Session Abstract – PMWC 2022 Silicon Valley


Track Chair:
Manoj Dadlani, CosmosID

Understanding mechanism of action and translating microbiome science into commercially viable therapeutics remains the biggest challenge in this emerging field. With that said, pharma and biotech across many different therapeutic indications and modalities are united in this global effort to bring novel microbiome-based therapies and diagnostics into the clinical domain. This session will include some of the most impactful and promising areas of the Microbiome field and panel discussions on the challenges for faster adoption.

    Sessions:
  • Regulatory Perspective
    - Scott Jackson, NIST
  • Pharma Drug Development
    Session Chair: Karim Dabbagh, Second Genome
    - Matthew Henn, Seres
    - Rangaprasad Sarangarajan, Metabolon
  • AI in Microbiome
    - Kaja Milanowska-Zabel, Ardigen
  • Direct-To-Consumer Testing/Technologies
    Session Chair: Nathan D. Price, Onegevity
    - Kiran Krishnan, Microbiome Labs
    - Emmanuel Hanon, Viome
    - Nicole Scott, Cybele Microbiome
  • Microbiome and Cancer
    - Sandrine Miller-Montgomery, Micronoma
  • The Role of the Human Gut Microbiome on Various Diseases
    - Colleen Cutcliffe, Pendulum Therapeutics
    - Tor Savidge, Baylor College of Medicine
    - Nikole Kimes, Siolta Therapeutics
    - Sarkis Mazmanian, Caltech
  • The Gut/Brain Microbiome
    - Mary Conrad, Axial Biotherapeutics
    - Rosa Krajmalnik-Brown, Arizona State University
    - Christopher Reyes, Bloom Science
  • Synthetic Biology in Microbiome
    - Jeff Hasty, UCSD
  • Showcase
    - Heloise Breton, DNA Genotek

 Session Chair Profile

Ph.D., President and CEO, Second Genome Inc.

Biography
Karim Dabbagh joined Second Genome in 2014. Prior, he served as Vice President of R&D at Pfizer where he led the Immunoregulation department, an R&D group focused on innovative approaches to elicit homeostatic immune responses for the treatment of immune related disorders. At Pfizer, he also led External R&D Innovation for Immunology, Neurosciences and Cardiovascular/Metabolic Therapy Areas. Before joining Pfizer, Karim was the founder of Modus BioMedicine, a biotechnology company focused on treatments for transplantation and autoimmune disease. Leading to that, Karim spent nine years at Roche in Inflammation Discovery Research. Karim obtained his PhD in Biochemistry from University College, London and his BSc (Hons) in Biotechnology from Imperial College, London. He completed postdoctoral fellowships at the Cardiovascular Research Institute at the University of California, San Francisco and at Stanford University where he worked on elucidating the role played by the microbiome in the hygiene hypothesis.


 Session Chair Profile

Ph.D., CEO, Onegevity, A division of Thorne HealthTech; Professor, Institute for Systems Biology

Biography
Dr. Nathan Price is the CEO of Onegevity, a division of Thorne HealthTech. In 2019, he was selected as one of 10 Emerging Leaders in Health and Medicine by the National Academy of Medicine.  He is also an (on leave) Professor at the Institute for Systems Biology, where he co-directs with Lee Hood the Hood-Price Lab for Systems Biomedicine.  He is Affiliate Faculty at the University of Washington and a previous co-founder of Arivale.  He is a Camille Dreyfus Teacher-Scholar, a Fellow of the American Institute for Medical and Biological Engineering, and received a 2020 Healthy Longevity Catalyst Award from the National Academy of Medicine.


 Session Chair Profile

Ph.D., MSC, DSC, Distinguished University Professor, University of Maryland College Park and Johns Hopkins Bloomberg School of Public Health, President, CosmosID, Inc.

Biography
Rita R. Colwell is a Distinguished University Professor at the University of Maryland and at the Johns Hopkins University Bloomberg School of Public Health. Colwell’s research interests are focused on global infectious diseases, water and health. She is currently developing an international network to address emerging infectious diseases and water issues, including safe drinking water for both the developed and developing world. Colwell served as the 11th director of the National Science Foundation from 1998 to 2004. Her major interests include K–12 sciences and mathematics education, graduate science and engineering education, and the increased participation of women and minorities in science and engineering. She has held many advisory positions in the U.S. government, nonprofit science policy organizations and private foundations, as well as in the international scientific research community. She is a member of the National Academy of Sciences, the Royal Swedish Academy of Sciences, Stockholm, the Royal Society of Canada, the American Academy of Arts and Sciences, and the American Philosophical Society.


