The Official Blog of the Annual Translational Microbiome Conference

The official blog of the Annual Translational Microbiome Conference provides readers with information, insight and analysis regarding the microbiome.

New Tools are Needed to Drive Microbiome Research to the Next Level

These microbiome insights are brought to you by Dr. Peter Christey of GALT, Inc., and Arrowhead Publishers. Dr. Christey will be presenting "Driving the Tidal Wave of Microbiome Discovery - a Next Generation Platform for Exploring the Microbiome" at Arrowhead's 4th Annual Translational Microbiome Conference, 18th-20th April, 2018.

I so much enjoy microbiome meetings and continue to be blown away by the speed at which the field is developing and the innovative work being presented. However, there is a sense of frustration with many of the presentations and publications we see in the literature. You would have seen them - studies where samples are taken from healthy patients, samples are taken from diseased patients, next generation sequencing of the microbiome is performed and the results are compared. We get shown lots of charts showing that population x goes up, population y goes down. Then of course PCoA and other statistical charts are presented to demonstrate some point or other. All during the presentation I'm waiting for the punch-line, the insight that helps me understand what is going on. What is the microbiome doing? Who are the key actors? How are they impacting the disease state? What is the underlying biology, chemistry here? Data and insights that quench my curiosity. But no, the presentation ends once the sequencing data analysis is complete - we are left with that empty feeling that something is going on, but it is beyond our ability to understand.

Sequencing is an incredibly powerful tool that has helped illuminate the wonderful complexity and richness of the microbiome. It's one of the few, if not the only, research tools we currently have that scales to the complexity of the microbial systems we are studying. But is it enough? I feel we are doing the equivalent of trying to cure cancer solely by sequencing a million tumor samples. Cancer is being defeated by insights derived from multiple avenues of investigation, including clinical trials, epidemiological data, analysis of the underlying genetics and, critically, wet lab work dissecting the core biological mechanisms and pathways. Wet lab work is critical to test hypotheses and new ideas under controlled conditions - the path to getting from correlation to mechanism. Then we can seriously develop informed interventions to improve the human condition.

Microbiome wet lab work is constrained by the current toolset. Mainstream microbiology technologies were invented over 100 years ago. Core tasks, such as isolating target microbes, creating comprehensive strain collections or studying model ecosystems, are often difficult or impractical. We need new tools to drive microbiome research to the next level.

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YUN Overcomes European Regulatory Issues Surrounding the Use of Live Probiotic Bacteria for Topical Skin Application

These microbiome insights are brought to you by Dr. Ingmar Claes, Chief Scientific Officer at YUN, and Arrowhead Publishers and Conferences. Dr Claes will be presenting YUN’s work at Arrowhead’s 4th Annual Translational Microbiome Conference, 18th-20th April 2018. (www.microbiomeconference.com).

We all know that the skin is critical for our health by serving as a protective layer against external factors, but we tend to overlook the importance of the skin microbiome. The skin microbiome, acid mantle and epidermal skin barrier functions as our first layer of defense against pathogens. Use of products with live beneficial bacteria, also known as probiotics, pharmabiotics, or live biotherapeutic products (LBPs), have the potential of improving dysbosis for a multitude of skin disorders. Such restoration of the microbiome using ‘live’ probiotic bacteria to treat disorders is known as probiotherapy.

YUN is a Belgian-based biotech company with a totally new vision on health and hygiene. YUN aims to take healthcare to the next level. YUN believes in maintaining and restoring the skin microbiome; and the importance of the microbiome for human health. Working closely with leading probiotherapy experts from the University of Antwerp over the past decade, YUN has developed a world premier range of skin products including treatments for pimples (ACN and ACN+) and athlete’s foot (FNG).

World Premier ACN and ACN+ Products
YUN’s ACN and ACN+ products are the first creams (oil in water cream) in the world that contain ‘live’ probiotic bacteria in a dose that will have an impact on the skin microbiome. This major breakthrough was made possible by the development of an innovative type of microcapsule. This new microcapsule contains the ‘live’ bacteria in a core suspension, surrounded by multiple layers to protect them from the water in the cream. Furthermore, YUN strains are ‘probiotic’ which are specifically selected lactobacilli strains. These have some shared mechanisms of action with other probiotic strains, but also have some very specific properties against a selection of pathogenic or problem-causing micro-organisms such as Propionibacteriuim acnes, Trichiphyton spp, Staphylococcus spp., Malassezia spp., Candida spp.

