Stanford Microbiome Summit Speakers and Panelists

Ami Bhatt, Stanford University, Assistant Professor of Medicine (Hematology) and of Genetics

The Bhatt laboratory studies the interplay between the human microbiome and noncommunicable diseases, such as cancer and cardiometabolic disorders. The laboratory uses next generation sequencing to define the microbiome and host immunological features in patients with hematological diseases, develops custom tools for the identification of novel microbes in immunosuppressed patient populations, and uses statistical and functional methods to understand the interplay between the human microbiome and the development of immunological diversity. Recently, the lab has become particularly interested in learning how to measure microbial genomic plasticity in clinical time scales and understanding the biological consequences of these genomic variations on bacterial adaptation. In addition to this, the lab studies methods to modify the microbiome, and the consequence of microbial metabolites on host biological processes.

Alexandra Boehm, Stanford University, Professor of Civil and Environmental Engineering and Senior Fellow at the Woods Institute for the Environment

Professor Boehm's research areas are coastal water quality and sanitation. These two research areas are linked by a focus on waterborne pathogens. The work on coastal water quality addresses the sources, transformation, transport, and ecology of biocolloids - specifically fecal indicator organisms, DNA, pathogens, and phytoplankton - as well as sources and fate of nitrogen. This knowledge is crucial to formulating new management policies and engineering practices that protect human and ecosystem health at the coastal margins. The work on sanitation aims to gain a better understanding of how pathogens are transmitted to humans through contact with water, feces, and contaminated surfaces. My research is focused on key problems in both developed and developing countries with the overarching goal of designing and testing novel interventions and technologies for reducing the burden of waterborne disease.

Josh Elias, Stanford University, Assistant Professor of Chemical and Systems Biology

The Elias lab endeavors to link three fields: Computational proteomics, antigen presentation, and host-microbe interactions in the gut. These may seem to be an odd combination, they are fundamentally interdependent: Antigen presentation is a pillar of nearly all immune-related diseases, from cancer to multiple sclerosis; whether an individual’s immune system interprets a particular antigen as something to be tolerated or not can often be traced to the trillions of commensal microbes living in our intestines. Proteins are arguably the major molecular class mediating host-microbe interactions and antigen presentation, but elucidating how these extraordinarily complex and dynamic systems interconnect will require new proteomic tools. Our recent efforts in each of the above three aspects include new tools based on de novo peptide sequencing for identifying proteins from ambiguous or unknown organisms; discovering new signatures of cancer and infection from peptide antigens presented by major histocompatibility complexes; an elucidating hallmarks of host responses to antibiotics, infection, and induced autoimmunity from stool. All of these experiments rely on our extensive expertise in mass spectrometry, and dozens of valued collaborations within Stanford University and with other research institutions.

Michael Fischbach, Stanford University, Associate Professor of Bioengineering

Michael Fischbach  is an Associate Professor of Bioengineering at Stanford University. Fischbach is a recipient of the NIH Director's Pioneer and New Innovator Awards, an HHMI-Simons Faculty Scholars Award, a Fellowship for Science and Engineering from the David and Lucille Packard Foundation, a Medical Research Award from the W.M. Keck Foundation, a Burroughs Wellcome Fund Investigators in the Pathogenesis of Infectious Disease award, and a Glenn Award for Research in Biological Mechanisms of Aging. His laboratory uses a combination of genomics and chemistry to identify and characterize small molecules from microbes, with an emphasis on the human microbiome. Fischbach received his Ph.D. as a John and Fannie Hertz Foundation Fellow in chemistry from Harvard in 2007, where he studied the role of iron acquisition in bacterial pathogenesis and the biosynthesis of antibiotics. Before coming to Stanford, he was an Associate Professor in the Department of Bioengineering and Therapeutic Sciences at UCSF, and before that spent two years as an independent fellow at Massachusetts General Hospital coordinating a collaborative effort based at the Broad Institute to develop genomics-based approaches to the discovery of small molecules from microbes.

