APRIL 16-18, 2019

BOSTON, MA USA

 

2019 Conference Agenda

 
 
 
PRE-CONFERENCE WORKSHOPS
 
APRIL 16, 2019
 
2:30 pm Workshop I
Microbiome NGS and Hands-on Bioinformatic Data Analysis with Strain Level Resolution
This workshop for microbiome researchers is divided into two parts and covers the end to end microbiome workflow. Part I focuses on microbiome sample handling and sequencing. We will uncover sources of error and bias along the workflow and offer insight into best practices for quality control, validation and standardization. During Part II you will receive hands-on training in microbiome data analysis – no bioinformatics or scripting experience is required and participants are invited to bring their own laptop computers.

You will receive an in-depth introduction to the user-friendly CosmosID cloud platform and explore published datasets of therapeutic relevance. The following concepts will be covered in detail: taxonomic profiling at strain level, comparative analysis across cohorts, comparison of alpha- and beta-diversity, and analysis of the community-resistome and virulence. Additionally, our tutors will guide you through the resolution of real-life research questions using published datasets. The data deep dive will explore the effect of an experimental oral drug on the antibiotic-mediated dysbiosis published by Connelly et al.1
Workshop Leaders: Nur Hasan, Ph.D., Chief Scientific Officer, Cosmos ID; Arne Materna, Ph.D., VP Product, Cosmos ID 

 
3:15 pm Workshop II
Patenting in the Microbiome Arena
Using a patent disclosure and patent prosecution scenarios based on actual patent applications, this workshop, presented by a team of U.S. and European patent attorneys, provides an in-depth look at issues encountered in obtaining patent protection for microbiome-related technology, from invention disclosure to allowed patent claims and beyond. 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. 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. Key takeaways for participants include:
• Strategies for obtaining meaningful patent protection, from U.S. and EPO perspective
• How to claim an organism – patent eligible subject matter issues, tension between definiteness and breadth
• Establishing Freedom to Operate by defining your position, from search and analysis of competitor IP, to opinions of counsel and design-around options
Workshop Leader: Mark Fitzgerald, Ph.D., Partner, Nixon Peabody LLP
 
5:30 pm Workshop III
What Investors Want, What Investors Notice and Value in a Pitch - The Secrets to Successful Venture Pitching
Everyone knows entrepreneurs need to have great pitches – live oral presentations of their ventures. Entrepreneurs must be able to articulate their ideas in a “pitch” to all types of “catchers” in order to obtain all types of important start-up resources like early employees to join them with little or no pay, benefits or structure, or first customers who are not convinced of functionality or ability to deliver and of course investors who could provide them with critical early financing.

While most entrepreneurs know they need to have their venture ideas clearly presented in terms of what the idea is, how it was developed, and how protected it is, they may not know what specifically investors notice and value during the pitch that leads them to prefer some ventures over others. Investors proudly state they evaluate the market potential and the management team above anything else when considering whether or not to invest. But the evaluation of the pitch comes much earlier in the investment process and contributes to the investors’ assessment of whether or not the management team is one they would like to back. When asked, investors cannot state with certainty that there are no certain ‘rules’ or qualities that must be met when they watch entrepreneurs pitching.

The pitch remains a critical component of the investors’ decision to fund. Almost no investor would fund without watching the entrepreneur pitch his or her venture. The popularity of shows like Shark Tank and Dragon’s Den highlight our fascination with the entrepreneur pitch-investor interactions. And though the context is entrepreneurship, crafting effective pitches is a skill that can be applied by any manager across any category in business. In this session, learn what works and why when pitching to investors, and a chance to practice your pitch to make successful hits.
Workshop Leader: Lakshmi Balanchandra, Ph.D., Assistant Professor, Entrepreneurship, Blank Center for Entrepreneurship, Babson College, Founder, Women's Venture Capital Network
 
MAIN SESSION 
 
APRIL 17, 2019
 
7:15 am Registration/Continental Breakfast

7:45 am Chairperson's Opening Remarks
Mollie Roth, JD, Executive Director, The Microbiome Coalition

8:00 am Keynote Address: Microbial life at Scale: Applications, Analytics and Lessons Learned From the Food Supply Chain
This presentation will detail the work IBM Research has done with the Sequencing the Food Supply Chain Consortium to analyze food microbiomes to understand pathogens, community dynamics, and ingredient authentication using deep sequencing. We will also detail some of the challenges and solutions we've generated in applications, analytics, and reference data repositories to study microbial life at scale.
Kristen L. Beck, Ph.D., Research Staff Member, Sequencing the Food Supply Chain, Almaden Research Center, IBM

