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
Read more


Shandrina Burns
Administrative assistant
burnss at mit dot edu
Tsultrim Palden
Lab manager
tpalden at mit dot edu
Katya Frois-Moniz
Research Scientist/Research Lead
kmoniz at mit dot edu


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
xiaofang Xiaofang Jiang
To adapt their physiology to gradual and sudden changes occurring in the host environment or during inter-individual transmissions, commensals exhibit remarkable genetic variation diversity at a population level. I am interested in the genetic variations of gut microbes and how the variations are beneficial for their effective colonization and successful survival. I am developing tools and mining genetic variations from isolate genomes and metagenomic data... 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
Sepideh Pakpour
Fangqiong Ling

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 mines 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
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... Read more
Haixin Sarah Bi
Isaac Rockafellow

Current Members

Former Members