2016 Archived Content

Targeting the Microbiome - Part 2 Header

This two-part Targeting the Microbiome meeting provides interactive sessions and panel discussions with leading researchers and thought leaders who 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 human health. Part Two of the Targeting the Microbiome Track, taking place September 21-22, 2016, features microbiome and biopharma companies discussing the potential of translational interventions and novel therapeutic targets based on microbiome R&D. Case studies will explore how to use the microbiome as a tool for therapeutic, diagnostic and product development. We will also explore issues around microbiome patent eligibility and legal changes that will have a major impact on microbiome research in the next several years.

Final Agenda

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Wednesday, September 21

11:20 am Conference Registration Open

11:25 Enjoy Lunch on Your Own

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


3:20 Chairperson’s Opening Remarks
Randal Eckert, Ph.D., Senior Director, Preclinical Biology, C3 Jian, Inc.

3:35 Correction of Microbiome Dysbiosis by Specifically-Targeted Antimicrobial Peptides (STAMP)

Randal Eckert, Ph.D., Senior Director, Preclinical Biology, C3 Jian, Inc.

The Specifically-Targeted Antimicrobial Peptide (STAMP) platform generates pathogen-specific drugs that target bacteria that drive dysbioses. Effective elimination of these organisms results in a microbiome reengineered to a healthy ecological state. Dysbiosis of microbiome communities has recently been implicated in several chronic diseases, such as dental caries, antibiotic-associated diarrhea, obesity, and IBD. Animal models and clinical studies have validated the STAMP platform, demonstrating remodeling of microbial communities. Updates to several STAMP development programs will be presented.

4:05 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.

4:35 Engineering Synthetic State Machines in Living Cells
Nathaniel Roquet, Ph.D. Graduate Student, Harvard Biophysics Program; Synthetic Biology Group (Professor Timothy Lu), Massachusetts Institute of Technology
State machines are circuits that combine logic and memory to execute complex decision-making, such as producing different outputs based on different orders of inputs. We have engineered state machines in E. coli by leveraging recombinases to perform controlled excision and inversion events on DNA. These state machines allow the cell to distinctly record and respond to all permutations of a set of chemical stimuli. We anticipate that our state machine devices may be useful for uncovering the temporal organization of environmental and cellular factors that drive microbial behavior inside the human body.

5:05 Refreshment Break in the Exhibit Hall with Poster Viewing

5:40 Rescuing the Infant Gut Microbiome

David Kyle, CEO, Evolve Biosystems, Inc.

The healthy human gut microbiome is a rich and diverse ecology throughout most of our lives. However, in one critical time period early in our development – from birth to weaning – the natural gut microbiome is remarkable in that it is dominated up to 80% by a single species: Bifidobactrium infantis (B. infantis). The presence of this single species is a consequence of its unique ability to consume the complex oligosaccharides (soluble fiber) found in in human milk. Unfortunately, the prevalence of the natural gut microbial phenotype in infants has been decreasing dramatically over the last 50 years in industrialized countries. We believe that the loss of this keystone species is due to the unintended consequences of the extensive use of antibiotics, the increasing use of infant formula, and Cesarean section births. Along with this precipitous loss of the natural gut microbiome phenotype in babies, there is a growing pandemic of lifelong metabolic and inflammatory disorders such as asthma, atopy, IBD, food allergies, Type I Diabetes, and obesity. Although these observations have not been directly linked, clinical research does indicate that the newborn immune system and early metabolic program are highly influenced by the gut microbiota. We have established that the infant’s natural gut phenotype (high in B. infantis) is dramatically different from that of the dysbiotic infant (little or no B. infantis) and that through a controlled supplementation with B. infantis, we can rescue the natural gut phenotype in babies regardless of their mode of delivery or nutrition. More importantly, we have shown that this natural gut phenotype is maintained long after supplementation ceases as long as those babies continue to receive breast milk as their primary source of nutrition.

6:10 Next Generation Immunotherapeutics from the Microbiome: Amrita Therapeutics’ Oncology Peptides

Susan Kling Finston, J.D./M.P.P., CEO, Amrita Therapeutics Ltd.
Amrita Therapeutics is pioneering commercialization of next generation immuno-oncology peptides from the microbiome, with lead candidate drug AT-01C and related SMAR1* biomarker (for precision medicine) heading to the clinic in the next 6 - 9 months. SMAR1 is a DNA binding protein and recognized master regulator with a critical role as a tumor suppressor. Amrita’s AT-01C is a p53 tumor suppressor derived from Mycobacterium Tuberculosis (M. bovis) Protein MPT63, also known as ATP-01, one of nearly 4,000 proteins in the bacteria utilized in early immune-oncology therapy BCG for bladder cancer. Amrita Therapeutics is in the vanguard of companies translating microbiome technologies into practical tools to promote human health, with research programs at discovery, early and late preclinical stages. Initially launched in Gujarat, India, Amrita Therapeutics fell outside the scope of American VCs. The company has incorporated in Washington DC in advance of planned human clinical research.