           

Sponsored by:

MAIN TRACK
          NUTRITION TRACK
8:30 am Biological, Chemical and Spatial Drivers of Microbiota Structure and Function: Therapeutic Implications
While fecal microbiota transplantation is highly effective for the treatment of recurrent Clostridium difficile infection, development of the next generation of therapeutics requires a deep mechanistic understanding of the dynamic host-microbiota relationship, as well as the inter- and intra-species relationships within the microbial community. We describe several basic research studies that are designed to elucidate the underlying biological, chemical, and spatial mechanisms that drive these relationships, the links to host physiology, and implications for microbial therapeutics.
Elliot 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
          8:30 am Bringing Probiotic Products from Bench to Market in the U.S.
Scientific and public interest continues to grow in the role of microorganisms in health maintenance as well as disease prevention and treatment. Consumers are looking for products with “good” or “helpful” bacteria to keep them healthy and marketers are looking for innovative new ways to deliver probiotics. The first stage of probiotic product development is determining if you intend to market a food, dietary supplement, or drug because each pathway to market is distinctly different and has a significant impact on the product development pipeline. This session will provide a topline discussion of the FDA regulatory requirements for bringing a probiotic product to market as a food, dietary supplement, or drug.
Andrew Shao, Ph.D., Sr. VP Scientific and Regulatory Affairs, Council for Responsible Nutrition

         
9:00 am Rapid Product Development: From Concept to Consumer Product
This talk will discuss BioCollective’s Approach to Rapid Probiotic/Prebiotic Prototyping using BioFlux™ Metabolic Modeling, existing extensive library of GRAS organisms/supply chain relationships, and small batch GMP production partners. Some of the most difficult challenges in formula development are:
• US Regulatory - GRAS status vs. new organisms (many organisms have similar functions - modeling can identify alternatives to deliver identical function with an already approved organism)
• Production - small batch photo-type product development, many vendors are already at maximum capacity and won’t do small production runs for prototyping-types
• Production - moving from small batch to scaled production
• Optimization - Organisms work as guilds, understanding the most synergistic combination can be simplified through metabolic modeling that closely mimics wet lab experiments
Martha Carlin
, Chief Executive Officer, The BioCollective
          9:00 am Supporting Infant Development by Supporting the Developing Microbiota
Infant development goes hand in hand with the development of the microbiota and thus provides a window of opportunity to support this development. Next generation sequencing and metabolomic techniques help us to understand what microbes reside in the gastrointestinal tract and what their metabolism is. This information may help us to optimize infant nutrition. This is already commonly done with probiotics and increasingly also with selected human milk oligosaccharides (HMOs). The use of next generation probiotics and combinations of HMOs may further improve the microbiota support and thereby infant development.
Arthur Ouwehand, Ph.D., Technical Fellow and Research Manager, DuPont Nutrition & Health

         
9:30 am The Skin is NOT the Gut: Optimizing DNA Extractions and Amplicon Sequencing for the Skin Microbiome
Most of the methods used in skin microbiome research have been borrowed from the gut field, often with little to no validation or optimization for skin microbes. I will discuss why this is problematic, with laboratory and clinical examples, as well as data-backed solutions for working with this distinctive community. Hint: I think we’ve been missing a lot!
Kelly N. Haas, Ph.D., Post Doctoral Scholar, Dermatology Department, University of California Davis
          9:30 am Perspectives on Future Success for Probiotics
Having spent the last 30 years in the probiotic field, Dr. Sanders has seen this area develop from being merely a fringe element to something that is very much part of the mainstream culture. But in order for it to continue to grow, companies must rely on something more tangible than simply asking consumers and medical professionals to trust them with respect to what’s in the bottle. Robust human clinical data and third party verification, akin to the USP label applied to vitamins and supplements, will be needed. Industry is poised to drive those standards. While safety may be presumed from prior use as a food or dietary supplements, next generation probiotics without evidence of safe use will need further safety assessment. Similarly the means to effectively communicate the benefits of this new generation of probiotics are required, with materials similar to ISAPPs infographics and videos, which are true to the science, targeted toward the educated lay person and professionals.
Mary Ellen Sanders, Ph.D., Principal, Dairy and Food Culture Technologies

         
10:00 am Networking/Refreshment Break           10:00 am Networking/Refreshment Break

