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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Ilana Ilana Brito
My main interest is understanding how microbes (and their genes) are transmitted among individuals and between individuals and their environments. Read more
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
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
josh Josh Michener
No gene exists in isolation. To be useful, a gene must be functionally expressed and its host must be able to deal with any resulting stresses. Most genes have had sufficient time in their current host that the gene and host have co-evolved to minimize deleterious interactions... Read more
smith Mark Smith
Mark's research uses high-throughput sequencing to gain insights into the structure, function and dynamics of the human microbiome, with a recent publication on the topic in Nature. Read more

manuTamminen Manu Tamminen
I'm investigating novel approaches to extract and analyze genomic and transcriptomic information from single cells. To achieve this exciting objective I use a variety of tools, including flow assisted cell sorting, microfluidics, molecular biology and computational analysis. This combination of laboratory and computational approaches has considerable benefits over metagenomics... 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


seanClarke Caroline Antolik
As Technical Assistant in the Alm lab, I help out with various aspects of lab members' projects. My main responsibilities include 16s library prep for Illumina sequencing and training for users on specialized equipment such as our Bioanalyzer and liquid handling robot.... Read more

Graduate Students

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
scott Scott Olesen
Microbial metabolisms transform the world around us, mediating key geochemical cycles and even determining human scent. I combine experimental design and computational techniques to assess and engineer the role of microbes in the environment and the human microbiome...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
smillie Chris Smillie
I'm interested in using computational methods to study the evolution and ecology of the human microbiome. Previously, I've collaborated with Sarah, Eli, and Paco to develop SLiME, a tool that uses machine learning to identify microbial signatures associated with disease... 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
yang Joy Yang
I am broadly interested in the evolution and ecology of pathogens. In particular, I would like to utililize high performance computing to study the effect of the intricate interactions among host, bacteria, and mobile genetic elements such as phage and plasmids on disease. Read more

Current Members
Former Members