 Speaker Profile

Ph.D., Leader – Complex Microbial Systems Group, National Institute of Standards and Technology

Biography
Scott Jackson joined NIST in May of 2014 after 11 years as a principal investigator with the FDA. At FDA, his research focused on characterizing the global genomic diversity of enteric pathogens, with applications for food safety, bioforensics and public health. At NIST, Scott is currently the leader of the Complex Microbial Systems Group in the Biosystems and Biomaterials Division. In this current role, Scott is leading efforts to improve microbiome and metagenomic measurements by organizing inter-lab studies, developing reference materials and reference methods, and developing in vitro tools that allow us to better understand microbial community resilience and evolution. Scott completed his PhD research in the biochemistry and biophysics departments at The University of Maryland and Johns Hopkins University, respectfully, where he focused on the evolution of mobile genetic elements using yeast as a model genetic organism. Scott performed huis undergraduate studies in Chemistry and Geology at the University of South Carolina.


 Speaker Profile

Ph.D., EVP, Chief Scientific Officer, Seres Therapeutics

Biography
Matthew Henn has over 20 years of combined research experience in microbial ecology, genomics and bioinformatics that spans both environmental and human disease applications. He has been involved in the discovery and clinical development of multiple microbiome therapeutics including all of Seres’ product candidates and has authored over 65 peer-reviewed publications. His research has focused on microbial physiology and the functional role of microbes in both environmental and human disease applications, and on the development of genomic and functional tools to study microbial systems. Prior to helping launch Seres in 2012, he was the Director of Viral Genomics and Assistant Director of the Genome Sequencing Center for Infectious Diseases at the Broad Institute of MIT and Harvard. He has served on various NIH working groups on antimicrobial resistance and microbiome research, as a scientific advisor for NIH’s Viral Pathogen Bioinformatics Resource Center, and as an ad-hoc reviewer and editor of various peer-reviewed journals. He currently serves on the scientific advisory board of Growcentia, Inc., an agricultural microbiome company.


 Speaker Profile

Ph.D., Executive Vice President & General Director of Microbiome Unit, Ardigen

Biography
Dr. Kaja Milanowska-Zabel is a microbiome enthusiast and a bioinformatics researcher. Her personal and professional ambitions led her to exploit the importance of microbiome in human health. In 2016, Kaja joined Ardigen and started research activities in the microbiome space primarily in the area of oncology. In 2018, after becoming one-third of Ardigen’s management board she took over a position of responsibility of the R&D projects. Kaja’s previous professional experience includes the position of assistant professor at the Department of Molecular and Systems Biology, The Institute of Bioorganic Chemistry of the Polish Academy of Sciences in Poznań, and the Department of Gene Expression at the Institute of Molecular Biology and Biotechnology at the University of Adam Mickiewicz in Poznań. Currently, Kaja is a General Director of a Microbiome Business Unit putting all her powers, passion and belief, that with an in-depth, data-science aid approach we can make a difference by decoding the microbiome to help patients.

Talk
Decoding Microbiome with Artificial Intelligence
AI is used in different microbiome research challenges, from signature discovery and time point analysis, to multi-omics, interpretability and more. Thanks to ML methods we are on the path to demystify the complexity of microbiome to unlock the secrets of the data.


 Speaker Profile

Ph.D., VP, Research & Development, Metabolon

Biography
Dr. Foster leads the software engineering, data science, IT operations, and biostatistics teams and guides data strategy. His teams build AI applications that enable and enhance Metabolon’s industry-leading capabilities. He holds a Bachelor of Science in Physics from Duke University and a Ph.D. in Physics from the University of Calgary.


Microbial Profiling Showcase:
Metabolon

Metabolon, the global leader in metabolomics, has a mission to deliver metabolomics data and insights that expand and accelerate the impact of life sciences research. Our industry-leading data helps to address challenging and pressing questions - accelerating research and development success.

