2015 Archived Content


The microbiome R&D is an emerging area of science that is starting to prove its importance. Basic and applied biomedical research from the Human Microbiome Project and other independent studies prove that a disruption of a stable microbiome ecosystem results in dysbioses. This imbalance leads to chronic disease and health conditions like inflammation, metabolic disorders, gut disorders, obesity, Type 2 Diabetes, autoimmune disorders, inflammatory bowel disease, neurodevelopmental disorders and more. Additionally, a PubMed search on the term “human microbiome” yielded 300 citations in 2003 and 4,498 citations in 2013. A fair amount of partnerships and commercial ventures have developed during recent years to identify and develop therapies and biomarkers for a number of chronic diseases and health conditions. There is great promise in correlating the microbiome compositions with these disease and using the microbiome as a tool for therapeutic development. Cambridge Healthtech Institute’s Inaugural conference, Targeting the Microbiome, 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 maintenance.

Final Agenda

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Tuesday, September 22

7:00 am Registration and Morning Coffee

8:00 Chairperson’s Opening Remarks
Joshua R. Korzenik, M.D., Director of Crohn's and Colitis Center, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital; Assistant Professor, Harvard Medical School

8:10 Keynote Presentation: Recent Advances in Understanding the Human Microbiome

Karen E. Nelson, Ph.D., President, J. Craig Venter Institute (JCVI)

Our recent studies on the human microbiome highlight a higher degree of microbial diversity within and across individuals than was previously appreciated as well as new microbial species whose roles remain unexplored. Studying healthy and diseased human populations, their microbiomes and circulating metabolites present new opportunities for defining novel diagnostics and therapeutic approaches for several human diseases. It is clear that the advent of metagenomics holds significant promise for increasing our understanding of many microbial diseases associated with the human body, inclusive of those that are yet to be characterized.

Dynamics of the Microbiome on Health and Disease – Computational Approaches, Ecological Perspectives & CLINICAL TRIALS

8:40 Computational and Synthetic Biology Approaches for Discovering Microbiome Interactions and Functions

Georg K. Gerber, M.D., Ph.D., MPH, Assistant Professor of Pathology, Harvard Medical School; Co-Director, Center for Clinical and Translation Metagenomics, Director, Computational Unit, Associate Pathologist, Department of Pathology, Brigham and Women’s Hospital

I will describe: (1) a new computational approach for accurately predicting microbiota dynamics, with applications to finding networks of bacteria that protect against a human enteric pathogen, and (2) a synthetic biology platform to functionally mine bacterial genomes for genes that contribute to fitness, with applications to finding genes important for colonizing the mammalian gut over time.

9:10 Studying the Microbiome Community Networks Across Different Body Sites

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)

The study aims to get an ecological view of microbiota from systems perspective across different body sites. Microbiome community networks were computed for samples from two different body sources, based on maximal information content. The patterns were compared and enriched with functional annotation to discover strong relationships between biological processes and microbes.

9:40 Grand Opening Coffee Break in the Exhibit Hall with Poster Viewing

Dynamics of the Microbiome on Health and Disease – Microbiota-Targeted Therapies and Interventions

10:25 Efficient Clinical Trials Leveraging the Microbiome

Nicholas J. Schork, Ph.D., Professor and Director, Human Biology, J. Craig Venter Institute

In this talk, I describe study designs which consider the microbiome (possibly among other endpoints) as the object of study for different interventions (e.g., dietary manipulations, fecal transplants, antibiotic use, etc.). These designs are meant to be efficient and cost-effective and include N-of-1 and aggregated N-of-1 studies, sequential studies, and multivariate profiling studies.

10:55 Engineering the Microbiome to Cure Clostridium Difficile Infection

Eric Alm, Ph.D., Director, Center for Microbiome Informatics and Therapeutics and Associate Professor, Biological Engineering, MIT; Associate Member, Broad Institute

Fecal Microbiota Transplantation (FMT) has proven very effective at preventing recurrent Clostridium difficile infection, yet the basic science behind FMT is poorly understood. In particular, little is known about the mechanism of action, or consequences of transplanting the gut microbiome from donors to patients. I will discuss efforts to build quantitative and predictive models of FMT, and what they reveal about the underlying biology of microbe-host interaction.

