[block background="#d3d3d3" color="#666" padding="15px" border="0" type=""]PRE-CONFERENCE WORKSHOPS [/block]
APRIL 18, 2018
1:15 pm pm Workshop I
Microbiome Characterization: Standards, Sequencing, and Bioinformatics
Bioinformatics is key to understanding and analyzing the microbiome. This workshop will give an overview of the power of bioinformatics in discovery, screening, diagnostics, and many additional aspects of microbiome analysis.
Workshop Leader: Nur A. Hasan, Ph.D., Vice President, Head of Research and Development, Cosmos ID
Workshop Leader: Manoj N. Dadlani, Chief Executive Officer, Cosmos ID
1:15 pm Workshop II
Scoping Out Patents in the Microbiome Arena
This workshop will allow participants to examine and better understand the challenges involved in protecting microbiome-related IP and strategies for overcoming them in both the U.S. and European Patent Offices (EPO), before applying these strategies in claims drafting and prosecution exercises using fact patterns drawn from actual patent file histories.
Workshop Leader: David Resnick, JD, Partner, Nixon Peabody LLP
4:00 pm Workshop III
The Microbiome, Mouse Models and Your Research
New roles of the microbiome are continuously being identified across a wide spectrum of diseases and conditions, highlighting the importance of advancing this research field.
Workshop Leader: Alexander Maue, Ph.D., Director Microbiome Products and Services, Taconic Biosciences
Workshop Faculty:
Barbara Rehermann, MD, Senior Investigator, Immunology Section, Liver Diseases Branch,, NIDDK, National Institutes of Health
Stephan Rosshart, MD, Postdoctoral Fellow, Immunology Section, Liver Diseases Branch, NIDDK, National Institutes of Health
Craig Franklin, Ph.D., Professor, Department of Veterinary Pathobiology, University of Missouri
6:30 pm Cocktail Reception
[block background="#d3d3d3" color="#666" padding="15px" border="0" type=""]MAIN SESSION [/block]
APRIL 19, 2018
7:15 am Registration/Continental Breakfast
7:50 am Chairperson’s Opening Remarks
Mollie Roth, JD, Executive Director, The Microbiome Coalition (TMBC)
8:00 am Keynote Address: Metagenome Diagnostics Across Earth and in Space
The avalanche of easy-to-create genomics data has impacted almost all areas of medicine and science, from cancer patients and microbial diagnostics to molecular monitoring for astronauts in space. Recent technologies and algorithms from our laboratory and others demonstrate that an integrative, cross-kingdom view of patients (precision metagenomics) holds unprecedented biomedical potential to discern risk, improve diagnostic accuracy, and to map both genetic and epigenetic states. Leveraging these data, the global profile of the world’s urban systems (MetaSUB.org) is being created to track the intra-city and inter-city shifts in antimicrobial resistance (AMR) markers. Finally, these methods and molecular tools work together to guide the most comprehensive, longitudinal, mutli-omic view of human astronaut physiology in the NASA Twins Study, which lay the foundation for future long-duration spaceflight, including sequencing, quantifying, and engineering genomes in space.
Chris Mason, Ph.D., Associate Professor, Department of Physiology and Biophysics, Weill Cornell Medicine, WorldQuant (WQ) Scholar, Director, WQ Initiative for Quantitative Prediction, Fellow, Information Society Project, Yale Law School
8:30 am Using DNA Methylation to Improve Metagenomic Analyses in Various Applications
DNA methylation is highly prevalent in bacteria yet had not been effectively studied in the context of microbiome analysis. Our recent work demonstrated that DNA methylation can be exploited as a natural epigenetic barcode to fundamentally improve the resolution and completeness of metagenomic analysis. Coupled with third-generation long read sequencing, this technology can resolve highly similar microbes into species and strains with megabase-long contigs associated with mobile genetic elements such as plasmids, directly from gut microbiome samples. This allows for improved analysis of microbiome samples that holds great promise in a variety of applications based on microbiome profiling or microbiome engineering with biomedical and clinical impact.