 Speaker Profile

Co-Founder and CSO, Microbiome Labs

Biography
Mr. Kiran Krishnan is a Research Microbiologist and has been involved in the dietary supplement and nutrition market for the past 20 years. Kiran established a Clinical Research Organization where he designed and conducted dozens of human clinical trials in human nutrition. Most recently, Kiran is acting as a Co-Founder and the Chief Scientific Officer at Microbiome Labs, a leader in microbiome and probiotic research. He is a frequent lecturer on the Human Microbiome at Medical and Nutrition Conferences. He is an expert guest on National Radio and Satellite radio and has been a guest speaker on several Health Summits as a microbiome expert. He is currently involved in over 18 novel human clinical trials on probiotics and the human microbiome. Kiran is also on the Scientific Advisory Board for 7 other companies in the industry. Kiran has published clinical trials in peer-reviewed, scientific journals and several global patents in his name.


 Speaker Profile

Ph.D., Global Head of R&D, Viome

Biography
As Global Head of R&D for the vaccine group at GSK, Dr. Hanon oversaw more than 3,500 employees across 50 countries dedicated to delivering discovery, development and management activities for the company's vaccine efforts. Dr. Hanon was responsible for the shared science and technology platforms supporting the entire vaccine business, managing technical development, clinical immunology, and preclinical stages of vaccine developments. Today, Dr. Hanon leads Viome's therapeutics efforts, leading our science team to identify host/microbial interactions from Viome's unique database of gene expression and to turn this knowledge into vaccines and drugs to prevent and intercept chronic diseases.

Talk
Reinventing Research & Development For Better Solutions Against Chronic Disorders
Viome has developed a unique platform capable of sequencing and quantifying RNA molecules from host and its microbiome at population scale. When combined with Artificial Intelligence, this platform allows to decipher the biological mechanisms underlying specific pathologies and paves the way for the discovery of better solutions against chronic conditions.


 Speaker Profile

Ph.D., M.P.H, CEO and Co-Founder, Cybele Microbiome

Biography
Nicole is a domain expert in the microbiome and data science with more than 20 years of experience, with the last 6 years in startups doing everything from marketing, business strategy, IP, data analysis, and fundraising. She studied at the University of Michigan and University of Chicago with Dr. Jack Gilbert, and was the first employee at Dr. Rob Knight’s microbiome startup Biota. She is cited more than 3000 times, published in prestigious journals such as Science and Nature, is the author of several book chapters and patents and is an active member of several NSF grant committees. She also serves as an advisor to several other startups in biotech.


 Speaker Profile

Ph.D, Pharm.D, CEO & President, Micronoma

Biography
Dr. Sandrine Miller-Montgomery is Micronoma CEO, a start-up company focusing on the development and commercialization of cancer diagnostic solution using Liquid Biopsy targeting the microbial markers. Previously, she was executive director of the Center for Microbiome Innovation, which she co-directed with Pr. Rob Knight at UC San Diego. Her team focused on expanding industry and academic collaborations of microbiome research in various domains such as clinical applications (new drug pathway identification, novel diagnostic biomarkers discovery – such as the IP that led to Micronoma), environmental science (e.g identification of natural products from ocean sediment), or consumer world (e.g. nutrition and diet role on our microbiome and metabolome). Before her foray in academia, she had a long career in Biotech and most recently had led MO BIO Laboratories, now a QIAGEN Company, having started as their director of sales and marketing where her team contributed to the consistent business growth resulting in its acquisition.

Talk
Cancer Microbiome and Diagnostic Application
This talk will cover recently published paper on leading the major paradigm shift that cancer tissues are not sterile, that their microbiome is specific and that we can use this discovery toward cancer diagnostic applications using blood samples even for solid tumors.


 Speaker Profile

Ph.D., CEO, Pendulum Therapeutics

Biography
Colleen has over 20 years of experience managing and leading teams in biotech, pharma and academia. Pendulum is a startup company based in San Francisco that uses biological and computational insights into the microbiome to develop interventions for a variety of health and disease conditions. Before starting Pendulum, Colleen served as the Senior Manager of Biology at Pacific Biosciences, which is where she met her two co-founders. Prior to that, Colleen was a Scientist at Elan Pharmaceuticals. Colleen completed her postdoctoral research at Northwestern’s Children’s Memorial Hospital, received her Ph.D. in Biochemistry and Molecular Biology from Johns Hopkins University and received her B.A. in Biochemistry from Wellesley College. Colleen currently resides in Menlo Park, CA with her husband, 2 daughters, 2 dogs, and 2 birds…all contributing to a diverse microbiome!