Tough Regulatory Approval Challenges
LBP products face tough regulatory hurdles. Unlike the US in which the FDA’s Center for Biologics Evaluation and Research (CBER) has issued LBP guidelines for industry, the EU lacks regulatory framework. Regulations are lagging behind the new innovations. As in all regulations, safety is considered the most important factor. Thus, safety should always be the first concern when using LBPs.

As a completely new field of products for topical application, YUN faced tough European regulatory approval challenges. YUN has been looking from the start to market its products outside the EU, and it is clear that there are differences in regulations between the US and Europe. Indeed, regarding the FDA LPB product guidelines, it is unclear whether YUN’s topical products fall under the FDA’s definition of LBPs.

Further complicating matters is there are major differences between the safety assessment of oral medical drugs and LBPs for topical use. Specifically, for topical application, the challenges regarding safety should not be neglected. Even though our epidermal skin barrier, the acid mantle layer and the skin microbiome seem to be protective for systemic problems, carefully selected safe ‘probiotic’ strains should be selected for topical application.

As YUN’s topical skin care LBP products are safe and work by restoring or maintaining the skin’s natural defense layer, namely the skin microbiome, they fall in the EU under the cosmetic regulations. These products must not cause damage to human health when applied under normal or reasonably foreseeable conditions of use (cfr. Regulation (EC) N° 1223/2009) and data proving the safety of the probiotic strains being used must therefore be provided.
YUN specifically substantiated for the safety of all their topical products, both at the probiotic strain level and the final product itself. YUN goes even one step further as it wants to address the issues at hand of many of the current topical products which neglect safety on the skin microbiome.

Probiotic Strain Safety Research
YUN specifically performed research for the safety of the probiotic strains both in vitro and in vivo. Indeed, Dr Claes emphasized the importance of the safety of YUN’s probiotic strains particularly during the pre-clinical in vitro screening phase of development. Consequently, all the YUN’s strains were thoroughly characterized at the strain level. Mobile antibiotic resistance elements and virulence factors were investigated and excluded. Furthermore, interactions with human cells were also investigated.

Final Product Level Safety Research
At the final product level, aseptic filling, absence of contaminant pathogenic bacteria and amount of ‘live’ probiotic bacteria had to be proven by YUN. Additionally, the products with ’live’ probiotic strains were clinically evaluated by YUN to underline their level of safety for topical application on the skin.

Quality Control Issues
YUN guarantees the viability of its probiotic bacteria through patented breakthroughs in new galenic formulation and the development of microcapsules shielding its ‘live’ probiotics from water present in creams. Keeping the bacteria in a water-free core suspension ensures a minimal viable dose for up to six months at room temperature as the bacteria’s metabolical activity is minimal in the water-free suspension.

New Regulatory Framework is Needed
Dr Claes explains that by constructing the safety documentation and quality controls in the production of YUN’s 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.

Furthermore, YUN is a member of the Pharmabiotic Research Institute (PRI) and hopes to constructively interact with the European Medicine Agency (EMA). YUN believes that for some specific applications and products a completely new regulatory framework should be proposed for these new innovative products, which in the first place should always tackle safety before efficacy.

Clearly, approval regulation is lagging behind innovation. European drug authorities must tackle regulatory challenges to produce concise guidelines for industry in the development of LBPs. YUN deserves much credit for not only developing the world’s first ‘live’ probiotic creams in a dose to maintain and restore the skin microbiome, but overcoming tough European regulatory approval challenges.

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Continuing Medical Education Credits Now Available for this Event

Joint-Providership Accreditation and Designation Statement

This activity has been planned and implemented in accordance with the accreditation requirements and policies of the Accreditation Council for Continuing Medical Education (ACCME) through the joint providership of the Office of Continuing Medical Education of the University of Virginia School of Medicine and Arrowhead Publishers. The Office of Continuing Medical Education of the University of Virginia School of Medicine is accredited by the ACCME to provide continuing medical education for physicians

The University of Virginia School of Medicine designates this live activity for a maximum of 8 AMA PRA Category 1 Credits.TM Physicians should claim only the credit commensurate with the extent of their participation in the activity. (The number of credits offered for this event is subject to change dependent upon future additions/revisions to the agenda.)