         
10:30 am A Targeted, Point of Care Solution for Microbiome Analysis
In order for the microbiome field to realize its promise to revolutionize health and wellness, we must translate both diagnostic and therapeutic discoveries out of the lab and into the clinic. Floragraph is advancing this promise in two ways: 1. Developing technology that make microbiome analysis simple, reproducible, rapid and accessible, and 2. Creating novel panels of rationally designed microbiomarkers, empirically validated for significance in disease. We will present preliminary results of biomarker validation in early detection and characterization of necrotizing enterocolitis (NEC) in stool samples from very low birthweight infants in the NICU.
Alicia Scheffer-Wong, Ph.D., Founder & CEO, Floragraph
          10:30 am Panel Session: Probiotics: Aligning Science and Government Regulatory Requirements on a Path to Market
In this panel session, the following topics will be covered:
• What traits to look for when selecting strains for probiotic applications - how to select beneficial strains
• FDA regulatory path (GRAS) for probiotics
• How to progress product candidates from in vitro and in vivo testing into clinical investigation
• Interpretation of the clinical microbiome/probiotic data
Moderator: Maciej Chichlowski, Ph.D., PMP, Principal Scientist, Reckitt Benckiser
Panelists:
Andrew Shao, Ph.D., Sr. VP Scientific and Regulatory Affairs, Council for Responsible Nutrition
Arthur Ouwehand, Ph.D., Technical Fellow & Research Manager, DuPont Nutrition & Health
Mary Ellen Sanders, Ph.D., Principal, Dairy and Food Culture Technologies

         
11:00 am Lessons Learned: Translating Metagenomics into Clinical Routine
The microbiome plays a vital role in human health and disease yet cause and effect in the host-microbiome interaction often remain elusive. There is an emerging consensus among microbiome researchers that delineating host-microbe interactions requires a combination of high-resolution approaches for taxonomic profiling and methods that explore metabolic function. In this presentation we will focus on experimental and analytical challenges along the workflow from target discovery, validation to the production of microbiome-based therapies. We compare performance characteristics of different sequencing and bioinformatic methods and explore the importance of validation and standardization. Concluding, we will illustrate effective approaches using case studies related to the gut, oral and skin microbiomes.
Nur Hasan, Ph.D., Chief Scientific Officer, Cosmos ID
          11:15 am Use of the Probiotic Lactobacillus GG in Managing Food Allergies in Infants
Studies in Finland many years ago suggested that Lactobacillus GG might be useful in ameliorating or even reducing the risk of atopic dermatitis due to cow milk protein allergy in infants. Subsequently studies have demonstrated therapeutic efficacy in infants with allergic colitis. Further studies have suggested that Lactobacillus GG may be useful in stimulating the development of immune tolerance to cow milk protein in previously allergic infants at an earlier age, a benefit subsequently followed by a reduction in symptoms suggestive of irritable bowel syndrome as these children get older.
Jon A. Vanderhoof, Attending Physician, GI/Nutrition, Boston Children's Hospital, Senior Lecturer in Pediatrics, Harvard Medical School, Professor Emeritus of Pediatrics, University of Nebraska College of Medicine

         
11:30 am Panel Session: Enhancing the Power of the Microbiome Through Partnership
Partnership in any business is a crucial component to success. In the growing arena of microbiome therapeutics, partnerships between scientific, clinical, governmental and corporate teams lend credibility, flexibility and speed to the development of novel technologies. Join in the discussion about how partnerships can accelerate the microbiome field and push the boundaries of innovation to help a broader class of patients.
Moderator: Edward Burd, Ph.D., Head of Regulatory Affairs, Rebiotix
Panelists:
Malcolm Kendall, CEO and Co-Founder, Microbiome Insights
Lindy Bancke, Pharm.D., Head of Clinical Development, Rebiotix
Greg Fluet, Microbiome Partnerships & Commercialization, Ferring (Rebiotix)
Tonya Ward, Ph.D., Senior Scientist, CoreBiome
          11:45 am Feeding Our Babies and Their Bugs: Optimizing Nutrition in the NICU
Each year, nearly 10% of all infants are born too soon in the Unites States. These infants require care in the Newborn Intensive Care Unit (NICU), where the majority survive and thrive, experiencing better health outcomes than ever before. However, the increasing number of infants who survive prematurity has been associated with a growing population of children at risk for impaired growth and neurodevelopment. Optimizing nutrition and early growth of premature infants while in the NICU requires strategies that extend beyond the administration of ideal macro and micro nutrients. It also requires interventions focused on intestinal biology and overall gut health. Analysis of the preterm infant intestinal microbiome in the context of nutritional interventions and health outcomes provides a foundation on which we can develop the next generation of therapies, aimed at helping premature infants thrive across the lifespan.
Tracy Warren, CEO, Astarte Medical
             