 Speaker Profile

Ph.D., Associate Professor, Department of Pathology & Immunology, Baylor College of Medicine

Biography
Dr. Savidge's research interests include studying microbial-neuroimmune interactions in the gastrointestinal tract and nervous systems. This work has established new disease susceptibility biomarkers to Clostridium difficile infection and Fecal Microbiota Transplantation failure, as well as identifying new precision-based microbial therapy for recurrent C. difficile infection based on population-scale metagenomics and functional microbiome analysis.

Talk
Pan-Microbiome Profiling Identifies Enterotype-Specific Taxa And Metagenomic Functions For Diarrheal Disease Classification


 Speaker Profile

Ph.D., Founder & Chief Executive Officer, Siolta Therapeutics

Biography
Dr. Nikole Kimes is Founder and Chief Scientific Officer of Siolta Therapeutics, a San Francisco-based biotech company developing novel microbiome-focused precision strategies for the prevention and treatment of inflammatory diseases. As the lead executive driving Siolta’s early-stage development, Dr. Kimes heads a talented team of scientists, blending microbiology, immunology, and bioinformatics expertise to leverage microbiome data for the improvement of patient stratification and development of precision microbial therapeutics. An inventor of Siolta’s technology, her research in Dr. Susan Lynch’s lab at the University of California San Francisco, provided the foundation from which the translational research program at Siolta Therapeutics has developed.

Talk
Disrupting the Atopic March: Utilizing the Gut Microbiome to Prevent Allergic Disease Development


 Speaker Profile

Ph.D., Luis & Nelly Soux Professor of Microbiology, Caltech

Biography
Sarkis K Mazmanian, PhD, is the Luis & Nelly Soux Professor of Microbiology in the Division of Biology & Biological Engineering at the California Institute of Technology (Caltech). His laboratory studies the human gut microbiome with a focus on developing novel therapies for immunologic and neurologic disorders, including Inflammatory Bowel Disease, Autism Spectrum Disorder, and Parkinson’s disease. Dr. Mazmanian has won numerous awards including a Searle Scholar, Young Investigator of the Year at Harvard Medical School, Damon Runyon Innovation Award, was named by Discover Magazine as one of the “Best Brains in Science under 40” and received the MacArthur Foundation “Genius” award. He is a founder of 3 biotech companies and serves on the Scientific Advisory Board of over a dozen companies, academic centers and not-for-profit foundations. Most importantly, Dr. Mazmanian has trained numerous students and fellows who have gone on to successful independent careers in academia, industry, and medicine.

Talk
Gut Microbial Metabolites in Health and Disease
We reveal that mice exposed to a microbial metabolite display autism-like behaviors and changes in functional brain connectivity. These findings reveal that gut bacteria may influence complex behaviors in mice via effects on oligodendrocyte function and myelination in the brain.


 Speaker Profile

Director, Microbiology, Axial Biotherapeutics

Biography
Mary leads microbiology and a drug discovery project team at Axial Therapeutics, a clinical stage company advancing a pipeline of gut-targeted small molecule therapies in areas of significant unmet patient need including Autism Spectrum Disorder and Parkinson’s disease, with a recent expansion into oncology. Prior to joining Axial in 2017, Mary spent two years at Kaleido Biosciences and nine years at Cubist Pharmaceuticals. Mary’s experience includes leading cross-functional teams in projects from exploratory through candidate selection stages to discover microbiome-inspired therapeutics and antibiotics, and building teams and drug discovery capabilities in microbiology, molecular biology, biochemistry, cell biology and the microbiome. Mary studied at Princeton University and in the department of bacteriology at the University of Wisconsin-Madison.

Talk
Intervening at the Level of Microbial Metabolites in Autism
Certain microbial metabolites have been associated with autism-like behaviors pre-clinically and found to be elevated in children with Autism Spectrum Disorder. Safety, tolerability and preliminary efficacy of AB-2004, a gut-restricted molecule targeting microbial metabolites, were assessed in an adolescent population with ASD.