The University of Virginia School of Medicine, as accredited provider, awards 8 hours of participation (consistent with the designated number of AMA PRA Category 1 Credit(s)TM ) to a participant who successfully completes this educational activity. The University of Virginia School of Medicine maintains a record of participation for six (6) years.

Shahram Lavasani, Ph.D.

Founder, Chief Executive Officer and Chief Scientific Officer
Immune Biotech

Shahram Lavasani is an international keynote speaker and entrepreneur in the field of the microbiome. He received his PhD in Immunology from Lund University in Sweden while studying the immunoregulation and immunotherapies in multiple sclerosis (MS). With more than two decades of teaching and research expertise on Gut-Brain axis, he has pioneered research in MS by demonstrating gut inflammation and barrier dysfunction and introduced microbiota-based therapies using probiotic bacterial consortia. He is the founder of ImmuneBiotech developing novel microbiome therapeutics. The company has access to a proprietary lactobacilli library and advanced selection technologies to design nutritional formulations for optimal management of the diseases. ImmuneBiotech´s first product GutMagnificTM has been designed to address the underlying causes of IBS and successfully launched to European market in October 2019.

Scott Jackson, Ph.D.

Group Leader, Complex Microbial Systems
NIST (National Institute of Standards & Technology

In this current role, Scott is leading international 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.

Rachel Clemens, Ph.D.

Commerical Innovation Manager, Life Science Lead
ISS US National Lab, Center for Advancement in Science in Space

Rachel Clemens has focused her career on advancing life science research and product development through experiments in space. In her current role as a Commercial Innovation Manager at the ISS US National Lab, she brings life science research to low earth orbit. She leads partnership development specifically with life science companies – from biotech start-ups to large pharmaceutical companies. She is eager to entertain even the craziest of ideas and passionate about finding novel solutions to Earth-bound problems.

Lynne Elmore, Ph.D.

Director, Translational Cancer Research Program
American Cancer Society

Lynne Elmore, PhD, is the director of the Translational Cancer Research program in the Extramural Grants department of the American Cancer Society (ACS). She manages a research portfolio focused on cell biology, infectious disease, the microbiome, molecular genetics, and cancer drug discovery.

Garth Ehrlich, Ph.D.

Professor of Microbiology & Immunology, Professor of Otolayngology - Head & Neck Surgery
Drexel University College of Medicine

Dr Ehrlich is Professor of Microbiology and Immunology, and Otolaryngology-Head and Neck Surgery at Drexel University College of Medicine (DUCOM) in Philadelphia, PA, USA. Dr. Ehrlich is also the founder and director of three Research Centers of Excellence in the Institute for Molecular Medicine and Infectious Disease: the Center for Genomic Sciences (CGS); the Center for Advanced Microbial Processing (CAMP); and the Center for Surgical Infections and Biofilms.

He also directs Drexel University’s Core Genomics Facility and the Meta-Omics Shared Resource for the Sidney Kimmel Cancer Center – an NCI-designated Cancer Center.

Momo Vuyisich, Ph.D.

Chief Scientific Officer
Viome

Momo Vuyisich is a co-founder and Chief Science Officer at Viome, a data-driven personalized nutrition company. Momo provides scientific leadership at Viome and his vision is to revolutionize healthcare from "symptoms management" to a true preventative medicine. He leads product development, clinical test implementation, and comprehensive clinical research portfolio.

Momo is also an Adjunct Professor at the University of New Mexico and New Mexico Tech. Before co-founding Viome in 2016, Momo spent 12 years at Los Alamos National Laboratory, where he led the Applied Genomics team, which developed the core technology used by Viome today.

Nancy Caralla

Founding President, Executive Director
C Diff Foundation

Nancy C Caralla is a three-time Clostridioides difficile infection (CDI) survivor. She has accumulated over 25 years of experience in the nursing profession blended with over 30 years in international construction management. Over the past several years, Nancy, in partnership with C Diff Foundation members, has focused on raising C. difficile awareness through education and advocating for Clostridium difficile infection prevention, treatments, clinical trials, AMR, and environmental safety worldwide. The C Diff Foundation is a non-profit organization that takes great pride in its volunteers, chairpersons, and committees.