12:15 pm Luncheon

1:15 pm Of Microbes and Monoamines: Stepping Stones from Dysbiosis to Psychiatric Disease
The microbiome is a rich target for drug discovery and therapeutic intervention, but in order for targeted approaches to be realized, a mechanistic understanding of the role of various microbial taxa is necessary. In an article recently accepted for publication at Trends in Neurosciences, S.D. Skolnick and Dr. Nigel Greig highlight three promising but largely overlooked metabolic pathways from the microbiome that have the potential to influence psychiatric and neurodevelopmental health. In this presentation, these pathways and their implications will be outlined in a manner appropriate for those with any level of neuroscience expertise, from layman to expert. Prospective research and challenges will be presented, and possible solutions discussed..
Stephen Skolnick, Translational Gerontology Branch, National Institutes on Aging, National Institutes of Health

1:45 pm Type 1 Diabetes: Primary Prevention Therapeutic Programs and First Pre-Autoantibody Biomarker Based on Association Between Autoimmunity and Dynamics of Amyloid-Producing E. Coli
We used a longitudinal microbiome analysis from Type 1 diabetic, HLA-susceptible children from birth to 3 years and analyzed it with an algorithm paying specific attention to gut amyloid-producing bacteria. Our analysis revealed an association between the development of autoantibodies in children with HLA-conferred susceptibility and significant (p<0.05) association between initially high gut amyloid-producing E. coli abundance among other things. Discovery of this new etiology and the mechanisms leading to autoimmunity in T1D that allowed us to develop novel biomarkers and a first-in-class diagnosis program of T1D in HLA-susceptible hosts.
George Tetz, MD, Ph.D., Chief Executive Officer, Human Microbiology Institute

2:15 pm The Human Microbiome: Towards Future Diagnostic and Clinical Solutions
The Human microbiome is a highly sophisticated system, much like the circulatory and immune systems, playing multiple roles within the human body. The most straightforward analysis of GI tract microbial compositions, “normal” and “deviated” (in case of various diseases) – is performed through sequencing of stool-derived DNA/RNA. The challenges associated with this approach include: stabilization of nucleic acids in the biological samples, minimization of bias upon DNA/RNA purification and sequencing, depletion of PCR inhibitors, process automation, and rapid “sample-to-answer”. All of these issues - and strategies around them - will be discussed in details. Ms. Jasti will overview the complete arsenal of tools enabling microbiota exploration, and highlight examples of workflow application towards studying effects of probiotics and diet on gastrointestinal tract bacterial populations, and rapid detection of pathogenic species.
Madhu Jasti, Scientist III R&D, Thermo Fisher Scientific

2:45 pm Strategies for Approaching FDA for Your First Clinical Trial
This talk will address common questions and concerns related to FDA Pre-IND meetings, including what the process is for requesting a meeting, when to approach FDA, what types of content to include and how to frame questions, and what types of outcomes can be expected.
Nicole Rempel, MS, MBA, Director of Regulatory & Strategic Development, Clinipace

3:15 pm Networking/Poster-Viewing/Refreshment Break

3:45 pm Developing Products to Unlock the Promise of the Microbiome in Health and Disease: A Novel Approach, Challenges and Common Opportunities
As the scientific knowledge of the microbiome grows and the tools to study it evolve so too does our understanding of the organ and its link to health and disease. Therapies directed at the microbiome organ are the next wave of medicines to be developed not only to treat diseases but also to maintain health and wellness. A number of different ways to target the microbiome are being developed, but there are also common learnings and knowledge that can inform the entire field as it continues to advance.In this presentation, Alison Lawton will discuss Kaleido’s unique chemistry-driven approach to leveraging the potential of the microbiome organ, and outline opportunities the field can address together to facilitate the development of safe and effective products aimed at targeting the microbiome.
Alison Lawton, Chief Executive Officer, Kaleido Biosciences

