Cambridge Healthtech Institute’s Annual

Microbiome-Based Precision Medicine

Using the Microbiome as a Tool for Translating Science into Useful Therapeutics

February 23-24, 2017 | Moscone South Convention Center | San Francisco, CA
Part of the 24th International Molecular Medicine Tri-Conference


Cambridge Healthtech Institute’s Inaugural Microbiome-Based Precision Medicine Symposium tracks the scientific and clinical research and applications being made in microbial targeted therapies for inflammation, metabolic disorders, immune disorders and other indications. Through interactive sessions and panel discussions, leading researchers and thought leaders will discuss how their work in this field has and will continue to have tremendous impact in generating personalized diagnostics and therapeutics to improve disease treatment and health status.

Thursday, February 23

7:00 am Registration and Morning Coffee


8:25 Chairperson’s Opening Remarks

Sudeep Basu, Ph.D., Practice Leader, TechVision-Innovation Services, Frost & Sullivan

8:30 Human Microbiome Market Analysis, Trends and Predictions

Sudeep Basu, Ph.D., Practice Leader, TechVision-Innovation Services, Frost & Sullivan

This presentation focuses on microbiome trends including a review of select technologies, markets and products. Additional insights will be provided on the policy and regulatory framework, in the context of the future pipeline - what companies and products are in clinical trials.

9:00 National Collaborations in Microbiome Research and Education

Alison Kim, Ph.D., Senior Director, Research and Innovation, American Gastroenterological Association (AGA)

The American Gastroenterological Association (AGA) established its Center for Gut Microbiome Research and Education in 2012 with a mission to advance research and education on the gut microbiome with the goal of improving human health. This talk will present the work of AGA and its center in organizing educational programs, publications, citizen science projects, and a national registry as a complement to the work of individual investigators and institutions studying the microbiome.

9:30 Presentation Moved from Friday & Replacement Presentation: The Mind-Gut Connection
Emeran Mayer, M.D., Ph.D., Executive Director, Oppenheimer Center for Stress and Resilience and Co-Director, Digestive Diseases Research Center, University of California at Los Angeles; Author, The Mind-Gut Connection: How the Hidden Conversation Within Our Bodies Impacts Our Mood, Our Choices, and Our Overall Health (published July 2016) Presentation delivered via narrated powerpoint

10:00 The Essential Ingredients for Decoding the Microbiome with Metabolomics

Kirk Beebe, Ph.D., Director, Application Science, Metabolon

The microbiome has an important role in health but lack of mechanistic understanding hinders the practical use of this information. We will illustrate how, through surveying the metabolites that broker microbe-host interaction, metabolomics can enrich insights into this association.

10:30 Coffee Break with Exhibit and Poster Viewing


11:15 Measuring Relevant Changes in the Microbiome

Colleen Cutcliffe, Ph.D., Co-Founder and CEO, Whole Biome

As various academic and commercial teams begin to develop interventions targeting the microbiome, we all find ourselves needing to answer two key questions: (1) Can we change an already existing microbial ecosystem in a predictable and desired way and (2) Can we change a person’s disease or healthy state in predictable and desired ways? The keys to answering these questions lie in the interventions themselves, but also in the methods that are used to measure and monitor the microbiome. In this talk, I will share some of Whole Biome’s learnings as we begin to explore the complexity of data acquisition and analytics required to enable us to answer these two key questions.

11:45 Standards for Microbiome and Metagenomics: Supporting the Commercial Translation of Microbiome Science

Scott Jackson, Ph.D., Molecular Genetics and Microbial Genomics, National Institute of Standards and Technology
In spite of the huge potential impact of microbiome science, current measurement capabilities are insufficient, particularly for translating discoveries and correlations observed in the lab into commercially viable products and services that improve our quality of life. Data are difficult to compare between experimenters, laboratories, or institutions. Emerging capabilities (e.g., next generation sequencing, metabolomics) are new and not fully characterized for microbiome investigations. Reference samples (i.e., for calibration or quality control) that mimic the complexity of naturally occurring communities are not available. Bioinformatic analysis packages and reference databases remain incomplete. At NIST, we are improving microbiome science and supporting the National Microbiome Initiative by developing standards for microbiome measurements that will enable federal, academic, and industry labs to reliably reproduce and advance each other's results. Microbiome standards will support research investigations and commercial translation of microbiome science by providing measurement assurance tools: standardized protocols, reference materials, validated measurements and critically evaluated reference data.