Rachel Teitelbaum, Ph.D.

Chief Executive Officer
Hervana

Rachel Teitelbaum, PhD is the founder and Chief Executive Officer of Hervana Bio Ltd. Dr. Teitelbaum earned her Ph.D. in microbiology and immunology at the Sue Golding Graduate Division of the Albert Einstein College of Medicine. Her academic research career spans more than 15 years, with a focus on research in infectious diseases, in particular relating to the host-pathogen interface, elements of the immune response to intracellular pathogens, the development of animal models of infection and the development of vaccines, in particular for providing effective mucosal immunity. With the founding of Hervana Bio Ltd, Dr. Teitelbaum has applied some of these principles to developing a probiotic therapeutic platform in Women’s Health applications, including the development of a non-hormonal, long-acting biologic contraceptive.

Sonia Timberlake, Ph.D.

Vice President of Research
Finch Therapeutics

Dr. Sonia Timberlake is the VP of Research at Finch Therapeutics, a microbiome therapeutics company. Sonia is an expert at designing NGS-based algorithms for applications in microbial genomics, immunogenomics, and evolution. Prior to joining Finch, she built and managed AbVitro's computational algorithms and infrastructure, supporting high throughput single-cell immune phenotyping and repertoire sequencing technology. This technology platform was acquired by Juno Therapeutics, where Sonia led a multidisciplinary team to harness native adaptive immune responses for developing engineered cell therapies in oncology.

Dae-Wook Kang, Ph.D.

Assistant Professor, Department of Civil & Environmental Engineering
University of Toledo

Dr. Kang received his BS and MS in Civil and Environmental Engineering from the Seoul National University and his PhD (also in Civil and Environmental Engineering) from the University of Wisconsin-Madison. Prior to joining the University of Toledo in 2019, Dr. Kang was a research scientist in the Biodesign Swette Center for Environmental Biotechnology at the Arizona State University where he was involved in groundbreaking work to establish the relationships between human gut microbiota and autism spectrum disorders. His broad research interests are employing multi-omics technologies and bioinformatics to advance understanding of the role of microbiota on human health, environment, and engineering systems, and eventually to improve human public health and environment sustainability.

Amy Feehan, Ph.D.

Research Scientist
Ochsner Health System

Dr. Feehan is an early stage investigator who received her BS and PhD in Neuroscience from The Brain Institute at Tulane University in New Orleans. She has conducted research in humans and rodents covering topics ranging from drug development of novel endomorphin analogs for pain, to sleep and circadian rhythms research and most recently the gut-brain axis and infectious disease. Her doctoral work led to two patents for a compound that reverses both acute and chronic pain with no observable risk of addiction. She currently works as a research scientist in the Infectious Disease department at Ochsner in New Orleans designing and executing investigator-initiated clinical trials.

Sangeeta Khare, Ph.D.

Research Microbiologist, Division of Microbiology, National Center for Toxicological Research
US Food & Drug Administration

Dr. Sangeeta Khare is a Research Microbiologist in the Division of Microbiology, at National Center for Toxicological Research, Food and Drug Administration. Dr. Sangeeta Khare leads an active team with a research emphasis on host-pathogen and host-microbiome interaction during perturbations with xenobiotic agents (nanoparticles, antibiotics and other drugs, natural products and additives). The main focus of Dr. Khare’s research group is on establishing innovative parameters of host intestinal toxicity.

Julius Goepp, MD

Chief Executive Officer
Scaled Microbiomics

Dr. Goepp is the inventor of “Systems and Methods for Altering Microbiome to Reduce Disease Risk and Manifestations of Disease,” filed as a PCT patent with USPTO on August 27, 2017 and assigned to Scaled Microbiomics, LLC. He has spearheaded the development of Scaled Microbiomics to date, including developing a research team, equipping a laboratory, designing the experiments that produced supporting data on use of IgY in microbiome applications, and interpreting the results.

Ze'ev Ronai, Ph.D.

