ALEX KOSTIC, Principal Investigator

My background and training is in computational biology, microbiology, and immunology. During my PhD thesis work with Matthew Meyerson and Wendy Garrett, we discovered an association between colorectal cancer and the gut microbiome constituent Fusobacterium nucleatum. We demonstrated that Fusobacterium accelerated intestinal tumorigenesis by a mechanism involving altered immune cell recruitment to the tumor, which we established after developing a mouse model with a humanized microbiome. As a postdoctoral fellow at Broad Institute working with Ramnik Xavier and Curtis Huttenhower, I worked to characterize the developing infant gut microbiome in dense, longitudinal metagenomic analyses of birth cohorts at risk for type 1 diabetes. We discovered a novel mechanism by which the human microbiome directly influences immune development and progression to type 1 diabetes. In my new lab, we focus on simplified microbial communities in gnotobiotic mice to discover basic lines of microbiome-host communication necessary for homeostasis and that underlie autoimmune disease.


    2008 Hon.B.Sc. Molecular Biology, University of Toronto

    2013 Ph.D., Biological & Biomedical Sciences, Harvard University

    2016 Postdoctoral Fellowship, Broad Institute of MIT & Harvard

    Assistant Investigator, Joslin Diabetes Center

    Member of the Faculty, Department of Microbiology and Immunobiology
    Harvard Medical School

TED CHAVKIN, Graduate Student

I’m a second year graduate student in the Biological and Biomedical Sciences (BBS) program at Harvard Medical School. My background is in bioengineering, molecular biology, and microbiology, and my current research is focused on applying synthetic biology tools to the gut microbiome to treat and manage diabetes. I’m also working on tackling gut microbiome interactions from a forward genetics approach, to better understand the microbe-microbe interactions and host-microbe interactions that cause disease states.


    REG Life Sciences, San Francisco, CA
    Research Associate, 2010 - 2012

    University of California Berkeley, Berkeley, CA
    Bachelors of Science, Bioengineering, May 2010

JACOB LUBER, Graduate Student

I am a PhD student in the Bioinformatics and Integrative Genomics (BIG) Program at Harvard Medical School in The Division of Medical Sciences under the aegis of The Graduate School of Arts and Sciences. I am a member of the Kostic Lab at the Joslin Diabetes Center where I work on elucidating host-gut microbiome interactions that lead to autoimmunity by integrating machine learning techniques with rapid experimental validation methods that leverage emerging sequencing technologies. My research interests are metagenomics, metatranscriptomics, host-microbe interactions, sequencing technologies, functional genomics, machine learning, ontology evaluation, genome structure, and personalized genomic medicine.


    Trinity University, San Antonio, TX
    Bachelors of Science, May 2016

BRADEN TIERNEY, Graduate Student

I am a second-year graduate student in the Biological and Biomedical Sciences program co-mentored by Alex Kostic and Chirag Patel. Research-wise, I’m interested in computationally modeling the relationship between microbiome gene content and host phenotype/genotype. Additionally, I am fascinated by the stability of microbial genomes, and how the presence or absence of different combinations of genes engender complex traits.

Prior to being at Harvard, I studied Biology and Economics at Duke University in Durham, North Carolina. During my time there, I worked with Philip Benfey on the development of the Arabidopsis root microbiome, Beth Shank on the soil microbiome, and AgBiome, a company focused on building microbial-based treatments for crop-based diseases.


    Duke University, Durham, NC
    Bachelors of Science in Biology, May 2016
    Bachelors of Science in Economics, May 2016

ISHAN MISHRA, Research Intern

I am a Computational Biologist working in Dr. Alex Kostic’s lab. Currently, I’m interested in researching the potential correlations between various genes in the human microbiome and various auto-immune diseases, including Type-1 Diabetes. I’m also a full-time Nanotechnology Engineering student at the University of Waterloo, Canada, where I’m about to begin my third year.

Before coming to Harvard Medical School, I was working as an Advanced Developer for CMOS Sensor Products at Teledyne DALSA, one of the world leaders in developing sensors for digital imaging. Prior to that, I was a Research Assistant under Professor Federico Capasso at Harvard University, working on meta-lenses. I’ve also worked in the past at Ryerson University, Canada (focusing on biomedical imaging) and the University of Toronto, Canada (working in particle physics).

ZHEN YANG, Research Intern

I’m a fourth year undergraduate student at the University of Waterloo, Canada, majoring in Mathematical Optimization with a specialization in Operations Research. I joined Kostic Lab as a Computational Biologist. I’m interested in building statistical tools and carrying out computational analysis with complex data sets. In particular, I hope to apply these skills in order to find relationships in metagenomic data to Type 1 diabetes.

Before joining the team, I worked as a quantitative analyst in NN Group, which is one of the largest insurance companies in the Netherlands.

MARSHA WIBOWO, Graduate Student

I am a second year Ph.D. student in the Biological and Biomedical Sciences (BBS) program at Harvard Medical School. I am from Indonesia and I did my undergraduate at MIT in biology, where I had a chance to work with David Page, Hidde Ploegh, and Harvey Lodish. My background is in molecular biology and my current research interest is in the role of the gut microbiome in obesity, metabolic syndrome, and type 2 diabetes.


    Massachusetts Institute of Technology, Cambridge, MA
    Bachelors of Science, Biology, May 2016

TAO XU, Postdoctoral Fellow

I am a molecular geneticist with expertise in molecular biology, bioengineering, and microbiology. My current research focuses on screening gut microbes that are actively involved in immune modulation, and more importantly, mining traits-conferring genes or gene clusters from isolates for the production of therapeutic molecules or the construction of genetically engineered cells to fight type 1 diabetes.


    University of Oklahoma, Norman, OK
    Ph.D., Microbiology, December 2016

    Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
    Masters of Science, Biochemistry and Molecular Biology, 2011

    School of Resources Processing and Bioengineering, Central South University, Changsha, China
    Bachelors of Science, Bioengineering, May 2008


My research background is microbiology and molecular biology, and also gut microbiota immunology and metagenomics. My current project focuses on the effect of the gut microbiome on the autoimmune response in type one diabetes in animal models such as non-obese diabetic and germ-free mice, trying to discover microbes with potential therapeutical activities and the development of T1D.


    Spanish National Research Council (IPLA-CSIC), Villaviciosa, Spain
    Ph.D., Microbiology, June 2016

    University of Oviedo, Oviedo, Spain
    Masters of Science, Food Biotechnology, 2012

    University of Oviedo, Oviedo, Spain
    Bachelors of Science, Biochemistry, 2010

RORY BROWN, Research Intern

I am a senior at Harvard College studying molecular and cellular biology with a secondary in global health and healthy policy. My work in the Kostic Lab is centered upon developing a genetic engineering platform for a minimal microbiome in mice. Our hope is that this tool will allow us to make specific alterations to bugs in this microbiome, ultimately allowing us to tease out the mechanisms behind host-microbe and microbe-microbe interactions.