Sampling Neighborhoods of the Gut Microbiome
The gut microbiome–composed of hundreds of different species of bacteria–is a complex community and a challenge for scientists to unravel. One specific challenge is the spatial distribution of different microbes, which are not evenly distributed throughout the gut. A new method developed by the lab of Dr. Harris Wang should help scientists locate and characterize these neighborhoods, which could shed light on how microbes influence the health of their hosts.
Techniques that can identify all species in the gut microbiome only work with homogenized samples (like stool), but methods that preserve spatial information can only cope with a handful of species.
Dr. Wang, assistant professor of systems biology and of pathology & cell biology, and graduate student Ravi Sheth in the Department of Systems Biology, tested the new technique with mice who switched from a low-fat to a high-fat diet. Diet is known to change the abundance of specific bacteria in the gut within days, but the new technique also revealed that the switch caused wholesale changes of microbial neighborhoods.
“Specific regions of bacteria were entirely lost with a switch in diet,” Sheth says. “This was exciting to us as it will give us clues to understanding how that change happens and how the change may impact health.”
The research, titled “Spatial metagenomic characterization of microbial biogeography in the gut,” was published July 22 in Nature Biotechnology.