Gang Fang, Ph.D., Assistant Professor, Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
9:00 am Driving the Tidal Wave of Microbiome Discovery - a Next Generation Platform for Exploring the Microbiome
In order to transition our understanding of the microbiome from correlation to causation and mechanism, wet lab investigations with live isolates, model consortia and controlled systems will be critical to complement insights from NGS. However traditional lab research tools available to the microbiome researcher have barely developed in the last 100 years, and lack scale and performance required to rapidly acquire isolates of interest or to address microbiome level questions. There is a critical need for new improved research tools to drive our understanding of complex microbial populations and their interactions with their environment, such as a high throughput, array based microbiome research platform. Our current focus is solving two core problems in microbiome research: 1) rapidly cultivating target microbes that are difficult or impossible to cultivate using current technologies, and 2) rapid screening of microbiomes, strain collections or engineered populations of microbes for target phenotypes or metabolites.
Peter Christey, Ph.D., Co-Founder and Chief Executive Officer, General Automation Lab Technologies (GALT)
9:30 am A Microbiome-based Approach to Precision Medicine and Personalized Nutrition
Precision medicine and personalized nutrition has been hailed as the new wave in health treatment and prevention. The gut microbiome – with its vast amount of microorganism that influence the health of the individual – is an important component to consider in optimal precision medicine and personalized nutrition regimes. In order to obtain useful information from the gut microbiome to this end, the genus level resolution obtained with the standard 16S amplicon sequencing technology will not give sufficient information. The reason for this is that different species and strains within a genus may have different characteristics, and may independently be up- or down-regulated to varying decrees. Bio-Me is developing GutCheck™, a high resolution, accurate, high throughput and low cost gut microbiome analysis platform. This talk will highlight some initial data from the development of this test, and point out possible useful applications within Precision Medicine and personalized nutrition.
Morten L. Isaksen Ph.D., Chief Executive Officer, Bio-Me AS
10:00 am Refreshment/Poster Viewing/Networking Break
MAIN TRACK
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CONSUMER TRACK
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10:30 am Translational Challenges in the Skin Microbiome
The skin microbiome plays a fundamental role in human health, and novel strategies have emerged to harness the skin microbiome to treat a plethora of diseases. Translating research to a commercial product, however, has particular issues in the skin, particularly in regulatory strategy, manufacturing and formulation activities, and commercialization strategy. These are even more complicated with a genetically modified LBP, which presents additional hurdles to the translational activities in the microbiome. All of these issues--and strategies around them--will be discussed in detail.Travis Whitfill, MPH, Co-Founder, Chief Scientific Officer, Azitra, Inc.
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10:30 am Presentation Title to be Announced
Robin Temmerman, Ph.D., Chief Executive Officer, Chrisal N.V.
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11:00 am Impact of Microbiome on Immunotherapy Response
While cancer therapy has benefitted greatly from immune checkpoint blockade agents, responses are variable and not always sustained. It has been well established in murine models that the gut microbiome can be modulated to enhance responses to immune checkpoint blockade. How do we strategize the timing of therapy for patients that have received antibiotics in order to avoid negatively impacting their gut bacteria? How do certain foods impact the gut bacteria and, subsequently, response to therapy? Should scientists be assessing the gut microbiome in pre-clinical models that are used to test therapeutic approach against cancer? And can the microbiome be manipulated to enhance the body’s immunosurveillance and prevent cancer altogether? In this presentation, Dr. Gopalakrishnan will address these questions and discuss ways in which the microbiome can be modified in clinical practice.
Vancheswaran Gopalakrishnan, Ph.D., Translational Scientist, Computational & Analytics Support, MD Anderson Cancer Center, The University of Texas Health Science Center at Houston
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11:00 am Using Live Bacteria for Topical Skin Application: Regulatory Issues
Our skin serves as a protective layer against external influences. Due to recent advances in NGS, the amount of data on the importance of the skin microbiome is rising. Use of products with live beneficial bacteria, also called live biotherapeutic products (LBPs), have the potential of improving symptoms of a multitude of skin disorders. The safety of our probiotic strains was the most important aspect during the in vitro screening phase. All the YUN strains were therefore thoroughly characterized at the strain level. Products with live probiotic strains were evaluated clinically to underline their level of safety for topical application on the skin. By building up the safety documentation and quality controls in the production of our products, they could be notified to EU authorities and placed safely on the market. It is therefore clear that safety is the most important aspect for LBPs and should always be addressed correctly. The added therapeutic benefits of these products for topical skin application might be the future for addressing specific skin disorders by using carefully selected probiotic strains.
