EXPERTS MEETING

Discovery of Novel ­Microbial Strains & the Impact of the Nagoya Protocol

Organized by BaseClear Thursday November 24th, 2020 All times are Central European Time (CET) AGENDA BaseClear hosts

Chair: Dr. Radhika Bongoni & Dr. Derek Butler Derek Butler Radhika Bongoni Derek is the commercial director of BaseClear. Radhika is Business Developer at BaseClear, SESSION 1: DISCOVERY OF NOVEL MICROBIAL STRAINS Derek completed a bachelor’s degree in with focus on markets for application of microbial Start at 10.30 ­Biotechnology at Dublin City University in 1995, genomics in food, feed and pharma industries. • Unlock: An open large-scale infrastructure for exploring new horizons specialising in Genetics and Immunology. He Radhika received her Ph.D. in Food technology for research on microbial communities continued his studies at University College Cork (2014) from Wageningen University & Research Dr. Peter Schaap | Associate Professor, WUR and in 2001 received his PhD degree for work on (the Netherlands) and an MBA (2015) from Tias • Expanding the metagenomics toolbox for novel enzyme and bioactive the genetic regulation of lactic acid bacteria. In the School for Business & Society (the Netherlands). compound discovery and production same year he took up a post-doctoral position at With techno-commercial expertise, she is involved Dr. Alexander Wentzel | Senior researcher, SINTEF the University of Groningen where his work focused in business growth and market penetration by • The importance of culturomics for unraveling microbial life in extreme environments on the identification of novel enzymatic activities fostering relationships with partners. Prior to Dr. Aleksandrina Patyshakuliyeva | Product Manager – BaseClear from thermophilic bacteria. In 2004 Derek joined BaseClear, Radhika was responsible for establishing Lactrys where he worked on vaccine development dietary supplements market in western Europe, SESSION 2: THE NAGOYA PROTOCOL AND RE-CLASSIFICATION OF STRAINS in probiotic bacteria before joining BaseClear in India, South Africa and Russia. Start at 14.30 2006. He has now more than 15 years’ experience • The Nagoya protocol: what you need to know working on microbial genomics research projects Dr. Martin Brink | Policy Advisor, Centre for Genetic Resources together with industrial partners. • Industry perspective on the Nagoya protocol Dr. Markus Wyss | Strain Director, Global Regulatory Affairs & Quality Management, DSM Nutritional Products • The impact of re-classification of microbial strains Dr. Adalberto Costessi | Product Manager Genomics & Regulatory Affairs, BaseClear

DEREK BUTLER, PHD RADHIKA BONGONI, PHD Commercial director Business Developer Illustration: Haans Industrial Design

Unlock: An open large-scale infrastructure for exploring new horizons for research on microbial communities. Peter J. Schaap Associate professor, Laboratory of Systems and ­Synthetic Biology, Wageningen University and Research

ABSTRACT BIO Microbial communities are of key importance challenges we have been able to isolate, study UNLOCK (https://m-unlock.nl) is a unique facility Peter Schaap is an associate professor at at different scales in our society, ranging from and use no more than 1% of the natural microbial for research on mixed microbial communities and Wageningen University and runs within the individual-based health issues related to microbial diversity, meaning that we have overlooked a will address exactly these three limitations, through chair of Systems and Synthetic Biology, the communities inhabiting the human body, to global major fraction of the microbial potential available enabling research on mixed microbial communi- Computational Systems Biology group. greenhouse gas (i.e. CH4 and N2O) emissions in nature. ties at an unprecedented scale and efficiency. (https://www.systemsbiology.nl/groups/ related to microbial activity. In light of these challenges, three major limitations The Unlock research infrastructure is composed computational-systems-biology/). His research Even though microbial ecosystems are charac­ exist in our current experimental procedures in of three complementary experimental platforms focus is on deriving a deeper understanding terized by an enormous diversity, and mixed research on microbial communities: (i) the lack of for high-throughput discovery and characterization of microbial systems by uncovering biological ­microbial communities inherently have interesting high-throughput cultivation facilities for parallel of microbial communities and a FAIR-data meaning from genome scale data and through emergent properties, fundamental and applied and comparative analysis of microbial ecosystems, ­platform for large scale data storage, data multiscale data integration. He has obtained microbial research historically have been focused (ii) the effective integration of these cultivation ­extraction and analysis of high-throughput data a PhD on a yeast Biochemistry subject from on a very limited number of isolated single strains. studies with molecular systems characterizations, in a cloud-based infrastructure. the Vrije Universiteit, Amsterdam and has This is because many of the key-microorganisms and (iii) tight integration and transparent and worked for many years with industrial fungus of microbial communities depend on symbiotic uniform storage and processing of the generated ­Aspergillus niger in a biotechnological interactions for growth and therefore are difficult to data. context. study and explore in isolation. Because of these