4:15 pm Panel Session: Confronting False Truths: On the Way to an IND, Is It Best to Avoid the FDA or Engage Early and Often?
There is a pervasive belief that engaging the FDA about your IND and clinical trial plans is something to be avoided lest you get locked into an approach you would prefer not to take. This panel brings together experts in the field of live biotherapeutic products (LBPs) that have first-hand knowledge working with the FDA to dispel this false narrative. Actual experience suggests that engaging early and often at the reviewer level actually allows the opportunity to walk through your thinking before you have gotten too far afield and have to invest more time and money in revising your approach or backtracking from it.
Moderator: Nikole Kimes, Ph.D., Founder and Chief Scientific Officer, Siolta Therapeutics

Panelists:
Susan Stewart, JD, Senior Vice President, Regulatory Affairs & Quality, Kaleido Biosciences
James R. Weston, Senior Vice President, Regulatory Affairs, Seres Therapeutics
Nicole Rempel, MS, MBA, Director, Regulatory and Strategic Development, Clinipace

5:00 pm The Asian Gut Microbiome: A New Therapeutics Discovery Opportunity
Almost 90 percent of the current translational microbiome research is focused on the Western gut microbiome. AsiaBiome has created the first horizontally integrated microbiome discovery platform in Asia. The company is linking together a microbiota bank, clinical network, and R&D discovery platform to launch microbiome products for both the Asia and global markets. They have strategic partnerships with Hong Kong University and the Genome Institute of Singapore. In this presentation Jonathan will discuss the following:
• How is the Asian gut microbiome different than the Western gut microbiome
• How does fecal microbiota transplant yield new drug discovery opportunities
• How the Asian gut microbes work in global population
Jonathan Krive, Co-Founder, CEO, AsiaBiome

5:30 pm Cocktail Reception
 
APRIL 18, 2019
 
7:30 am Continental Breakfast

8:00 am Keynote Address: Understanding the Role of the Microbiome in Cancer Immunotherapy
In this presentation, Dr. Wargo will describe known associations of the microbiome with response to immunotherapy in patient cohorts. She will also discuss putative mechanisms through which gut microbiota may influence immunity, and mechanisms to target them. Lastly, she will delineate the role of microbiota on toxicity to therapy, and highlight needs for the field as we move forward.
Jennifer Wargo, MD, Associate Professor, Department of Surgical Oncology, Division of Surgery, The University of Texas MD Anderson Cancer Center

             
MAIN TRACK
          TRACK TWO
8:25 am Integrative Analyses of Microbiota, Environment, Tumor, and Immunity for Precision Medicine
Any disease state including neoplasm represents fundamentally heterogeneous pathological processes due to cellular and molecular alterations and influences of the exposome (including the microbiome) and the immune system. To address this, the integrative scientific field of molecular pathological epidemiology (MPE) can investigate influences of the exposome (microbial, dietary, lifestyle, environmental, pharmacological, and other exposures) on tumor-immune interactions, thereby informing immunoprevention and immunotherapy research. Using over 1500 colorectal cancer cases with rich data on immune response, whole exome sequencing of tumor and normal DNA, tumor neoantigens, tissue microorganisms (e.g., Fusobacterium nucleatum), and clinical outcomes, our proof-of-principle microbiology-immuno-MPE studies have shown that several cancer risk factors appear to influence carcinogenic processes through their influences on tumor-microbial-immune interactions. These new research paradigms can provide possible paths for precision prevention and therapy.
Shuji Ogino, MD, Ph.D., MS, Chief, Program in MPE Molecular Pathological Epidemiology, Dept of Pathology, Professor of Pathology, Professor, Brigham & Women's Hospital, Dana Farber Cancer Insitute, Harvard Medical School, Harvard T.H. Chan School of Public Health
          8:30 am Ultra-high Resolution Microbiome Taxonomic Profiling Enabled by Novel High-throughput, High-resolution Assay Design
Strain level microbiome profiling is needed for a full understanding of how microbial communities influence human health. Microbiome profiling of rRNA gene amplicons is a well-understood method that is rapid and inexpensive, but standard 16S rRNA gene methods generally cannot differentiate closely related strains. Whole genome/shotgun microbiome profiling is considered a higher-resolution alternative, but with decreased throughput and significantly increased sequencing costs and analysis burden. Specialized microbiome-focused protocols were developed to achieve strain-level taxonomic differentiation using a rapid, high throughput rRNA gene assay. The protocol integrates lysis and DNA preparation improvements with a unique high information content amplicon and associated novel database to enable taxonomic differentiation of closely related microbial strains.
Mark Driscoll, Ph.D., Co-Founder and Chief Scientific Officer, Shoreline Biome