Professor
Sanford Burnham Prebys Medical Discovery Institute

Ze'ev Ronai obtained his Ph.D. in 1985 from The Hebrew University, Jerusalem Israel and performed his postdoctoral research with I.B. Weinstein at the Cancer Center of Columbia University in New York. He established the Molecular Carcinogenesis Program at the American Health Foundation in Valhalla, New York, and in 1997 moved to the Ruttenberg Cancer Center at Mount Sinai School of Medicine in New York, where he was a tenured professor up to 2005. During 2004, Dr. Ronai moved to Sanford Burnham Prebys Medical Discovery Institute (formerly known as Sanford-Burnham Medical Research Institute) in La Jolla CA, where he is a Professor. He served as the Director of the Signal Transduction Program (2005-2013), as the Deputy Director for the Cancer Center (2008-2014), and as the Scientific Director for the La Jolla site (2014-2016). He established a cancer center at the Technion in Israel (Technion Integrated Cancer Center), while maintaining his activities at SBP (2016-2018). He is currently Chief Scientific Advisor and Professor at Sanford Burnham Prebys Medical Discovery Institute (SBP), La Jolla CA.

Henrik Bjorn Nielsen, Ph.D.

Chief Scientific Officer
Clinical Microbiomics

Henrik Bjørn Nielsen, PhD, is Chief Scientific Officer (CSO) at Clinical Microbiomics where he is part of the leadership team together with the CEO and CBO. As CSO he is responsible for directing the science team and the scientific innovation, in addition to overseeing all client projects. Bjørn has an outstanding background as both group-leader at the Technical University of Denmark (DTU) and has been a frontrunner in the field of microbiome research for more than a decade. He has published more than 20 high-visibility publications within the microbiome field, covering biomedical discoveries and a series of key analysis concepts for microbiome data. Bjørn has extensive expertise in analysing, integrating and managing diverse types of data. With his experience and innovative mindset, Bjørn has played a key role in establishing Clinical Microbiomics as the leading CRO for advanced microbiome analysis.

Cecile Clavaud, Ph.D.

Project Leader in Skin Microbiome, L'Oreal Advanced Research
L'Oreal

Research and Innovation, France Dr. Clavaud's initial expertise is chemistry and biochemistry to design new radiolabelled probes for medical imaging (Commissariat à l’Energie Atomique, Saclay, FRANCE) followed by four years post doc in the Aspergillus Unit (Institut Pasteur, Paris, FRANCE) to characterize the molecular mechanisms involved in the fungal cell wall polysaccharides biosynthesis. Dr. Clavaud joined L’Oréal Research and Innovation in 2011, to work in an open innovation mode, establishing partnership with international academic experts in the skin and scalp microbiome field. At that stage, she explored the ecology of skin microbiota members (bacteria, fungi and viruses) observed in various skin physio-pathologies and body sites in order to identify key determinants involved in the interaction with skin. Since 2017, she has been involved in building a laboratory dedicated to the skin – microbiota interactions in 3D reconstructed skin models, to better understand how commensal microbiota can impact positively the skin barrier function and the skin quality. Today, she is leading transformation projects turning the recent microbiome knowledge into anti-aging applications.

Anandh Babu Pon Velayutham, Ph.D.

Associate Professor, Department of Nutrition and Inegrative Physiology
University of Utah

Dr. Anandh Babu Pon Velayutham is an Associate Professor in the Department of Nutrition and Integrative Physiology at the University of Utah. His research focuses on identifying novel dietary compounds for the prevention of vascular disease in diabetes and metabolic syndrome. His current research examines the vascular effects of blueberries and strawberries with special emphasis on the microbial metabolites of berry anthocyanins and the molecular signaling mechanisms involved. Dr. Velayutham's research aims to understand the causal association between dietary berries, gut microbiome and vascular health.

Sara Ferrando Martinez, Ph.D.

Research Scientist
AstraZeneca

Dr. Sara Ferrando-Martinez is a Research Scientist at AstraZeneca. Sara is an immunologist that focused on understanding the mechanisms underlying the deterioration of the immune system and how to rejuvenate and recover immune responses as a strategy for immunotherapy. Within AZ Sara is trying to uncover the link between microbiome, microbiome-related products and immune modulation and its impact in health and disease.

