Research

openbiome_0

Stored fecal microbiota transplants

 

Fecal microbiota transplants

Fecal microbiota transplants (read: transferring microbes from someone else’s feces into your colon, with help from a medical professional) have emerged as effective treatments for gastrointestinal diseases caused by imbalances in the gut microbiome—the trillions of microbes that live inside the human intestine. Infections of Clostridium difficile, for example, sicken 500,000 people annually, killing approximately 14,000 patients. Such imbalances often occur after patients take antibiotics, which clear out normal, healthy gut flora and allow opportunistic bacteria to take over. I am developing new sequencing methods to separately profile living and dead microbes from complex samples. We aim to use this new method to screen fecal transplants and clarify the mechanisms of transplant efficacy.

This project is a part of Eric Alm’s lab in Biological Engineering at MIT. It is in close collaboration with our partners and friends at OpenBiome, who are leading the way to offer fecal treatments to hospitals and patients in a safe, controlled manner.

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Sampling elkhorn coral (Acropora palmata) tissue for metagenomic studies

Sampling elkhorn corals (Acropora palmata) for metagenomic studies

 

Coral microbial dynamics

Coral reefs are economically and aesthetically crucial, but over the past few decades, we have seen a staggering decline in coral abundance. One cause of this decline is the rise of coral diseases. We know very little about how microbial communities in and around corals interact to prevent or cause these diseases. I use metagenomic techniques to track how coral microbial communities change with seasons, species, sites, and disease states. With baseline information like this, we might better be able to target conservation strategies to stave off further declines in coral reefs.

This project was done at the Smithsonian Tropical Research Institute’s (STRI) Bocas del Toro Station. It was supported by a Fulbright Fellowship, STRI Fellowship, and the National Science Foundation.

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Scallop fishing in the Atlantic Ocean

Atlantic sea scallop population genomics

The Atlantic sea scallop fishery is a prime example of how protected areas can help fish stocks rebound and even bring back fisheries from near collapse. In the early 1990s, scallop catches were at record lows. In response to the crisis, three areas of Georges Bank were closed to fishing in 1994. Since then, the fishery has come back, producing nearly $500 million of scallops every year. To understand the dynamics of this recovery and how current populations are connected, we are using a suite of population genomics techniques. With these tools, we hope to identify key fishery areas (“source” populations) that support less densely settled areas (“sink” populations), allowing the fishery as a whole to grow.

This project is at Northeastern University’s Marine Science Center . It is supported by the National Oceanic and Atmospheric Association’s Research Set-Aside Program, which allocates a portion of each annual catch to study the biology of the scallop fishery.

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Phylogeography of Nucella lapillus in the NW Atlantic

Phylogeography of Nucella lapillus in the NW Atlantic

Intertidal phylogeography and adaptation genomics.

How do populations of the same species adapt to different environments? How do environmental factors affect how populations are connected and how genes flow between them? These are some of the questions I asked when analyzing populations of the marine snail Nucella lapillus in the northwestern Atlantic. Using next-generation sequencing tools, we found previously undetected genetic structure among populations and latitudinal polymorphisms in heat stress genes, which might have arisen from from temperature-related selection.

This project was done at Northeastern University’s Marine Science Center with Steven Vollmer and Geoffrey Trussell. It was supported by Brown University and the National Science Foundation.

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