Tad Fukami, Stanford University,  Associate Professor of Biology

Tadashi Fukami studies how species assemble into ecological communities. He is particularly interested in understanding historical contingency, or when and why the structure and function of communities are contingent on the history of species immigration. One of the study systems that his lab currently uses for this research is the bacteria and yeasts that colonize floral nectar via flower-visiting animals such as hummingbirds and bees. This work is aimed at addressing fundamental questions that are relevant not only to the floral microbiome, but to a range of communities, including the human microbiome. For more info, see the Fukami Lab web site: http://web.stanford.edu/~fukamit/

Aida Habtezion, Stanford University, Associate Professor of Medicine (Gastroenterology and Hepatology)

Dr. Habtezion studies leukocyte trafficking and immune responses pertaining to the gastrointestinal organs in states of both health and disease. Her lab demonstrated a beneficial role and mechanism for the stress inducible anti-inflammatory enzyme, hemeoxygenase-1, and its downstream effectors in acute pancreatitis. In chronic pancreatitis her lab demonstrated cellular crosstalk that contributes to disease progression and fibrosis. More recently her lab showed a mechanism via which environmental factors such as smoking promote immune and pancreas stellate cell interaction leading to progression of chronic pancreatitis. Her lab is currently working to elucidate targetable immune pathways that alter or reverse the course of pancreatic diseases. A second major project in the lab pertains to understanding immune responses in the intestine and in inflammatory bowel disease (IBD). The lab is currently trying to understand disease heterogeneity among IBD patients using immune profiling and approaches that determine host immune-microbiome interactions. In addition, using experimental models, her lab is actively pursuing immune-enteric nervous system interaction and intestine-specific leukocyte recruitment in order to develop intestine specific therapeutic targets to ameliorate disease.  

Susan Holmes, Stanford University, Professor of Statistics, Bass Fellow and member of BioX

Susan Holmes and her group have been developing open source statistical and computational tools for the analysis of microbiome data for more than 10 years. She specializes in the fusion and integration of clinical covariates with  of the different domains of information (genomic, phylogenetic, metatranscriptomic and metabolites) available in microbiome studies. The Bioconductor and R programs developed in her group (phyloseq, dada2, structSSI, treeDA) have been used in hundreds of published studies. She has designed many microbiome studies, including a large perturbation experiment funded by an NIH transformative research award jointly with David Relman.

She has dedicated herself to the creation of templates for optimizing reproducible research in the analysis of the human microbiome using nonparametric statistics and rigorous experimental design. All her papers are supplemented with extensive code that enable researchers to reproduce computations on their own data.

KC Huang, Stanford University, Associate Professor of Bioengineering and of Microbiology and Immunology

My group is uniquely positioned to combine computational and experimental methods across multiple length and time scales, to uncover how cells achieve robust morphogenesis and respond to mechanical perturbations. My lab has repeatedly pioneered new technologies that have yielded dramatic conceptual advances in our understanding of bacterial growth. I have been trained as a theoretical physicist with an appreciation for the natural cooperation of theory, computation, and experiment. My research continues to evolve into three areas that all focus on the physical interplay among molecules, cells, and their environment:
(1)  How cell growth responds to changes in osmotic environment, exploiting comparisons across organisms in three kingdoms;
(2)  Biophysical tools to uncover the genetic and macromolecular determinants of bacterial cell stiffness; and
(3)  How integration of cytoskeletal mechanics and spatial organization produces robust rod-shaped bacterial morphogenesis.
Our focus is now extending these efforts to cellular communities, to probe how physical perturbations impact the spatial organization, physiology, and function of the gut microbiota.

Britt Koskella, UC Berkeley, Assistant Professor of Biology

Britt Koskella is an evolutionary ecologist interested in multi-species interactions, with a particular focus on host-pathogen coevolution. Her lab currently has two main research avenues: (i) exploring the role of bacteriophages in shaping the microbiome, and (ii) studying both host-microbiome and pathogen-microbiome coevolution. We are using tomato (short-lived) and tree (long-lived) hosts as models to understand these fundamental processes. By expanding the interactions under study to multi-species, we are also seeking to determine whether theoretical predictions for host-pathogen coevolution and host-commensal interactions can be and should be applied to more complex communities and host-microbiome ‘holobionts,’ or whether a new body of theoretical work need be developed. Our work – as with most current microbiome research - is grounded in basic science, but has clear application to human and agricultural health which we hope to further develop moving forward.