Ingmar Claes, Ph.D., Chief Scientific Officer, Yun Probiotherapy
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11:30 am Panel Session: Microbiome and Cancer Therapies
This panel will consider and discuss:
• Can the microbiome be a predictor of cancer therapy outcomes?
• What is the role of the microbiome within the tumor microenvironment?
• Can the microbiome be a co-therapy to existing cancer therapies?
• Can the microbiome be modulated to make existing cancer drugs work better?
• What types of studies/trials should we do?
Moderator: Take Ogawa, Director Marketing, Second Genome
Panelists:
Deepak Gopalakrishnan, Ph.D., Translational Scientist, Computational & Analytics Support, MicrobiomeDx
Dario Gutierrez, Ph.D., Immuno-Biology Lead, Merck Exploratory Science Center
Bernat Olle, Ph.D., Chief Executive Officer, Vedanta Biosciences
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11:30 am Presentation Title to be Announced
Maciej Chichlowski, Ph.D., Principal Scientist, Mead Johnson Nutrition
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| 12:15 pm Luncheon |
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12:00 pm Luncheon |
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1:15 pm Reverse Translation for Therapeutic Development in the Human Microbiome
To date, one of the great challenges of translational research in the microbiome has been the interpretation of correlations observed in human cohort studies or causal relationships observed in murine models. However, with the increasing abundance of clinical interventional data from experience with fecal microbiota transplantation (FMT), there is an opportunity to develop therapeutic insights directly from clinical observations. Finch Therapeutics is deploying its platform for identifying microbial therapies from observing patterns of microbial engraftment that drive clinical responses to develop a new generation of Rationally Selected Microbiota therapies.
Mark Smith, Ph.D., Chief Executive Officer, Finch Therapeutics |
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1:00 pm Panel Discussion to be Announced |
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1:45 pm Novel Therapeutic Approach To IBD Through Microbiome Modulation
Whereas existing medications for IBD offer symptomatic relief to the chronic, lifelong condition of the disease, BiomX’s IBD program addresses a potential cause of the disease, and thus holds the promise for a disease-modifying treatment. Using its advanced discovery and development capabilities in phage therapy, BiomX is advancing BX002, a phage composition customized to specifically target and eradicate the IBD associated pro-inflammatory gut bacteria. In this presentation we will share multiple challenges for developing a novel therapy, including understanding FDA guidelines, deciding on the phase I clinical setting for a proof of mechanism, identifying the target patient population and meeting GMP standards to establish a final customized therapy which addresses potential bacterial resistance.
Assaf Oron, Chief Business Officer, BiomX |
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1:45 pm Presentation to be Announced |
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2:15 pm Probiotics For Serious Medical Conditions; How To Select The Right One
There has been a significant surge in the use of probiotics around the world in recent years in many conditions with claims spanning from “feeling good” to reducing infections and serious inflammatory conditions affecting many organ systems. While some claims are soft, there is a concomitant increase in scientific enquiry to back some of these evidences. Dr. Panigrahi will discuss results of a recently published large clinical trial of a synbiotic preparation using L. plantaum and fructo-oligosaccharide that reduced neonatal sepsis by 40% in India. Unexpected reduction in lower respiratory tract infections led to early demonstration of efficacy and termination of the trial. It is intriguing to question the mechanism(s) of action of the probiotic strain used in our trial as we question the role of microbiome and changes in the gastrointestinal milieu in newborns and developing young infants. Although speculative, our data as well as that available in the literature strongly points toward immunomodulation by such early microbial exposures. A reverse immunology approach in repeat trials will shed light on the mechanisms of action of these observations.
