Keynote Speakers
September 20, 2019
More than 1,000 species of bacteria, archaea, viruses and fungi live in the human gut. Far from being passive passengers, these organisms strongly interact with one another and with their host’s metabolism and immune system. Compelling early experiments have demonstrated associations between the intestinal microbiome composition and obesity, cardiovascular diseases, and certain cancer chemotherapies’ efficacy. Yet teasing apart the mechanisms by which microbes impact host health has been challenging. To accelerate an otherwise challenging, slow and tedious process and to deconstruct mechanisms, we must critically examine our existing “tool kit” for studying the microbiome, and mature our measurement tools to meet these challenges. Our translational laboratory builds and designs observational and interventional clinical cohorts to study. We have also steadfastly worked to develop genomic tools to study strain level dynamics of the microbiome, how microbial genomes change over time and how microbes use hidden “microproteins” to communicate with each other and their human hosts. In this presentation, I will speak about three recent developments in our lab: (1) I will introduce the importance of absolute quantification in microbiome research, and our efforts toward that. This will form the basis of revised estimates of the number of microbial cells in a human body. (2) I will give an overview of a new computational workflow called “Phanta”, which enables simultaneous taxonomic profiling of eukaryotes, bacteria and viruses in a human gut metagenomic sample. (3) I will share exciting new unpublished work on our discovery of intragenic inversion as a previously unappreciated mechanism of generating genetic diversity in microbial genes.
Ami Bhatt is an Associate Professor at Stanford University in the Departments of Medicine (Hematology; Blood & Marrow Transplantation) and Genetics. A physician scientist with a strong interest in microbial genomics and metagenomics, she received her MD and PhD from the University of California, San Francisco, followed by residency and fellowship training at Harvard Medical School. She joined the faculty at Stanford University in 2014 after completing a post-doctoral fellowship focused on genomics at the Broad Institute of Harvard and MIT.
Prof. Bhatt has received multiple awards including the Chen Award of Excellence from the Human Genome Organisation (HUGO), the Distinguished Investigator Award from the Paul Allen Foundation, and the Sloan Foundation Fellowship; she is also an elected member of the American Society of Clinical Investigation. Her team’s research program seeks to illuminate the interplay between the microbial environment and host/clinical factors in human diseases. Her translational laboratory develops and applies novel molecular and computational tools to study strain level dynamics of the microbiome, to understand how microbial genomes change over time and predict the functional output of microbiomes. She is keenly interested to understand how microbes “talk” to one another and to host cells, and to leverage this understanding to improve health and treat diseases. She has also worked collaboratively to mine microbial enzymes from mobile genetic elements and develop these as genome editing/engineering tools.
In addition to carrying out research at Stanford University, Prof. Bhatt has active collaborations world-wide including in Nigeria and South Africa. She is committed to ensuring that advances in research touch the lives of individuals in all income settings – and thus, in her spare time, enjoys volunteering for the nonprofit she co-founded, Global Oncology and serves as the Director for Global Oncology for Stanford’s Center for Innovation in Global Health. Outside of work, Ami enjoys reading fiction, hiking and climbing in the great outdoors, and has been working on perfecting her vegan ramen recipe.
Bacterial Metabolism and Competition in the Mammalian Gut
Microbiome research in the Wolf Lab encompasses two areas: bacterial metabolism of dietary ingredients and microbiota-mediated protection against infectious diseases (including Mycobacterium tuberculosis and Shigella). We combine human microbiome data, laboratory models, and computational analyses to ask questions about the role of diet, microbial competition, and host factors in gut microbiome structure and function.
Ashley Wolf is an Assistant Professor jointly appointed in the Center for Computational Biology and the Division of Infectious Diseases and Vaccinology at Berkeley Public Health. Ashley graduated from Princeton University with a degree in Molecular Biology and certificates in Applications of Computing as well as Quantitative and Computational Biology. She completed a senior thesis with Bonnie Bassler studying inter-bacterial signaling. For her Ph.D. in Systems Biology, she interrogated mitochondrial RNA biology with Vamsi Mootha at Harvard University. Ashley completed her postdoctoral fellowship in the lab of Jeffrey Gordon at Washington University School of Medicine. Throughout her career, Ashley’s work has integrated experimental and computational approaches to questions spanning basic and translational science.