11:25 Harnessing the Gut Microbiome: Separating the Hype from the Evidence

Lee Jones, CEO, Rebiotix Inc.

Lead product RBX2660 (microbiota suspension), a next-generation version of fecal microbiota transplant, is targeted at recurrent Clostridium difficile infection. This new drug is currently being assessed in a Phase 2B study under an FDA IND. Work on other applications and formulations is underway.

C3 Jian11:55 Re-engineering the Microbiome through Targeted Elimination of Specific Pathogens

Brian Varnum, Ph.D., Chief Development Officer, C3 Jian, Inc.

Treatment of microbiome-associated diseases is best approached with use of pathogen-specific antimicrobials. Our platform technology creates targeted antimicrobial peptides to treat and prevent microbial dysbiosis. C16G2, our lead molecule for dental caries, has demonstrated clinical efficacy, as measured by microbiome reengineering. A targeted treatment for Clostridium difficile infection is progressing towards the clinic. Updates for both programs will be presented.

12:25 pm Session Break

12:35 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:15 Refreshment Break in the Exhibit Hall with Poster Viewing

1:50 Chairperson’s Remarks
Willy Valdivia, CEO, Orion Integrated Biosciences, Inc.

2:00 Innovative Microbiome Therapeutics: Understanding the Ecologies of Disease Associated with CDI

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

SER-109, a first-in-field oral microbiome drug, is in advanced clinical development for the prevention of recurrent Clostridium difficile infection. Clinical outcomes, effects on the gastrointestinal microbiome of patients, and lessons for drug development will be presented.

2:30 Therapy for Gastrointestinal Microbiome-Associated Diseases Requires Dietary Diversity

Mark L. Heiman, Ph.D., FTOS, Vice President, Research and CSO, MicroBiome Therapeutics

Diet is the principal regulator of the gastrointestinal (GI) microbiome, an ecosystem in our GI tract, especially the colon, comprised of trillions of bacteria (microbiota) in a solution of unabsorbed macro- and micro-nutrients. Loss of dietary diversity shifts the microbiome to unhealthy states. I will present 2 strategies to improve dietary diversity by supplementing the habitual uniform diets with GI microbiome modulators (GIMMs).

Enterome Bioscience3:00 Metagenomic Approaches for Drug Discovery 

Laurent Chene, Ph.D., Head, Drug Discovery Platform, Discovery, Enterome Bioscience

Using Enterome’s expertise on metagenomic, we identify commensal bacteria associated with diseases and use specific meta/genomics libraries to screen bacterial components regulating biological functions. This approach is used to identify components regulating cytokine secretion from IEC and is extended to identification of compounds that modulate gut hormones secretion or could improve immune anti-tumoral responses.

3:15 Role of Commensal Bacteroidetes in Defense against Clostridium difficile Infection 

David Haslam, M.D., Associate Professor of Pediatrics, Cincinnati Children’s Hospital

Alteration of the commensal microbiome is the major risk factor for Clostridium difficile infection (CDI). I will describe our studies using a mouse model of CDI that identified members of the commensal microbiota that confer protection from CDI and the mechanisms involved in protection.

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

4:10 Engineered Probiotics: The Next Frontier for Microbiome Therapeutics

Bernard Malfroy-Camine, Ph.D., President & CEO, ViThera Pharmaceuticals

ViThera Pharmaceuticals with its collaborators at Inserm and Inra in France is a pioneer in the concept of using genetically engineered probiotic bacteria as vectors for delivery of therapeutic proteins targeting the intestinal epithelium for inflammatory bowel disease.

4:40 Micro Biome Restorative Therapy in Dogs and Cats Using Ozone Therapy to Reduce the Biofilm

Margo Roman, DVM, Main Street Animal Services of Hopkinton (MASH)


5:10 Interactive Breakout Discussion Groups 
This interactive session provides conference delegates and speakers an opportunity to choose a specific roundtable discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion.  