         
8:50 am Leveraging Gut Microbiota Networks to Impact Tumor Immunotherapy
In this presentation, Dr. Jayaraman will discuss the following:
• The concept of “reverse translation” as a strategy for microbiome drug discovery - Identification of a microbiome signature and its association with treatment and response
• Use of metagenomics and metabolomics to deconvolute functional fingerprints of complex ecology to identify specific species and strains
• Integration of computational strategies with empirical phenotyping and screening to drive drug design
• Designing compositions of microorganisms that form “functional ecological networks” and can impact response to therapy
Lata Jayaraman, Ph.D.
, VP, Oncology, Seres Therapeutics
          9:00 am Genomic Features: An Actionable Key for Gut Microbiota Modulation in Cancer Treatment
There is a growing body of research on the gut microbiome's correlation with the effectiveness of immune checkpoint inhibitor cancer therapies and specifically that a gut microbiota modulation may alter the response rate of checkpoint therapies. Actionable units - specific bacterial strains that can be used to modulate the gut microbiome - require the focus to be put on entities directly associated with specific functionalities. Ardigen demonstrates that the BiomeScout technology is able to build a study-specific catalog of genomic features allowing for the description of differences between responder and non responder groups. Such Genomic Features also make it possible to identify the strains responsible for the difference and could be used to design microbiome-derived therapies and diagnostics in the area of immuno-oncology.
Kaja Milanowska, Ph.D., Executive Vice President, Head of Immunology & Microbiome R&D, Ardigen

         
9:15 am Panel Session: Immuno-Oncology and the Microbiome - An Extended Q&A with the Morning’s Speakers
Moderator: Mollie Roth , Executive Director, The Microbiome Coalition
Panelists:
Jennifer Wargo, MD, Associate Professor, Department of Surgical Oncology, Division of Surgery, The University of Texas MD Anderson Cancer Center
Shuji Ogino, MD, Ph.D., MS, Chief, Program in MPE Molecular Pathological Epidemiology, Dept of Pathology, Professor of Pathology, Professor, Brigham & Women's Hospital, Dana Farber Cancer Insitute, Harvard Medical School, Harvard T.H. Chan School of Public Health
Lata Jayaraman, Ph.D., VP, Oncology, Seres Therapeutics
          9:30 am Multicenter Evaluation of the Role of Gut Microbiota in the Outcome of Hematopoietic Cell Transplant Patients
Allogeneic hematopoietic cell transplantation (allo-HCT) is a curative immunotherapy for hematologic malignancies. However, complications such as infection, graft-versus-host disease and relapse are barriers to a successful therapy. Gut microbiota of allo-HCT patients from four transplantation centers in three continents was evaluated in terms of its dynamics, injury over time and association with patient outcome. A microbiota signature trained in the largest could independently assess the mortality risk in the other cohorts. This work provides a multi-center understanding of microbiota and patient outcomes with promise for the development of biomarkers and therapeutic applications.
Antonio Gomes, Ph.D., Computational Biologist, Sr., Memorial Sloan Kettering Cancer Center

         
10:00 am Networking/Refreshment Break           10:00 am Networking/Refreshment Break

         
10:30 am New Modeling Tools to Predict Dynamics of Microbial Ecologies
This session will describe an ongoing collaboration between the Bucci Lab and Vedanta Biosciences to develop and experimentally validate new modeling tools to predict dynamics of microbial ecologies. The speakers will also present a specific application of the tools in the optimization of rationally designed bacterial consortia drugs.
Vanni Bucci, Ph.D., Assistant Professor, University of Massachusetts Dartmouth
Bernat Olle, Ph.D., Chief Executive Officer, Vedanta Biosciences
          10:30 am Panel Session: Reference Standards for Microbiome Research: Essential for the Clinic and Beyond
The implementation of well-characterized, homogeneous and stable reference materials in microbiome-based discovery is essential for robust and reliable results. The use of standards can facilitate product design and contribute to a more efficient evaluation of regulatory submissions, ultimately likelihood of funding and improving time to market. This open forum of discussion will address key issues in microbiome quality control and methods validations from the metagenomic, proteomic and bioinformatic perspective.
Moderator: Raul Cano, Ph.D., Chief Operating Officer & Scientific Director, The BioCollective
Panelists:
Nur Hasan, Ph.D., Chief Scientific Officer, Cosmos ID
Denise Kelly, Ph.D., Venture Advisor, Seventure Partners
Michael Weinstein, Ph.D., Scientist, Zymo Research