Second Genome12:15 pm Improving the Utility of Microbiome Research

Cheryl-Emiliane Chow, Ph.D., Bioinformatics, Scientist Solutions, Second Genome

Understanding which microbes influence health is critical to research in human biology. Through hardware and software development, Second Genome has built strategies to: achieve strain-level taxonomic resolution, improve functional insights, and achieve reproducible results. Through identification of key microbes, these findings can be applied to develop microbiome-based diagnostics and therapeutics.

12:30 Session Break

12:45 LUNCHEON PANEL DISCUSSION: The Charles River Microbiome Think Tank

This Microbiome Think Tank Luncheon Panel Discussion features leading researchers and thought leaders discussing novel research towards clinical applications to improve disease treatment and human health.

Iva Morse, CSO, Vice President, Charles River

John Ho, M.D., Corporate Senior Vice President & Chief Strategy Officer, Charles River


Kirk Beebe, Ph.D., Director, Application Science, Metabolon
Lynn Bry, M.D., Ph.D., Associate Professor, Pathology and Director, Massachusetts Host-Microbiome Center + Crimson Core, Brigham & Women's Hospital

David Cook, Ph.D., Executive Vice President of R&D and CSO, Seres Health
Audrey Goddard, Ph.D., Vice President, Research and Development, uBiome

Christiane Honisch, Ph.D., Director, Microbiology Markets, Illumina

Mohan S. Iyer, Chief Business Officer, Second Genome

Scott Jackson, Ph.D., Molecular Genetics and Microbial Genomics, National Institute of Standards and Technology 
Andreas M. Kogelnik, M.D., Ph.D., Director, Open Medicine Institute 
Deepak K. Rajpal, Ph.D., Director, Computational Biology-Target Sciences, GSK

1:45 Session Break


2:20 Chairperson’s Remarks

Bonnie Feldman, D.D.S., MBA, Digital Health Analyst and Chief Growth Officer, DrBonnie360

2:30 Precision Microbiome Engineering in Agriculture and Beyond

Nick Conley, Ph.D., CEO & Co-Founder, EpiBiome

In lieu of small-molecule antibiotics, EpiBiome deploys bacterial viruses known as phages, which are abundant in nature and kill about half of the bacteria on the planet every two days. This talk provides an understanding of how modern tools of molecular and microbiology, such as high-throughput discovery methods and next-generation sequencing, can give an old idea (phage therapy) new life.

3:00 Rapid Detection of Enteric Pathogens and Characterization of the Intestinal Microbiome in Health and Disease

Rita R. Colwell, Ph.D., D.Sc., Distinguished Professor, Center for Bioinformatics and Computational Biology and University of Maryland Institute of Advance, University of Maryland College Park

High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. A retrospective case control study comprising samples of known and unknown etiology, as well as healthy individual samples will be discussed. The results of this study showed that the intestinal microbiome could differentiate healthy, diseased, and asymptomatic carriers, as well as individuals in the early stages of infection and disease.

3:30 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall

4:15 New Presentation: Challenges in Microbiome Therapeutic Development

Emma Taylor, M.D., Co-founder and CEO, Naked Biome

Naked Biome is developing live biologic therapeutics for skin disease with a focus on acne. Their company is harnessing information from the human microbiome project and translating this into the first science-based topical live biologic therapeutic using healthy skin bacteria. This is a novel therapeutic area without precedence and the company is navigating challenges in several of the areas below to develop antibiotic alternatives and effective microbiome-based therapies for dermatologic conditions. Discussed will be: challenges in microbial therapeutic development, strain selection, intellectual property, RX vs DTC, manufacturing, formulation, regulatory strategy, and clinical trial.

4:45 The Oral Microbiome, Autoimmunity and Personalized Nutrition

Bonnie Feldman, D.D.S., MBA, Digital Health Analyst and Chief Growth Officer, DrBonnie360

Advances in big data analytics, next-generation sequencing, and systems immunology are fueling our understanding of the human microbiome. This emerging science is changing our understanding and approach toward oral health and systemic immunity. Bacteria in the mouth seed the GI tract to the tune of 1 trillion bacteria every day. The status of our oral health may be an early indicator of other systemic diseases such as diabetes, heart disease, and rheumatoid arthritis.

