THE GUT MICROBIOME
EXPLORING COMPLEX MICROBIAL COMMUNITIES

WE ADDRESS FUNDAMENTAL
BIOLOGICAL QUESTIONS...


INTERACTIONS
What makes natural microbial communities robust? What governs the stability of different states in microbial communities? How do microbes modulate their environment and thereby their host?

SYSTEMS + CONTROL
What physical principles govern the dynamics of microbial communities? What principles govern how these communities affect their hosts? How do physicochemical effects shape microbial environments? How do gut microbiota influence host physiology/ behavior?

CULTIVATION
How can we culture “unculturable” microbes?

We use innovative methods, such as...

IMAGING + BIOINFORMATICS ANALYSES
FISH, RNA-seq, real-time imaging, bioinformatics

CONTROL OF THE MICROENVIRONMENT
Splitting SlipChips, droplets, gene- and function-based microbial isolation, anaerobic chambers, gnotobiotic animals

MICROFLUIDICS
We are experts in microfabrication, device design, microfluidic culture, single-cell recovery, culture, treatment, nucleic acid extraction and single-cell gene expression

POLYMER PHYSICS

 

 

SOME OF OUR MOST RECENT PUBLICATIONS IN THIS FIELD

Datta et al. 2016. Polymers in the gut compress the colonic mucus hydrogel. PNAS. 113(26):7041-7046.

Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host–microbe interactions and drug delivery. Here, we demonstrate that gut polymers ... regulate mucus hydrogel structure, and that polymer–mucus interactions can be described using a thermodynamic model based on Flory–Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo.

"Dietary Fiber and Microbes" NEWS STORY

 

Yano et al. 2015. Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis. Cell  161 (2). pp. 264-276.

The gastrointestinal (GI) tract contains much of the body’s serotonin (5-hydroxytryptamine, 5-HT), but mechanisms controlling the metabolism of gut-derived 5-HT remain unclear. Here, we demonstrate that the microbiota plays a critical role in regulating host 5-HT.

Ma et al. 2014. Gene-targeted Microfluidic Cultivation Validated by Isolation of a Gut Bacterium Listed in Human Microbiome Project's Most Wanted taxa. PNAS 111(27):9768-9773.

This paper describes a microfluidics-based workflow for genetically targeted isolation and cultivation of microorganisms from complex clinical samples. … Here, we describe a method that enables genetically targeted cultivation of microorganisms through a combination of microfluidics and on- and off-chip assays. We validated this targeted approach by cultivating a bacterium, here referred to as isolate microfluidicus 1, from a human cecal biopsy. Isolate microfluidicus 1 is, to our knowledge, the first successful example of targeted cultivation of a microorganism from the high-priority group of the Human Microbiome Project’s “Most Wanted” list.

“Busted!” NEWS STORY LINK

Ma et al. 2014. Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. Integr. Biol. 6(8):796-805.

Isolating microbes carrying genes of interest from environmental samples involves the use of genetic assays that often require lysis of microbial cells, which is not compatible with the goal of obtaining live cells for isolation and culture. This paper describes the design, fabrication, biological validation, and underlying physics of a microfluidic SlipChip device that addresses this challenge.

We are currently hiring postdoctoral researchers!

Please see our "Positions" page for more details.