Our Research

Microbiome research is among the most exciting and promising areas of science today due to many technological advances, particular in high throughput DNA and RNA sequencing, that allow us to determine in complex environments which microbes are present and their metabolism. A prominent component of our research is using genomic and computational methods to understand the ecology and evolution of gut and forest soil microbiomes. Our laboratory is set up for standard molecular biology and microbial physiology research and contains specialized equipment for isolating and culturing anaerobic bacteria. The research we do has led to the discovery of new bacterial species and metabolic processes that have have far ranging impacts from developing probiotics to understanding climate change. Our research is currently funded by the National Science Foundation, Department of Energy, and the United States Department of Agriculture. Below are overviews of some of our current funded project areas.

Global warming and forest soil microbiomes

Human activities are having a major impact on the global balance of exchange between carbon reservoirs. Three quarters of the carbon in terrestrial ecosystems is found as organic matter in soils, most of which is derived from plant litter. Our ability to understand carbon cycling by microbial communities is being transformed by rapid advances in DNA sequencing technology. We are developing new bioinformatic approaches for understanding microbial communities and their evolution. Our research involves field research in three experimental warming plots at the Harvard Forest, the oldest of which was established in 1991. This project involves collaboration with Prof. Kristen DeAngelis (UMass - Microbiology), Prof. Serita Frey (UNH), Dr. Linda van Diepen (UNH) and Dr. Jerry Melillo (MBL).

Increasing rates of plant decomposition using C. phytofermentans (Cphy) and microbial consortia

Clostridium phytofermentans (Cphy) was discovered in anaerobic forest soil from the Quabbin Reserve by Dr. Susan Leschine and Tom Warnick. Cphy can directly convert a broad range of biomass sources directly to ethanol without expensive thermochemical pretreatment. Using genome-based technologies we are able to measure changes in the DNA sequences and gene expression levels of all of these parts as they change in response to environmental cues. These data are then integrated in genetic and physiological models to improve biofuel production and tested using molecular genetic and biochemical approaches. The questions we are asking include: How can we increase the rate of fiber breakdown? How are carbohydrate uptake mechanisms regulated? This project involves collaboration with Prof. Susan Leschine (UMass - Vet & Animal Sciences) and Prof. Lynmarie Thompson (UMass - Chemistry).

Function and Evolution of Bacterial Microcompartments

Clostridium phytofermentans contains three genetic loci coding for bacterial microcompartments. Bacterial microcompartments are an intracellular organelles composed of a proteinacous shell that encapsulates metabolic products that maybe harmful to the cell. Unlike other types of organelles, no lipids are associated with the microcomartments. These structures are icosahedral in shape, akin to bacterial phages and capsid viruses and are subject to frequent horizontal gene transfer and loss. We have determined that one genetic locus in C. phytofermentans is responsible for the metabolism of the cell wall carbohydrates fucose and rhamnose. In the genome of C. indolis we have identified a new type of microcompartment and are working on the function and evolution of microcompartments.