5:15 Diversity of Key Players in the Microbial Ecosystems of the Human Body

Corrado Priami, Ph.D., Professor, Computer Science, The University of Trento; President and CEO, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)

Coexisting bacteria form various microbial communities in human body parts. We analyze the interaction network among bacterial OTUs in 11 locations of the human body. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks.

5:45 Reception with Exhibit and Poster Viewing

6:45 Close of Day

Friday, February 24

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Registration Open


8:25 Chairperson’s Remarks
Take Ogawa, Director, Second Genome, Inc.

8:30 Microbiome-Based Precision Medicine Tools for Personalized Treatment Approaches

Purna C. Kashyap, MBBS, Assistant Professor of Physiology and Assistant Professor of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic

Every individual harbors a unique gut microbiome. The inter-individual differences make it difficult to design treatment strategies targeting the microbiome that would apply to all individuals; rather, it highlights the need for personalized therapies. At the same time, inter-individual differences in microbiome may be predictive of individual susceptibility to microbiota related disease, drug therapy and pathogenic infections, hence serving as a diagnostic and therapeutic biomarker. Microbiome represents an important component of the next generation of precision medicine tools.

9:00 The Human Skin Microbiome: Metagenomes to Therapeutics

Julia Oh, Ph.D., Assistant Professor, The Jackson Laboratory

Metagenomic analyses of the human skin demonstrate that contrasting forces of the skin’s biogeography and individuality shape the skin microbiome and its temporal dynamics. Striking changes in the skin’s microbiome are observed in skin disease and other host factors like age or immunodeficiency. Understanding the function, structure, and dynamics of the microbiome is important to design therapeutics that precisely target the pathogen of interest, yet spare the surrounding beneficial microbiota.

9:30 Skin Microbiome

Larry Weiss, M.D., CMO, AOBiome, LLC

AOBiome is exploring the role of Ammonia Oxidizing Bacteria (AOB) as an ancestral human skin commensal. The company is developing live topical therapeutic and cosmetic formulations on Nitrosomonas eutropha for the prevention and treatment of inflammatory disorders of the skin. This presentation will discuss discovery of AOB as skin commensals; biology of Nitrosomonas eutropha; clinical development of AOB as a dermatologic therapeutic, and consumer products as a tool in therapeutic development.

10:00 High-Resolution Taxonomic Profiling to Enhance Translational Microbiome Research

James Robert White, Ph.D., Founder, Resphera Biosciences

Despite advancements in high-throughput DNA sequencing technologies, current microbiome profiling strategies often suffer from insufficient taxonomic characterization, thus hindering identification of reliable biomarkers and the design of follow-up experiments. This presentation will describe a new method for high-resolution taxonomic assignment of 16S rRNA sequence data and highlight two recent collaborative studies with FDA that employ this approach for detection of Salmonella enterica and Listeria monocytogenes. We will further report on applications in the context of Clostridium difficile infection and colorectal cancer.

10:30 Coffee Break with Exhibit and Poster Viewing

11:15 Talk Title to be Announced

David Cook, Ph.D., Executive Vice President of R&D and CSO, Seres Health


11:45 Bioactive Small Molecules from the Human Gut Microbiome

Dylan Dodd, M.D., Ph.D., Instructor of Pathology, Sonnenburg Lab, Department of Microbiology and Immunology, Stanford University School of Medicine

The bacteria within our gut synthesize many small molecules that have important effects on our bodies including modulating drug metabolism, altering the immune system, and predisposing to cardiovascular disease. Targeting the production of these compounds represents an important new strategy to treat human disease. To achieve this, we need to understand how these molecules are produced and develop strategies to predictably alter their levels.

12:15 pm New Presentation: The Human Microbiome: Data Challenges and Solutions

Andreas M. Kogelnik, M.D., Ph.D., Open Medicine Institute
Examination of various human microbiomes is yielding valuable, clinically-relevant information; however, there is still much to learn. Human microbiome analysis is the study of microbial communities found in and on the human body. The goal of human microbiome studies is to understand the role of microbes in health and disease. High throughput methods have enabled increasingly relevant studies with increasing clinical impact that is both surprising and broad-reaching at times. There remains enormous work to be done for data analysis and for application of these technologies.

12:45 Close of Symposium

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