Pinaki Panigrahi, MD, Ph.D., Professor, Department of Epidemiology and Pediatrics; Director of Center for Global Health and Development, University of Nebraska Medical Center, College of Public Health |
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2:15 pm Presentation to be Announced |
2:45 pm Refreshment/Poster Viewing/Networking Break
3:15 pm Presentation Title to be Announced
Dr. Stefan Jennewein, Managing Director, Jennewein Biotechnologie GmbH
3:45 pm Effects of the Microbiome on Clinical Responses to Cancer Therapeutics and Vaccines
Numerous preclinical and clinical studies have shown that the microbiome is the newly-discovered “organ” that is involved in numerous aspects of fundamental physiology and pathology. Recent discoveries are starting to shed the light on the precise mechanisms by which the microbiome regulates both innate and adaptive immune responses, and are beginning to appreciate why and how this regulation affects disease initiation, progression, and treatment response. However, most current studies are performed using rodent animal models discoveries in which often fail to translate into human therapies. At the Merck Exploratory Science Center (MESC) in Cambridge we are using a systems biology approach to integrate human and microbiome pathways using well-curated clinical data to identify molecular mechanisms by which the microbiome regulates responses to vaccines and cancer immunotherapy.
Olga Danilchanka, Ph.D., Microbiome Lead, Exploratory Science Center,Merck & Co.
4:15 pm Panel Session: Talking the Talk and Walking the Walk with Investors: Best Practices For When Microbiome Meets the Street
Moderator: Chris Shibutani, MD, Managing Director, Heathcare-Biotechnology, Senior Research Analyst, Cowen, Inc.
Panelists:
Jeffrey M. Solomon, Chief Executive Officer, Cowen
Others to be Announced
5:00 pm From Dysbiosis to Recovery in the Infant Gut Microbiome
Over 20 years of research at the University of California at Davis has established that the natural microbiome of the human infant is dominated by a single commensal species through its unique and dominant ability to consume Human Milk Oligosaccharides (HMOs). Astonishingly, this natural microbiome has changed slowly, but extensively over the past 100 years due to the near extinction of this commensal species through the unintended consequences of extensive infant formula use, the multigenerational use of antibiotics, and recent increases in the C-section rate. We have now established that this new pandemic dysbiosis in gut of infants in developed nations can be returned back to the natural state simply through the reintroduction of this natural dominant commensal into the population along with breast-feeding or otherwise supplying HMOs to the infant. This new data now sets the path forward to a major worldwide reestablishment of the natural infant microbiome over the next few years.
David Kyle, Ph.D., Chief Scientific Officer, Evolve Biosystems
5:30 pm Cocktail Reception
APRIL 20, 2018
7:15 am Continental Breakfast
8:00 am Keynote Address: The Human Skin Microbiome: Metagenomes to Therapeutics
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 for rational design of engineered microbial therapeutics that can precisely target an underlying etiology, a pathogen of interest, or enhance immunomodulatory properties.
Julia Oh, Ph.D., Assistant Professor, Jackson Laboratory
8:30 am Known Unknowns - An Outsiders Perspective On The Cost Of Being at The Forefront Of Biotech's New Chapter
This talk will focus on two pain points of being a new entrant into the microbiome industry. First, the impact of being an outsider and an amateur in the space and the cost it played on two young biotech founders. Second, the cost of working in an industry filled with so much uncertainty and of being among the few in the space that's pushing forward with new forms of medicines in a world slowed down by speculations and regulations.
Adham Alijahmi, CEO and Co-Founder, Blue Turtle Bio
9:00 am Panel Session: Startup 101: Navigating the Pitfalls and Perils of Microbiome Translation and Commercialization
The potential of the microbiome to affect the entire spectrum of health and disease makes it an unprecedented investment opportunity, but challenges remain in translating science into commercialized products. Determining the proper partner, both from an investor and start-up perspective, is paramount to overcoming the translational roadblocks on the way to market. This panel will share insights into the future of the microbiome industry, how to navigate the investment landscape and what investors look for in an emerging company.
