Ravi U. Sheth

SAMPL-seq identifies spatial hubs in the human gut microbiome by sampling micron-scale sub-communities and analyzing microbial co-occurrence across individuals and time.

The paper describes a ribonuclease-based method for rRNA depletion in bacterial RNA-seq, validated on gut microbiota isolates and providing probe sets and an online tool for custom probe libraries.

The paper introduces DIVERS, a method to quantify spatiotemporal dynamics and noise in microbiota abundances using replicate sampling and spike-in sequencing, applied to the human gut microbiome.

This study uses engineered CRISPR-Cas to capture real-time horizontal gene transfer events from gut microbiota at nucleotide resolution, revealing extensive and rapid transfer of plasmid types, particularly IncX.