         
11:15 am Statistical and Computational Tools for Functional Microbiome
Human microbiome research is quickly moving towards functional microbiomics in order to understand how microbes in the human gut affect host immunity and physiology, disease initiation and treatment outcome. Alterations in microbiome-associated metabolite levels and small molecules may explain such associations. In this presentation, I will describe several new machine learning methods for (1) predicting and quantifying metabolic potentials of a microbial community using shotgun metagenomics data, (2) understanding the complex network of interactions between the intestinal mucosal immune system and the microbiome by integrating CyTOF and shotgun data. I will demonstrate the insights we gain from applying these methods to study IBD, infant early growth dynamics and effects of diet on host metabolism.
Hongzhe Li, Ph.D., Professor of Biostatistics and Statistics, Chair, Graduate Program in Biostatistics, Director, Center for Statistics in Big Data, University of Pennsylvania
          11:15 am Beyond Sequencing: Closing the Research Tools Gap in Microbiome Research
The rapid acceleration of research into the microbiome has highlighted a significant gap in the tool set necessary to thoroughly understand and characterize the role of microbes and microbial communities. Molecular techniques alone cannot provide all the answers we need to understand these complex, vibrant ecosystems. We need new tools to support research strategies that complement and validate insights generated by sequencing based approaches. A core need is the ability to cultivate and screen microbes at the efficiency and scale necessary to support functional and mechanistic studies using well characterized systems.
Peter Christey, Ph.D., Chief Executive Officer, General Automation Lab Technologies, Inc. (GALT)

         
11:45 am From Conceptualization to Launch: A Case Study of a GI Microbiome Modulator
Perhaps no other rapidly emerging space of innovation so confounds and comingles the disparate industries of nutrition and pharmaceuticals, as does the field of the microbiome. A collision of sorts is occurring now and will unfold over the coming years between the nutritional industry’s notions of the microbiome and the resultant emerging products with those of the pharmaceutical sector. Neither side seems fully prepared for the inevitable challenges and yet the prospects for breakthroughs and benefit are sufficiently high for strong optimism and commitment to the sector. The scientific insight and conceptualization of a potential therapy translated into a plan for scientific validation and regulatory compliance frequently runs in parallel with overcoming the hurdles of financing, and eventually, to product positioning, launch, marketing campaigns and consumer response. Such a life-cycle of any novel genre of product is usually tortuous and perhaps this has never been truer than with the emergent class of microbiome-derived products. The product life-cycle of one particular GI microbiome modulator will be reviewed in the context of these challenges from both the nutritional and pharmaceutical industry point of view.
Dale Pfost, Ph.D., Chief Executive Officer, MicroBiome Therapeutics, General Partner, Advent Life Sciences
          11:45 am Culture-Free Metagenomic Deconvolution, Plasmid-Host Association, and Strain Genome Assembly Using Hi-C Proximity-Ligation Technology
In this presentation, Dr. Liachko will discuss the application of Hi-C data to a number of diverse microbiome samples. For example, they have been able to discover hundreds of novel strains and species from fecal and infected samples, as well as identify novel plasmid/phage host interactions. They have also been able to identify the host for a number of AMR genes within novel species, underscoring the value of proximity-ligation data to microbiome research.
Ivan Liachko, Ph.D., Chief Executive Officer, Phase Genomics
             

         
12:15 pm Luncheon           12:15 pm Luncheon
             

         
1:15 pm A Survivor's Perspective: The Bigger Picture of the Patient Journey
Too often, manufacturers of therapeutics forget that the patient is more than simply someone taking a pill, but a person on an often long and arduous journey; a journey in which a therapeutics manufacturer can and often should become more than simply a supplier, but a trusted partner. In this presentation, Nancy C. Caralla, Founder of the C Diff Foundation and three time C difficile survivor, will share first-hand knowledge of one patient's journey that will bring needed perspective to the audience and new insights that should be front of mind for anyone developing new microbiome therapies.
Nancy Caralla, Founding President, Executive Director, C Diff Foundation
          1:15 pm Patenting in the Microbiome Arena
Using a patent disclosure and patent prosecution scenarios based on actual patent applications, this presentation provides an in-depth look at issues encountered in obtaining patent protection for microbiome-related technology, from invention disclosure to allowed patent claims and beyond.
Mark Fitzgerald, Ph.D., Partner, Nixon Peabody LLP
             