4 5 Expanding the ­

(meta)genomics toolbox for BIO novel enzyme and ­bioactive Dr. Alexander Wentzel works as a Senior Researcher at SINTEF Industry, Dept. of Biotechnology and compound discovery Nanomedicine, in Trondheim, Norway. He studied and production Biology at the Georg-August-University in Göttingen, Germany, where he finished his PhD in Microbial Dr. Alexander Wentzel Molecular Biology in 2003. During his post-doctoral Senior researcher, SINTEF period at NTNU and SINTEF in Trondheim from 2005- 2010, he was working on research projects within the fields of microbial upgrading of crude oil and Systems Biology understanding of the metabolic switch to ABSTRACT antibiotics production by the model Actinobacterium Latest estimates suggest a microbial bio­ Our focus at SINTEF and collaborators has 1200 selected isolates have been Streptomyces coelicolor.Dr. Wentzel’s current main diversity on earth in the range of more than in recent years been on developing efficient genome sequenced by BaseClear. research focus and interest is on developing efficient 1 trillion (1012) different species of bacteria, tools for a more rapid exploitation of micro­ A set of advanced bioinformatics tools tools for accessing the vast biodiversity of archaea and fungi. However, only a negligible bial biodiversity for novel industrial enzymes has been applied to assess taxonomic microorganisms in nature for the discovery and fraction of that has so far been described and for the bioeconomy and bioactive ­novelty and to extract a wide range of development of new products for the enzyme, bio-based explored for biotechnological applications. ­compounds for pressing medical needs. biosynthetic gene clusters encoding chemicals and biopharmaceuticals markets, following Technological advances in recent years are This included both sequence- and function-­ potentially new bioactive compounds of both in silico and functional metagenomics approaches. enabling us today to more efficiently explore based (meta)genomics approaches applied pharmaceutical value, as well as novel Within this field, he currently coordinates the ERA- microbial biodiversity for new enzymes for a to extreme environments ranging from deep enzymes for the conversion of biomass CoBioTech project BESTER and the Centre for Digital Life wide range of industrial applications, and sub-surface oil reservoirs to high Arctic soils in the production of bio-based Norway project INBioPharm. In addition, he is SINTEF PI novel bioactive natural products to fight and covering both terrestrial to marine niches. ­chemicals and fuels. In silico data mining in several Norwegian national and European projects, microbial infections and other severe Central in these efforts has been a large approaches are thereby consequently including the Horizon 2020 projects MetaFluidics and ­diseases, including cancer. collection of marine Actinobacteria isolated combined with functional screening AtlantECO, the ERA-net projects MarBioTech (MBT) and from the Trondheim fjord of which approx. approaches for which new technology is AquaHealth (BlueBio). being developed, deployed, and continuously improved.

6 7 ABSTRACT The discovery of microorganisms that inhabit extreme environments shed light on a wide variety of unique strategies and mechanisms they have evolved and developed to live under harsh conditions. Moreover, the discovery of ­extremophiles has added high value to mult­i­ billion-dollar industries, including agricultural, chemical synthesis, laundry detergents and pharmaceuticals. Despite their ecological ­importance and commercial potential, the majority BIO of microbial diversity in extreme environments Aleksandrina Patyshakuliyeva is product remains uncultured and poorly characterized. manager Microbiome & Animal Performance Culturomics is one of new innovative tools to and Health at BaseClear. She did a PhD in study microbial diversity derived from various fungal physiology at Westerdijk Institute The importance of ­environments. This approach involves the (KNAW), the Netherlands investigating plant ­application of multiple cultivation conditions biomass utilization by fungi and obtained a to capture the vast diversity of microorganisms, PhD from the University of Utrecht, the ­culturomics for their isolation and further identification. Netherlands. She has worked as a post­ The importance of ­culturomics methods is that doctoral researcher at Utrecht University, it allows isolation of novel strains which are unique Wageningen University and NIOO-KNAW and ­unraveling microbial sources for ­completely novel enzymatic reactions was a visiting researcher in INRA, France and and ­pathways, enzymes with a desirable Helsinki University, Finland. During this time, ­characteristic or ­functionality, and bioactive her research centred on applications in life in extreme secondary ­metabolites. sustainable food production, sustainable agriculture and bioremediation. She has explored production of extracellular enzymes, ­environments organic acids, siderophores, metabolic pathways and regulators controlling the Dr. Aleksandrina Patyshakuliyeva microbial response to the substrates (plant, Product Manager – BaseClear algal biomass, asbestos).

