Lab Members

PI: Eric Alm

ericAlm The human microbiome plays a key role in human health and disease. Research in my group includes both computational/theoretical and experimental approaches to understanding and engineering the human microbiome. Our research is focused on translating basic science discoveries rapidly into the clinic, where they can contribute to better outcomes for patients. Some areas of special interest include:
  • Developing therapeutics based on synthetic microbial communities
  • Personalized medicine
  • Monitoring human activities through Smart Sewers
  • Smart Toilets that track human health
  • Discovering low-cost non-invasive biomarkers
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mBansal Christopher Corzett
I am interested in how microbes survive and thrive in diverse and dynamic environments. This includes understanding how bacteria sense and respond to environmental change, the metabolic machinery required for different feeding strategies, and how microbes adapt and evolve various lifestyles... Read more
sean Sean Gibbons
Microorganisms form the foundation of all ecosystems on Earth and are responsible for driving the major biogeochemical cycles. From generating the air that we breathe and the food that we eat, to maintaining our health and well-being, microbial communities are essential components of the biosphere. Read more
mathieu Mathieu Groussin
Broadly speaking, I am interested in the inference of biological properties of ancient prokaryotic life and in how bacterial and archaeal communities evolve. My main interests focus on the study of genetic data (DNA, proteins) to understand the main evolutionary processes... Read more
thomas Thomas Gurry
The relationship between our health and our microbial inhabitants is poorly understood and likely to be vast in its implications. I am interested in integrating different types of physiological data that have been collected in a continuous fashion, including data pertaining to the microbiome... Read more
tami Tami Lieberman
During my doctoral research in Roy Kishony's lab, I developed new genomic approaches for understanding how bacteria evolve during infections of individual people. I also studied antibiotic resistance and microbial evolution more broadly, using my favorite tools of experimental evolution and genomic sequencing. Read more
mathilde Mathilde Poyet
I am an ecologist with a special interest in biological communities. During my PhD, I characterized the invasion processes of an insect (Drosophila suzukii) and its impact on the invaded communities at different levels of organization. Now, I keep on studying community and ecosystem stability... Read more
avihu Avihu Yona
During my doctoral research I utilized experimental evolution to study the evolutionary dynamics of genomic duplications like aneuploidy and tRNA genes. Now, Im interested in the way complex communities evolve as an integral entity and in how evolutionary forces can be applied to reshape such communities towards desirable traits.... Read more

Graduate Students

Nathaniel Nathaniel Chu
I am fascinated by two questions: What processes govern the evolution and ecology of microbial communities? And how can we harness these processes to create practical solutions to problems in human and ecological health? Read more
Claire Claire Duvallet
Studying the relationships between the microbiome, health, and lifestyle provides incredible opportunities for translational medical discoveries and public health impacts. I'm excited by the possibility of using various physiological data to predict disease states, both on the individualized and broader community levels. Read more
seanKearny Sean Kearney
Microbes rule the world; our very existence is dependent on the once free-living oxygen-respiring bacteria now known as mitochondria. We cannot even begin to imagine how interlocked our own lives are with those of 4000 million year old organisms. I am interested in studying how microorganisms influence evolution and ecology over vast temporal and spatial scales.... Read more
marianaMatus Mariana Matus
My research aims to mine health data from human waste to better inform personal- and community-level health practices through three major projects: (1) personal analytics of ulcerative colitis patients, (2) Underworlds: Smart Sewers, and (3) salt, microbiome, and hypertension. Read more
tu Tu Nguyen
Our body is in constant interaction with the microbial communities inhabiting not only our gastrointestinal tract but also our respiratory system, skin and the reproductive tissues. These diverse microbial communities outnumber our own cells by a 10 to 1 ratio and have been increasingly reported to play important roles in human health and diseases... Read more
allison Allison Perrotta
My current focus in the lab is to create and test high throughput methods for preparing 16s Illumina sequencing libraries from diverse environmental sources. Our lab researches the microbial ecology found in a myriad of environments and under diverse conditions... Read more
spencer Sarah Spencer
I'm interested in how ecological principles play out at the resolution of single cells. To explore this I'm developing high-throughput sequencing technology that can immobilize interacting cells for downstream 16S profiling. I'm starting to apply this technique to aquatic communities, but eventually I'd like to adapt the protocol to address other problems in microbial evolution and ecology. Read more
annie Xiaoqian (Annie) Yu
I am particularly interested in investigating two things: how does bacterial diversity affect ecosystem processes and how genetic variations of Carbohydrate Active Enzymes in Vibrios are distributed according to their ecological context. We also hope that these investigations will help us become more capable of harnessing the enzymatic capabilities of bacteria for biofuel production. Read more
jay Shijie (Jay) Zhao
The sequencing revolution has immense promises for improving human health. In the Alm lab, I have the opportunity to apply cutting edge genomic technique to study the interplay of microbes and human diseases. One of my current work is to study fecal microbiota transplant... Read more

Current Members
Former Members