         
1:45 pm Beyond Bacteria: Harnessing the Virome to Improve Our Understanding of Human Health and Inform Diagnostic and Therapeutic Applications 
Although the human microbiome consists of broad diversity of bacteria, archaea, viruses, fungi, and small eukaryotes, the majority of human microbiome studies have limited their focus to bacteria. Viruses represent the most abundant group of organisms living in and on our bodies and are known to influence health and disease. Although our broader understanding of the virome is still being shaped, recent studies suggest that the human virome has the potential to be harnessed for both diagnostic and therapeutic applications. This presentation will address the challenges associated with virome sequencing and highlight virome applications.
Emily Hollister, Ph.D., VP, Information Technology & Analytics, Diversigen
          1:45 pm Working with a Major Healthcare Company to Mine for Health Specific Microbiome Profiles: A Small Biotech’s Perspective
Next generation microbiome profiling platforms like PMP™ combined with access to world-class microbiome Biobanks like HUNT in Norway makes novel microbiome profiles and biomarkers discovery related to various health conditions readily available. Bio-Me recently signed an agreement with a major consumer healthcare company to capitalize on this opportunity. In this presentation, Dr. Isaksen will cover some of the key aspects of this project and highlight some of the benefits that can be utilized for others seeking to uncover novel microbiome-related biomarkers to various diseases.
Morten Isaksen, Ph.D., Chief Executive Officer, Bio-Me
             
2:15 pm Microbial Signatures of Gut Wellness Through Multi-Study Integratlon of Human Stool Metagenomes
In this presentation, Dr. Sung will present results from a meta-analysis on an integrated, multi-cohort dataset of 4,347 publicly available stool metagenomes from healthy and non-healthy cohorts. Using probabilistic approaches that identifies frequent patterns across individual microbiome samples, I will show a set of microbial species and functions consistently observed within the healthy population, but not as frequent in disease. From these results, a gut microbiome health index, composed of multi-dimensional microbiome information, was developed to quantitatively assess the health status of a human gut.
Jaeyun Sung, Ph.D., Assistant Professor of Surgery, College of Medicine, Senior Associate Consultant I, Division of Surgery Research, Mayo Clinic
2:45 pm Networking/Poster-Viewing/Refreshment Break
 
3:15 pm Panel Session: Microbiome Discovery Needs Systems Biology Like Bricks Need an Arch: Building on Lessons Learned from Multi-omics Experimental Design and Computational Analysis
There has been a lot of talk about the need to move from associations to mechanisms of action, but not enough discussion about how to do this meaningfully. The aim of this panel is to positively shift the balance by highlighting opportunities and challenges ahead, and sharing some wisdom from industry and academia.
Moderator: Aaron Del Duca, VP Technology & Microbiome Program Lead, DNA Genotek
Panelists:
Stephan Reiling, Ph.D., Senior Fellow & Computational Scientist, Kaleido Biosciences
Annie Evans, Ph.D., Research and Development Director, Metabolon
Dan Knights, Ph.D., Professor, Department of Computer Science & Biotechnology Institute, University of Minnesota, Co-Founder, CoreBiome
David Riglar, Ph.D., Post-Doctoral Fellow (Silver Lab) Microbiome Engineering, Department of Systems Biology, Harvard Medical School

4:00 pm The First 1000 Days: Babies, Nutrition and Gut Health
Every time an infant is born marks the start of a new symbiosis between a human host and microbial communities that are essential for health. Microbial colonization patterns are partly determined by gestational age, delivery method, feeding practices, and many other, still poorly understood factors. There are numerous challenges in trying to deliver technology platforms to analyze the gut health and to optimize nutrition of preterm infants in the neonatal ICU and beyond. In this presentation, we will talk about the challenges in sample acquisition and processing, data analysis, and technical standards, both focused on our specific goals, as well as in the setting of current hopes and hypes of the microbiome field.
Katherine Gregory, Ph.D., Scientific Co-Founder, Astarte Medical, Assistant Professor of Pediatrics, Brigham & Women's Hospital

4:30 pm End of Conference
 
Please check back in the coming days for additions to this agenda. Join our mailing list and receive regular updates regarding this event. 
 

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Microbiome Analysis at Strain-Level: Study Design for Pre-Clinical and Clinical Drug Development

April 3, 2019 | 1:00 PM CDT

Learn about common challenges specific to microbiome studies and solutions along all phases of drug development using real-world examples.