Kabir Peay, Stanford University, Assistant Professor Biology

Our lab studies the ecological processes that structure natural communities and the links between community structure and the cycling of nutrients and energy through ecosystems. We focus primarily on fungi, as these organisms are incredibly diverse and are the primary agents of carbon and nutrient cycling in terrestrial ecosystems.

Much of our research focuses on plant-fungal root associations, better known as mycorrhizas, which constitute one of the most pervasive mutualisms in terrestrial ecosystems. We work on questions at three scales of this symbiosis, (1) how does environmental variation and functional variation in mycorrhizal fungi affect the symbiosis at the root tip scale, (2) how does dispersal contribute to the predictability of community assembly patterns at the landscape scale, and (3) how does biogeography affect mycorrhizal community structure and ecosystem function? By integrating these three levels of research we hope to build a 'roots-to-biomes' understanding of plant-microbe symbiosis.

Katie Pollard, UC San Francisco,  Professor of Epidemiology & Biostatistics, Director and Senior Investigator  at the Gladstone Institute

Dr. Pollard earned her PhD in Biostatistics from the University of California, Berkeley and was a comparative genomics postdoctoral fellow at the University of California, Santa Cruz. She was awarded the Thomas J. Watson Fellowship in 1995 and the Sloan Research Fellowship in 2008. She is a member of the California Academy of Sciences and a Chan-Zuckerberg Biohub Investigator.

The Pollard lab develops bioinformatics methods for comparative analysis of massive biological datasets, with a focus on genomics and other transformative technologies. The lab’s mission is to enable statistically rigorous, quantitative comparisons across species, developmental stages, and conditions. A major emphasis is creating open source bioinformatics software. Pollard and her team developed industry standard tools for gene expression analysis, detecting evolutionary conservation and acceleration, and quantifying abundances of microbial genes from metagenomes.

David Relman, Stanford University, Thomas C. and Joan M. Merigan Professor of Medicine, and of Microbiology and Immunology

Relman was an early pioneer in the modern study of the human indigenous microbiota. Most recently, his work has focused on human microbial community assembly, and community stability and resilience in the face of disturbance. Ecological theory and predictions are tested in clinical studies with multiple approaches for characterizing the human microbiome. Previous work included the development of molecular methods for identifying novel microbial pathogens, and the subsequent identification of several historically important microbial disease agents. One of his papers was selected as “one of the 50 most important publications of the past century” by the American Society for Microbiology.

Dr. Relman received an S.B. (Biology) from MIT, M.D. from Harvard Medical School, and joined the faculty at Stanford in 1994. He served as vice-chair of the NAS Committee that reviewed the science performed as part of the FBI investigation of the 2001 Anthrax Letters, as a member of the National Science Advisory Board on Biosecurity, and as President of the Infectious Diseases Society of America. He has received an NIH Pioneer Award, an NIH Transformative Research Award, and was elected a member of the National Academy of Medicine in 2011.

Tiffany C. Scharschmidt, UC San Francisco, Assistant Professor of Dermatology

Dr. Scharschmidt is a physician-scientist with training in microbiology, immunology in Dermatology.  In the clinic, her focus is on treating patients with complex inflammatory skin disease. In the lab, her passion is trying to understand how our immune system establishes and maintains a healthy relationship with our skin microbiota. In 2016, following her clinical and postdoctoral training, Tiffany established her own research group at UCSF, where she is a faculty member in the Biomedical Sciences, Immunology and Microbial Pathogenesis & Host Defense programs. Research in her lab aims to elucidate host-directed and microbe-directed mechanisms that promote healthy dialogue between skin commensals and the adaptive immune system, with a focus on early life events.

Justin Sonnenburg, Stanford University, Associate Professor of Microbiology and Immunology

Justin Sonnenburg, PhD, is currently an associate professor at Stanford University School of Medicine, where he studies the gut microbiota in health and disease and co-directs the Center for Human Microbiome Studies.  His laboratory at Stanford is currently focused on understanding basic principles that govern interactions within the intestinal microbiota and between the microbiota and the host. An ongoing objective of the research program is to devise and implement strategies to prevent and treat disease in humans via the gut microbiota.
He and his wife Erica, are the authors of the book The Good Gut:  Taking Control of Your Weight, Your Mood, and Your Long-Term Health