8 9 The Nagoya Protocol:­ what you need to know Dr. Martin Brink Policy Advisor, Centre for Genetic Resources

ABSTRACT BIO The Nagoya Protocol is about Access The objective of the Nagoya Protocol is In the EU, access rules are implemented Martin Brink has been working as a policy advisor at the and Benefit Sharing (ABS), which refers “the fair and equitable sharing of the on the national level, while the Centre for Genetic Resources, the Netherlands (CGN) to the regulation of access to genetic benefits arising from the utilization of ­compliance aspects of the Nagoya since 2012. His work is focused on genetic resources resources (GR), and the sharing of genetic resources (...), thereby contri­ Protocol are implemented at the EU policies, especially on Access and Benefit-Sharing (ABS) benefits from the use of these GR buting to the conservation of biological level. Any person, company or principles and practices. He is the National Focal Point on between providers and users. ABS is diversity and the sustainable use of its ­organisation doing R&D on genetic ABS for the Netherlands and is supporting the activities relatively new and stems from the components”. Genetic resources cover resources has to exercise ‘due diligence’ of the Netherlands in international genetic resources fora, recognition that many genetic resources material of plant, animal, microbial or to ascertain that the genetic resources such as the Convention on Biological Diversity (CBD), the from developing countries were other origin, while the Protocol also they use have been legally acquired and Nagoya Protocol, the International Treaty on Plant transformed in IPR-protected products contains provisions on derivatives and that benefits are shared. Genetic Resources for Food and Agriculture (ITPGRFA) in developed countries. traditional knowledge. Access is and the FAO Commission on Genetic Resources for Food provided on the basis of permission of This means that users in the EU have and Agriculture (CGRFA). He is involved in the the provider country authorities (Prior to be aware of the access rules of the development of new official EU-guidance on the Informed Consent, PIC) and a contract ­country that provided the genetic Regulation implementing the Nagoya Protocol in the between provider and user (Mutually resources, to obtain PIC and MAT where European Union, to be published by the end of 2020. Agreed Terms, MAT). An important required, to keep all documentation for He is also active, as a coordinator and a teacher, in principle of the Nagoya Protocol is 20 years after use, to submit a ‘due training courses on genetic resources management that compliance to ABS rules is to be diligence declaration’ in certain and policies. Martin holds a PhD degree in Agricultural ­monitored by the countries where the ­situations, and to pass on information to Sciences from Wageningen University in the Netherlands. genetic resources are used. further users of the genetic resources.

10 11 Industry ­perspective on the Nagoya protocol Dr. Markus Wyss Strain Director, Global Regulatory Affairs & Quality ­Management, DSM

ABSTRACT BIO The 2020 year marks the 10-year anniversary of the Nagoya Markus Wyss builds on 25 years of professional Protocol. An increasing number of countries are implementing experience in the chemical and biotechnology industries, laws on how and under which conditions “genetic resources” first at F. Hoffmann-La Roche, and since 2003 at DSM. can be accessed in their territory. An important focus of the He has held various managerial positions in R&D, international negotiations currently is whether also “Digital technical product management, human resources, project Sequence Information” should formally be included in the and program management. Since 2013, he is DSM’s scope of formal ABS obligations. This presentation will Strain Director in the Global Regulatory Affairs and address the opportunities and challenges of the Nagoya Quality Management department. Since 2019, Markus Protocol, will highlight the risks of including DSI in the formal Wyss is the chair of the ABS Task Force of the scope of benefit sharing obligations, and will call for engage- International Chamber of Commerce (ICC). ment of both academia and industry in shaping the ABS system of the future.

12 13 ABSTRACT BIO Recently, a seismic shift occurred in the probiotics Adalberto is BaseClear’s expert on the world when the entire Lactobacillus genus under- application of whole genome sequencing The impact of went reclassification and renaming. There were technologies to regulatory affairs. Adalberto several very sensible reasons why this was done. graduated in Medical Biotechnology at the The Lactobacilli had become a behemoth: the University of Trieste and he specialized in re-classification genus was one of the largest among the bacteria molecular biology and next generation and consisted of microorganisms from diverse sequencing during his PhD at the Radboud environments and with differing phenotypes, which University in Nijmegen. of microbial caused communication confusion. In addition, new genome sequencing techniques allow a more reliable classification of microbes, and the current strains taxonomy of Lactobacillus was considered to be highly irregular. Despite these practical advantages, Dr. Adalberto Costessi the name change will have negative consequences Product Manager Genomics & for regulatory bodies, industry and the general Regulatory Affairs, BaseClear public as we have to get used to the new names and the microorganisms that they represent.

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