Moderator: Dirk Gevers, Ph.D., Global Head, Janssen Human Microbiome Institute, Janssen Research and Development
Panelists:
Marian Nakada, Ph.D., Vice President, Venture Investments, Johnson & Johnson Innovation
Denise Kelley, Ph.D., Investment Advisor, Seventure Partners
Adham Aljahmi, CEO and Co-founder, BlueTurtle Bio
9:45 am Refreshment/Poster Viewing/Networking Break
MAIN TRACK
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NUTRITION TRACK
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10:15 am Rodent Microbiomes and Their Role in Pre-clinical Reproducibility, Translatability, and Discovery
The gut microbiome is now recognized as a key factor in host susceptibility to many different diseases and conditions. Similarly, the microbiome of research animals is an integral part of mouse and rat model phenotypes and recent data suggest that inadvertent changes in the composition of the microbiota might explain lost or altered phenotypes. From a translational standpoint, there is also reason to believe that traditional sources of research animals and husbandry practices limit the richness and antigen experience, thus implying a need for methods of working with alternatively sourced animals while maintaining biosecurity. This presentation will provide data on seemingly benign factors capable of altering the microbiota of research rodents and provide real-world examples, explore important considerations regarding the use of “dirty mice” in a research setting, and describe methods of turning instances of poor reproducibility into opportunities for discovery.
Aaron Ericsson, DVM, Ph.D., Assistant Professor, University of Missouri, College of Veterinary Medicine, Director, Missouri University Metagenomics Center |
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10:15 am Eating for Two: Developing Nutritional Interventions and Naturally-derived Products that Consider Host and Microbial Requirements for Improved Human Health
The design of new nutritional measures and therapies will be advanced through an integrated approach incorporating knowledge of host nutrition, GI biology, our bacterial symbionts and the many intersecting metabolic pathways. The presentation will summarize ongoing efforts to develop nutritional interventions for IBD, the use of traditional Chinese botanicals to develop drugs for GI health and the mining of bacterial culture collections for beneficial strains.
Paul Giannasca, Ph.D., Global Scientific Lead, GI Health, Nestle Health Science |
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10:45 am ATCC Microbiome Standards: Addressing the need for Standardization in Microbiome Research
The complexities involved in 16S rRNA and shotgun metagenomic analysis methods pose significant challenges for microbiome research. Significant biases can be introduced during sample preparation, DNA extraction, PCR amplification, library preparation, sequencing, or data interpretation. One of the primary obstacles in assay standardization is the limited availability of reference materials. To support this need, ATCC has developed microbiome reference standards from fully sequenced and characterized ATCC strains that were selected on the basis of phenotypic and genotypic attributes or their availability in clinical or natural environments. To further enhance the use of microbiome reference standards and eliminate the bias associated with data analysis, we have also developed a data analysis module in collaboration with One Codex that provides simple output in the form of true-positive, relative abundance, and false-negative scores for 16S rRNA community profiling and shotgun metagenomic sequencing.
Dev Mittar, Ph.D., Lead Scientist, American Type Culture Collection (ATCC) |
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10:45 am Diet, the Gut Microbiome, and its Metabolome in Inflammatory Bowel Disease: Therapeutic Opportunities
The environment of the gut, namely the microbiota and diet, plays an important role in the pathogenesis of the inflammatory bowel diseases (IBD) that afflict approximately 3 million patients in the U.S. alone. Characterization of the impact of diet on both the composition of the gut microbiota as well as the metabolites that are produced might lead to the discovery of alternative strategies to treat IBD by engineering the environment of the gut. Using defined formula diets as a therapeutic probe, we describe several human subject studies that are designed to help determine better diets for patients with IBD that can be used to treat and/or prevent the recurrence of active disease.
Elliott Friedman, Ph.D., Senior Research Investigator, Division of Gastroenterology, Technical Director, Microbial Culture & Metabolomics Core, PennCHOP Microbiome Program, Perelman School of Medicine, University of Pennsylvania
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11:15 am Gut Check, Scoping Out Patents and the Microbiome
Patent protection is key to thriving in the microbiome space and is possible with careful drafting and consideration of what is allowed by the PTO. This presentation will discuss the challenges involved in protecting microbiome-related IP and strategies for overcoming them in both the U.S. and European Patent Offices (EPO). Issues commonly encountered in technology commercialization will be considered, including establishment of a Freedom-to-Operate position and options for challenging competitors’ IP in the U.S. and EPO, before turning to an examination of challenges and benefits of working with academic institutions from an IP perspective.