The Human Microbiome: Implications in Diagnostics and the Challenge for Regulatory Agencies

Willy Valdivia, CEO, Orion Integrated Biosciences, Inc.

  • Addressing taxonomic diversity in complex microbiome samples
  • Is the engineering of the microbiome the next frontier for antimicrobial development?
  • Intellectual property and complex microbial communities, a viable commercial venture?
  • The microbiome and personalized medicine, multiple paths for one individual

On the Road Towards Causality: the Opportunities and Challenges of the Mouse Model in Microbiome Research

Yanjiao Zhou, MD, PhD, Research Scientist , The Jackson Laboratory for Genomic Medicine, Farmington CT

  • Current understanding of the mice microbiome
    -The healthy mice gut microbiome 
    -Genetically engineered mice, inbred mice or diversity outbred mice to map host genes impacting the microbiome 
    -Germ free mice to test the causality vs correlation
  • Practical issues and solutions in the mice microbiome experimental design
    -Maternal effect-Cage effect
    -Batch effect
    -Fecal transplant
  • Outlook on improving the mice microbiome research
    -Enrich the mice gut taxonomical and gene catalogue 
    -Customized mice microbiome service

6:10 Welcome Reception in the Exhibit Hall with Poster Viewing

7:15 Close of Day

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Wednesday, September 23

7:30 am Registration and Morning Coffee

Dynamics of the Microbiome on Health and Disease – Microbiota-Targeted Therapies and Interventions

8:00 Chairperson’s Remarks
Jennifer Russo Wortman, Director of Bioinformatics, Seres Health, Inc.

8:10 Probiotic Skin Microbiome against S. aureus Infection

Eric Huang, Ph.D., Professor, Division of Dermatology, University of California, San Diego

Mounting evidence indicates that the fermentation of normal intestinal microbiota can positively influence immune responses and protect hosts from pathogen infection. Our publications demonstrate for the first time that skin commensal bacteria can employ the carbohydrate fermentation process against Staphylococcus aureus (S. aureus) pathogens. The molecular mechanisms of fermentation in the human skin microbiome as the probiotic immunity will be presented.

8:40 The Lung Microbiome in Respiratory Diseases

James R. Brown, Ph.D., Director, Computational Biology, GlaxoSmithKline, Collegeville, PA

Increasing evidence suggests that the lung microbiome plays an important role in chronic obstructive pulmonary disease (COPD). We will present an overview of lung microbiome clinical studies which potentially suggest novel precision medicine approaches for the future treatment of COPD patients.

9:10 Microbiome, Microbial Metabolites, and Metabolic Diseases

Deepak K. Rajpal, Ph.D., Director, Computational Biology, GlaxoSmithKline, King of Prussia, PA

We present a case study of gut microbial modulation resulting in metabolic improvements, which are important for developing novel therapeutic intervention strategies for metabolic diseases. Additionally, we share our initial observations on utilizing the microbial metabolites for developing hypotheses for drug discovery programs.

9:40 Coffee Break in the Exhibit Hall with Poster Viewing

10:25 Metagenome Analysis of the Microbiome to Assess Survival to Disease
Willy Valdivia, CEO, Orion Integrated Biosciences, Inc.

10:55 Keynote Presentation: Exploring the Medical Microbiome 
George M. Weinstock, Ph.D. Professor and Associate Director, Jackson Laboratory for Genomic Medicine, Farmington CT
The Human Microbiome, the collection of microbes colonizing the human body, is coming under increasingly sophisticated scrutiny as genomic technologies and analytic tools advance. Microbiome research continues to find correlations between the microbial ecology of the human body and diseases, lifestyles, and other factors. The most recent projects bring together studies of the host with that of the microbes and involve large multidisciplinary datasets that present complex profiles to be mined for diagnostic and mechanistic clues to health and disease. The fruits of this research are leading to new concepts in treatment of disease.

11:25 Enjoy Lunch on Your Own

12:55 pm Plenary Keynote Program

2:40 Refreshment Break in the Exhibit Hall with Poster Viewing

3:25 Close of Conference

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