A. Stewart Campbell, Ph.D.

VP, Early Stage Development
Axial Biotherapeutics

Dr. Campbell brings more than 25 years of drug discovery and development experience to the team. He has built and led R&D teams involved in a variety of environments from early stage research through to advanced clinical development in small start-ups to mid-sized companies. With capable colleagues he has been fortunate to have triaged several drug candidates from discovery to clinical proof-of-concept in multiple therapeutic areas. He received a Ph.D. in Organic Chemistry from the Queen’s University, which was followed by post-doctoral research at Duke University. He has consulted for several start-up companies in multiple technology and therapeutic areas in the Greater Boston area and is co-inventor on more than 15 issued patents.

Gregg Silverman, MD

Professor of Medicine & Pathology
NYU School of Medicine

Dr. Silverman is Professor of Medicine and Pathology, Associate Director of the Division of Rheumatology, and the Director of the Laboratory of B-cell Immunobiology at the NYU School of Medicine. He is an elected member of AOA, ASCI and the Henry Kunkel Society. After training in Internal Medicine at UCSD, he was a fellow at The Scripps Research Institute in rheumatology and clinical immunology, with a focus on molecular immunology and the structural basis of immune recognition. He has authored over 160 publications and he is on the editorial board of several prestigious journals. Work in his lab is highly translational, with a special interest in B cells and the properties of autoantibodies. and more recently the contributions of the gut microbiome to autoimmune disease.

Mahmoud Ghannoum, Ph.D.

Professor, Department of Dermatology
Case Western University and University Hospitals Cleveland Medical Center

Dr Mahmoud Ghannoum received MSc in Medicinal Chemistry and PhD in Microbial Physiology from University of Technology in England, and an MBA from the Weatherhead School of Management at Case. Presently he is a tenured Professor and Director of the Integrated Microbiome Core and Center for Medical Mycology, Case Western Reserve University and University Hospitals Cleveland Medical Center (UH) where he established a multidisciplinary Center of Excellence that combines basic and translational research investigating medically important fungi from the test tube to the bedside. More recently he pioneered the studies on the fungal communities residing in our body and coined the term ‘Mycobiome”.

He is also a fellow of the Infectious Disease Society of America and past President of the Medical Mycological Society of the Americas (MMSA). In 2016, Dr Ghannoum received the Rohda Benham Award presented for his continuous outstanding and meritorious contributions to medical mycology from the Medical Mycological Society of the Americas and he also received the Freedom to Discover Award from Bristol-Myers Squibb for his work on microbial biofilms. In 2017, he was inducted as a fellow of the American Academy of Microbiology. Beside his academic career Dr. Ghannoum is an entrepreneur-scientist who launched a number of companies focusing on the treatment of biofilm infections as well as microbial dysbiosis as it relates to gut health.

Pamela Silver, Ph.D.

Elliot T. and Onie H. Adams Professor of Biochemistry and Systems Biology
Harvard Medical School

Pamela Silver received her BS in Chemistry and PhD in Biochemistry from the University of California where she was an NIH Pre-doctoral Fellow. She was a Postdoctoral Fellow at Harvard University in the Dept of Biochemistry and Molecular Biology where she was a Fellow of the American Cancer Society and The Medical Foundation. Subsequently, Pam was an Assistant Professor in the Dept of Molecular Biology at Princeton University and then moved to the Dana Farber Cancer Institute where she was a Professor in the Dept of Biological Chemistry and Molecular Pharmacology at Harvard Medical School. Pam became one of the founding members of the Department of Systems Biology at Harvard Medical School and the first Director of the Harvard University PhD Program in Systems Biology and one of the first members of the Harvard University Wyss Institute for Biologically Inspired Engineering. Her work has been recognized by an Established Investigator of the American Heart Association, a Research Scholar of the March of Dimes, an NSF Presidential Young Investigator Award, Claudia Adams Barr Investigator, an NIH MERIT award, the Philosophical Society Lecture, a Fellow of the Radcliffe Institute, and election to the American Academy of Arts and Sciences. She is among the top global influencers in Synthetic Biology and her work was named one of the top 10 breakthroughs by the World Economic Forum. She serves on numerous public and private advisory boards including the board of the Internationally Genetics Engineering Machines (iGEM) Competition, and she is the co-founder of several biotech companies.