, we assess the resilience of the gut ecosystem to …

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

The gut microbiota is a dense and diverse microbial community governed by dynamic
microbe–microbe and microbe–host interactions, the status of which influences whether enteric …

The composition of the gut microbiome in industrialized populations differs from those living
traditional lifestyles. However, it has been difficult to separate the contributions of human …

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 …

Improved understanding of the interplay between host and microbes stands to illuminate
new avenues for disease diagnosis, treatment, and prevention. Here, we provide a high-…

Intestinal microbiotas contain beneficial microorganisms that protect against pathogen
colonization; treatment with antibiotics disrupts the microbiota and compromises colonization …

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