 Speaker Profile

Ph.D., Professor, Center Director, Arizona State University

Biography
Dr. Rosa Krajmalnik-Brown is a Professor at the School of Sustainable Engineering and The Built Environment and the Director of the Biodesign Center for Health Through Microbiomes at Arizona State University. Her research focuses on understanding microbe-microbe, microbe-environment, and microbe-host interactions. Her research team was the first one to describe gut microbiome changes after gastric bypass surgery, and the first research team to design and implement a successful microbiota-based therapy to improve gastrointestinal and autism symptoms. Her interests and research also include bioremediation, the use of microbial systems for bioenergy production, and the human intestinal microbial ecology and its relationship to obesity, metabolism, and autism.

Talk
Microbiota Transfer Therapy for Autism
Recent studies in human cohorts and mouse models have shown links between gut microbiota and autism. We pioneered an autism-targeted open-label clinical trial of microbiota modification. Gastro-intestinal symptoms and behavior improved significantly, and most improvements remained two years after treatment.


 Speaker Profile

Ph.D., CEO & Founder, Bloom Science

Biography
Dr. Reyes is a biophysicist and entrepreneur with a passion for creating solutions to improve our health, environment and economic sustainability. Dr. Reyes has founded two companies focused on developing therapeutics to address serious medical needs as well as a tech company focused on connecting people to socially conscious commerce solutions. His first company Eclipse Therapeutics, a cancer stem cell focused start-up, resulted in a successful acquisition in 18 months. Dr. Reyes has a Ph.D. in Biophysics at the University of California, San Francisco and B.A. in Molecular and Cell Biology, Biophysics from the University of California, Berkeley. Dr. Reyes was a postdoctoral fellow at The Scripps Research Institute. Dr. Reyes has received honors from the National Science Foundation, the Ford Foundation and was a McNair Scholar.

Talk
Developing The Next Generation Of Living Medicines
Bloom Science is developing genetically optimized living medicines that target diseases in neurology, immunology and oncology. Our unique approach elucidates connections between clinical outcomes, the microbiome, and critical disease pathways. We then use genetic tools to engineer superior biopharmaceutical properties in our microbiota therapeutics.


 Speaker Profile

Professor, Bioengineering, UC San Diego

Biography
Jeff Hasty engineers synthetic gene networks in order to gain insight into the general modules of gene regulation. These modules include subnetworks that act as switches or oscillators, as well as networks that communicate across a population of cells. The work provides a framework for predicting and evaluating basic gene regulatory motifs that govern protein production at the genomic level. Hasty develops and uses mathematical models to analyze gene networks and employs experimental techniques to construct the networks according to the model blueprint. For example, he has developed a model of a positive feedback loop, in which a gene produces a protein which in turn causes that gene to become more active. He has confirmed this model in experimental studies with E-coli. Hasty believes there are many such modular mechanisms that taken together, control the function of cells. Understanding genetic networks is a first step towards logically controlling and monitoring the function of cells. Hasty’s long-term goal is to build synthetic genetic switches or oscillators which could be inserted into a patient’s cells to tightly regulate the expression of a desired protein, or even to cause an undesirable cell to self-destruct. Hasty has been an invited speaker on gene regulatory networks at more than 20 professional meetings, and his work has been covered in the popular press including CNN and Business Week.


 Speaker Profile

Ph.D., Product manager, Microbiome & Metabolomics, DNA Genotek Inc

Biography
Ms. Breton joined DNA Genotek in 2015, starting in the customer facing team and later moving into product management. Using her years of experience working with researchers in human genomics and microbiome, she currently leads product management for microbiome and metabolomics devices. During her PhD, Ms. Breton studied chemical and microbial signatures of forensically relevant samples in collaboration with Dr. Rob Knight's laboratory. She has previous experience as an environmental microbiologist and is a member of the Canadian College of Microbiologists.


Microbial Profiling Showcase:
DNA Genotek Inc

DNA Genotek Inc., Novosanis and Diversigen are subsidiaries of OraSure Technologies, Inc. working to provide high-quality sample collection products and comprehensive services for sample processing, sequencing, and bioinformatic analysis. Our solutions enable microbiome discovery for academic, pharmaceutical, biotechnology, agricultural and environmental applications.

OMNIgene.SKIN - A Validated Skin Microbiome Collection System
Low biomass samples like those obtained from human skin are a challenge to collect and analyze. OMNIgene®•SKIN is the first skin sampling device validated for microbiome applications with demonstrated ambient temperature stability and reliable profiling.