*Scaffold Matrix Attachment Region Binding Protein 1 

6:40 End of Day 

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Thursday, September 22

7:30 am Registration Open and Morning Coffee


8:30 Chairperson’s Remarks

Susan Kling Finston, J.D./M.P.P., CEO, Amrita Therapeutics Ltd.

8:45 The Gut-Brain-Axis: Neurotransmitter Modulation by the Microbiota

Phil Strandwitz, Ph.D., Postdoctoral Research Associate, The Lewis Lab, Northeastern University Antimicrobial Discovery Center

The gut microbiota has been shown to influence numerous disease of the gastrointestinal system. Surprisingly, recent work has shown the influence of the gut microbiota reaches beyond the gut, and can effect behavior and mental health disorders. In this presentation, several key studies on the gut-brain-axis will be discussed, and new work showing the ability of the microbiota to modulate the neurotransmitter GABA will be reported. Such discoveries will likely have profound implications on how to treat mental health disorders, and pave the way for microbiota-based therapeutics.

9:15 Targeted High Molecular Weight Protein Complexes for Microbiota Engineering

Dean Scholl, Ph.D., Director of Research, AvidBiotics Corporation

Avidocin proteins are engineered high molecular weight bacteriocins targeted to kill chosen bacterial species by manipulating the Avidocin cellular receptor binding motif. In vivo data show that Avidocin proteins can remove a targeted bacterial species from the mouse gut without disrupting normal microflora. We are developing these novel antimicrobials for microbiota engineering by selectively removing key species associated with dysbiosis and metabolic disorders.

9:45 Silencing Harmful Bacterial Activity with Non-Antibiotic Drugs

Ward Peterson, Founder & CEO, Symberix, Inc.

The gut microbiome can be pharmacologically targeted to improve human health with a new class of drugs that act on bacteria without killing them. Symberix is targeting the sugar-metabolizing GUS enzyme in gut microbiota that is responsible for causing serious intestinal injuries associated with many pain and cancer drugs. The therapeutic, regulatory and commercialization implications of “drugging the microbiome” will be discussed.

10:15 Coffee Break in the Exhibit Hall with Poster Viewing and Poster Competition Winner Announced

11:10 Protection of the Gut Microbiome from Antibiotics

Jean de Gunzburg, Ph.D., CSO, Da Volterra

Antibiotics are life-saving drugs but inflict severe damage to the gut microbiome with short and long term consequences. We have devised a product, DAV132, which delivers a powerful adsorbent to the late ileum of humans, and show in a randomized controlled study on human volunteers that its co-administration with the fluoroquinolone moxifloxacin enables to protect the gut microbiome without jeopardizing the systemic exposure to the antibiotic. Furthermore, we show the product prevents the occurrence of Clostridium difficile infections in several preclinical settings. Our data suggests that DAV132, which has the capacity to adsorb a broad spectrum of different antibiotics, may constitute a breakthrough in antibiotic treatments, by protecting the gut microbiome and preventing adverse health consequences.

11:40 Precision Medicine and Microbiome Targets: Treatment of IBS-C and Prevention of C. difficile Infections

Klaus Gottlieb, M.D., FACG, Vice President, Clinical & Regulatory Affairs, Synthetic Biologics, Inc.

Microbiome research is currently dominated by sequencing efforts and hypothesis-free discovery. To date, hypothesis-driven translational efforts, e.g., a specific microbiome-directed intervention which results in a specific clinical benefit, are few. The presentation will provide an update on two clinical programs currently in development that demonstrate it may be possible to utilize established pathomechanisms, or mechanisms of action, in an entirely new way to protect the gut microbiome while targeting pathogen-specific diseases. Lead candidates in Phase 2 clinical trials and Phase 3 program development include: 1) SYN-010 which is intended to reduce the impact of methane producing organisms in the gut microbiome to treat an underlying cause of irritable bowel syndrome with constipation (IBS-C), and 2) SYN-004 which is designed to protect the gut microbiome from the unintended effects of certain commonly used intravenous (IV) beta-lactam antibiotics for the prevention of C. difficile infection and antibiotic-associated diarrhea (AAD).

12:10 pm Enjoy Lunch on Your Own

1:30 Refreshment Break in the Exhibit Hall with Poster Viewing


2:15 Chairperson’s Remarks

Susan Kling Finston, J.D./M.P.P., CEO, Amrita Therapeutics Ltd.