David Resnick, JD, Partner, Nixon Peabody LLP |
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11:15 am Presentation to be Announced
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| 11:45 pm Microbiome Engineering For Disease And Wellbeing
Dr. Guell will present details regarding S Biomedic's experience using the natural microbiome for modulating the skin disease and well-being.
Marc Guell, Ph.D., Co-Founder and Non-Executive Director, S Biomedic
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11:45 am Panel Discussion to be Announced |
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| 12:15 Luncheon |
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12:30 pm Luncheon |
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1:15 pm PANEL SESSION: What Should Be the Role of Evidence Based Data in Microbiome Drug Development?
Regulatory decisions around FMT and stool banks operating in the space have substantial implications for microbiota drug development. The value and use of evidence based medicine as it pertains to Randomized Controlled Trials (Level 1 clinical data) has become a hot topic. Beyond simply impacting the trajectory of drug development, the decisions (or non-decisions) being made also raise questions as it pertains to patient safety and outcomes data. This panel will explore:
• How critical regulatory decisions are impacting microbiome drug development
• The value of Randomized Controlled Trials in microbiome drug development
• The impact of those decisions on patient safety considerations in microbiome drug development
Moderator: To be Announced, Rebiotix
Panelists: To be Announced |
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1:30 pm Presentation to be Announced |
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2:00 pm Microbiome Characterization: Standards, Sequencing, and Bioinformatics
Bioinformatics is key to understanding and analyzing the microbiome. This presentation will provide an overview of the power of bioinformatics in discovery, screening, diagnostics, and many additional aspects of microbiome analysis.
Manoj Dadlani, Chief Executive Officer, CosmosID |
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2:00 pm Presentation to be Announced |
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2:30 pm Powering Microbiome Discovery with Big Data
The gut microbiome is an important determinant of health. Important next steps include shotgun metagenomics sequencing to determine key microbial genes and enzymes related to performance. This talk will show that shallow shotgun sequencing of 500K-1M reads/sample matches ultra-deep sequencing for species-level taxonomic and functional annotation and biomarker discovery, allowing researchers to increase power by sequencing more samples per study.
Dan Knights, Ph.D., Chief Executive Officer, CoreBiome
3:00 pm Refreshment/Poster-Viewing/Networking Break
3:30 pm Panel Session: Addressing Reproducibility Challenges in Microbiome Research: Wet and Dry-Side Approaches
Next-generation sequencing (NGS) is increasingly the primary analytical method in microbiome research. However, while the depth of information NGS provides is immense, the data itself is large, complex, and often contains errors and significant biases introduced before, during, and after sequencing. Further complications include irreproducible bioinformatics pipelines and related computational challenges. Collectively, these deficiencies pose enormous barriers to reproducibility and validation. This panel will focus on reproducibility across “sample to answer” microbial NGS workflows: ranging from sample collection to library prep and sequencing to informatics and reporting. It will cover both challenges with current approaches, emerging standards and best practices, and new techniques for improving the reproducibility of microbiome studies.
Moderator: Kashef Qaadri, VP, Marketing, One Codex
Panelists:
Alex Kostic, Ph.D., Assistant Professor, Joslin Diabetes Center, Harvard Medical School
Aaron Del Luca, Vice President, Technology, Head, Microbiome Business Unit, DNA Genotek
Jillian DeWalt, Co-Founder, Head of NGS and Discovery Lab, Solarea Bio
4:15 pm Promoting Peak Performance: Identifying and Isolating Novel Probiotics From Athlete Microbiomes
Over the past two years Harvard University has recruited and sequenced the microbiome of athletes to identify the bacteria associated with peak performance and recovery. The work reveals unique differences between the microbiomes of athletes and non-athletes, as well as bacteria that change before and after athletic events. This has led to the identification of novel probiotic candidates with the potential to promote recovery and energy metabolism. Based on this work Jonathan describes the specific microbial profile of elite athletes and how probiotics can enhance their performance. His presentation will share:
• Results of pre-clinical studies into a novel probiotic candidate that can break down lactic acid
• Evidence for athletes’ distinct microbial communities and the dynamic behavior of those communities during sports performance and recovery
• How next-generation sequencing can identify novel probiotic species and strains
Jonathan Scheiman, Co-Founder, Fitbiomics
4:45 pm End of Conference
