Characterizing complex microbial communities with single-cell resolution has been a long-
standing goal of microbiology. We present Microbe-seq, a high-throughput method that …

The potential of commensal bacteria to modulate host immunity remains largely
uncharacterized, largely due to the vast number of strains that comprise the human gut …

Microbiota therapeutics that transplant faecal material from healthy donors to people with
mild-to-moderate ulcerative colitis have shown the potential to induce remission in about …

Despite identification of numerous associations between microbiomes and diseases, the
complexity of the human microbiome has hindered identification of individual species and …

Functional characterization of the microbiome's influence on host physiology has been
dominated by a few characteristic example strains that have been studied in detail …

When examining bacterial genomes for evidence of past selection, the results depend
heavily on the mutational distance between chosen genomes. Even within a bacterial …

We present Microbe-seq, a high-throughput single-microbe method that yields strain-
resolved genomes from complex microbial communities. We encapsulate individual …

Quantifying the contributions of possible environmental sources (“sources”) to a specific
microbial community (“sink”) is a classical problem in microbiology known as microbial …

The functional potential of the gut microbiota remains largely uncharacterized. Efforts to
understand how the immune system responds to commensal organisms have been …