2:20 Targeted Delivery of Bacteriophage-Derived Lysins as Microbiome-Sparing Antimicrobials for Gastrointestinal Infection

Gerard Honig, Ph.D., Founder & CEO, Symbiotic Health, Inc.
Symbiotic Health is dedicated to addressing pressing unmet medical needs by combining insights from microbiome biology with innovative drug delivery engineering. Our lead candidate, SHP-01, is an ultra-targeted, ultra-rapid antimicrobial against C.difficile infection. Conventional antibiotic treatments for C.difficile infection injure and deplete the healthy gut bacterial ecosystem of the gut, increasing the risk of infection recurrence. SHP-01 is an engineered bacteriophage-derived lysin enzyme; lysins target carbohydrate cell wall structures which are highly pathogen-specific. As a result, lysin-based antimicrobials have the potential to eradicate pathogens with exceptional speed while sparing healthy gut microbiota. In order to address challenges which have limited the development of orally administered recombinant proteins, SHP-01 incorporates a novel polymer-based platform technology for delivery of proteins and bacterial cells to the lower gastrointestinal tract for local therapeutic action. The development of SHP-01 is an opportunity to demonstrate the general potential of an innovative and disruptive therapeutic strategy with applications in infectious disease and gastrointestinal pathologies.

2:50 Developing a Room Temperature Stable, Orally Delivered Microbiota-Based Drug for the Prevention of Recurrent C. difficile Infection

Matt Adams, Vice President, Technical Operations and Business Development, Rebiotix

Disruption of the intestinal microbiota by factors such as antibiotic use has been implicated in Clostridium difficile infection (CDI). Fecal microbiota transplantation (FMT) has been demonstrated as a very effective for preventing recurrences of CDI. However, product preparation and delivery can be burdensome. A room temperature-stable microbiota-based drug that could be delivered orally in capsules could greatly simplify many aspects of the therapy for patients and physicians alike. The formulation has the potential to increase availability and access to a non-antibiotic therapy for recurrent CDI that does not disrupt the intestinal microbiota. Additionally, the drug formulation has broader applicability to other indications and disease states. This talk discusses the development and validation of an oral room-temperature stable microbiota-based drug formulation and updates on a clinical study program both for the prevention of recurrent CDI and other indications.

3:20 Session Break

3:30 Catalyzing Safe Fecal Microbiota Transplantation: From Current Practices to Future Therapies

Zain Kassam, M.D., MPH, FRCPC, CMO, OpenBiome; Gastroenterologist, Epidemiologist and Research Affiliate, MIT Center for Microbiome Informatics & Therapeutics

Fecal microbiota transplantation (FMT) is a promising emerging therapy for the treatment of recurrent C. difficile infections (rCDI). FMT has already advanced significantly from a DIY therapy using minimally screened individual donors to a highly standardized process, using universal donors subject to rigorous screening. As an example of this transformation, OpenBiome, the first public stool bank, has delivered over 11,000 treatments to over 600 hospitals in 7 countries, with less than 3% of prospective donors passing the 178-point clinical assessment and 30-item laboratory screening panel required for enrollment. The field continues to evolve rapidly with new synthetic microbial therapies under development for rCDI, and a wide range of new indications emerging as targets for microbial engineering.


4:00 The Changing Legal Landscape for Microbiome Research

John M. Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina, Chapel Hill; Counsel, Robinson Bradshaw & Hinson

This presentation will review three sets of legal changes that will have a major impact on microbiome research in the next several years. These changes are occurring in patent law, making it much harder to get and enforce patents on both biological substances and analytic methods; in the Common Rule for protecting human research subjects; and in the U.S. and international law of privacy.

4:30 Microbiome, Industrial Product Development and Their Patent Protection: Key Emerging Issues

Ananda Chakrabarty, Ph.D., Department of Microbiology & Immunology, University of Illinois College of Medicine

The US patent laws are in the US Constitution (Article I, section 8, clause 8) to promote the progress of science and useful arts as well as to ensure that ingenuity should receive a liberal encouragement (Thomas Jefferson, 1793). As part of such Constitutional mandate, the US Supreme Court in the case Diamond v. Chakrabarty (447 US 303, 1980) boldly declared that ‘anything under the sun that is made by man’ is patent eligible in the US so long as it meets the statutory requirement of patentability. Since then many purified products of nature which were novel, non-obvious and with great utility not recognized before, including our bacterial anticancer protein azurin, and its peptide fragment p28, have been patented. A sea change has, however, occurred since the 2012 Supreme Court’s verdict in the case Mayo Collaborative Services v. Prometheus Laboratories, Inc. and the 2013 decision on Myriad Genetics BRCA gene patents (Association for Molecular Pathology v. Myriad Genetics) on inventions involving natural process, natural phenomenon or product of nature that appear to have imposed strict limitations on what are patentable subject matters under the US patent laws. Many microbiome-related inventions may fall under such legal limitations and prevent their marketing because of lack of patent protection, as illustrated by the recent CAFC decision on Sequenom v. Ariosa Diagnostics. This talk will deal with such issues to sensitize both academic/industrial researchers and entrepreneurs on the limits of patent protection for many microbiome inventions of great practical and industrial importance.

5:00 Q&A Discussion: Patent Eligibility Issues of Microbiome Innovations

This interactive discussion will provide attendees an opportunity to explore direct questions regarding patent eligibility of microbiome innovations and IP issues involved.

5:15 Close of Conference

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