The Marine Microbiome - Discovery & Innovation

Open Science Conference

Wednesday 29 June

At a Glance Sci Con 29 07 2016

Please click here for the full Conference Programme.

Session 1: The diversity of the oceanic microbiome

Much debate still persists regarding the extent of the microbial diversity of the oceanic microbiome. This applies to all three domains of life: Eukarya, Bacteria and Archaea. How many species really exist? How are they distributed in the ocean? How many new species are there and where can they be found? Can we find new species with interesting values in extreme marine environments, the deep sea or the deep-sea sediments? Or would the most interesting microbes be symbiotic with marine animals, plants or other microorganisms? This session attempts to give an overview of the present knowledge in relation to these questions.

Foto Overmann

Accessing the marine microbiome through novel cultivation approaches

Prof. dr Jörg Overmann (DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) received his PhD from the University of Konstanz. After a postdoc at UBC, Vancouver, and the Habilitation at the ICBM, Oldenburg, he became Professor of Microbiology at the LMU München. Since 2010 he is Director of the Leibniz-Institut DSMZ and Professor of Microbiology at the TU Braunschweig. Prof. Overmann has published over 150 articles, received the Ph.D. award of the VAAM, and was Inaugural Douglas Leigh Lecturer of the Waksman Foundation for Microbiology in 2013. He is member elect of the review panel of the German Science Foundation, and serves in Editorial Boards and several scientific advisory boards.


Microbiomics at global scale: From human gut to TARA oceans

Prof. dr Peer Bork (Structural and Computational Biology, EMBL Heidelberg, Germany) is Senior Group Leader and Joint Head of the Structural and Computational Biology unit at EMBL, a European research organisation where he also serves as strategic head of bioinformatics. In addition, he holds an appointment at the Max-Delbrück-Center for Molecular Medicine in Berlin. Prof. Bork received his PhD in Biochemistry (1990) and his Habilitation in Theoretical Biophysics (1995). He works in various areas of computational and systems biology with a focus on function prediction, comparative analysis and data integration. In addition to an outstanding academic career, he has also co-founded five successful biotech companies, two of which went public.

Session 2: Novel (meta)genomic approaches in marine microbiology

Next Generation (high throughput) Sequencing (NGS) presents unprecedented possibilities for uncovering the marine microbiome. It allows for the reconstruction of metabolic pathways and uncovering of metabolic networks. Metagenomic (including transcriptomics, proteomics, metabolomics) techniques will infer novel functions and it may inform strategies for how to isolate and grow novel marine microbes. These techniques are so precise they allow for investigation even on a single cell level. Metagenomics can be used as an approach for targeted isolation of microorganisms with interesting properties. It can also uncover the diversity and distribution of secondary metabolites. Cloning and expression of genes in the (meta)genomes can be used to find novel products. This session will discuss state-of-the-art techniques in this field and present an outlook on the possibilities and impossibilities of these approaches to understand the function of the marine microbiome and how to mine it for novel applications. 


Integrated (meta) genomic and synthetic biology approaches for bioactive biodiscovery

Prof. dr Fergal O’Gara  (BIOMERIT Research Centre, School of Microbiology, National University of Ireland, Cork [UCC], Ireland) is Director of the Biomerit Research Programme at UCC. He is also Emeritus Professor of Microbiology at the University and is Distinguished Research Fellow at Biomedical Science at Curtin University and at the Telethon Kids Institute Perth WA Australia. Professor O’Gara’s research interests focus on the genetics and molecular biology of microbe-host interactions in medical and environmental biotechnology including marine biodiscovery.  


Targeting taxonomic blind spots and functional traits via single-cell approaches

Dr Tanja Woyke (DOE Joint Genome Institute, Walnut Creek, CA, USA) joined the DOE Joint Genome Institute (JGI) in 2004 after receiving her PhD from the Eberhard Karls University of Tübingen, Germany. Since 2009, she has been heading the Microbial Genomics Program at the JGI and she holds appointments as Adjunct Scientist at the Bigelow Laboratory for Ocean Sciences and as Adjunct Associate Professor in the School of Natural Sciences at the University of California, Merced. Her research is focused on metagenomics and single-cell genomics to study ‘microbial dark matter’, and including the development of functionally targeted single-cell approaches.

Thursday 30 June

At a Glance Sci Con 30 07 2016

Session 3: Marine systems microbial ecology

Marine microbial systems should be studied as functional entities formed by the microbial diversity and the biogeochemical cycles they encompass. In this systems ecology approach the network of different microorganisms, and the way they communicate, can be studied by using meta-omics (metabolomics) and numerical modelling. This session aims at bringing together the newest developments in systems microbial ecology.


Ecogenomics of marine microbial communities

Prof. dr Gerard Muyzer (Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, The Netherlands) is Professor in Microbial Systems Biology at the University of Amsterdam, The Netherlands. His research interests are diversity and ecophysiology of bacteria that play a role in the sulphur cycle of freshwater, marine and extreme environments. Within his research he is using a systems biology approach including different meta-omics techniques. For more information, see


Single-cell analysis of microbial activity in benthic marine environments

Dr Anne Dekas (Department of Earth System Science, Stanford University, CA, USA) is a geomicrobiologist interested in how microbial life affects the chemistry and climate of our planet today and throughout time. She obtained her PhD in Geobiology at the California Institute of Technology in 2013, and her BA in Earth and Planetary Sciences at Harvard University in 2004. She joined the Earth System Science Department at Stanford University as Assistant Professor in September 2015.

 Session 4: Novel cultivation approaches of marine microbes

Hitherto, only a small number of marine microorganisms have been brought into culture. It is of great importance to increase the number of marine microorganisms in culture because it is the only way to understand their nature, their function in the marine microbiome, and their properties, including potential pharmaceutical or biotechnological applications. Culturing the uncultured and the "unculturable" is MaCuMBA’s motto as we seek to make progress after several decades of focus on cultivation-independent techniques. In this session we will discuss the state-of-the-art of isolations and culturing techniques and approaches, including co-cultivation of microorganisms and microbial consortia, use of environmental signals and cell-to-cell communication, and mimicking natural conditions.


New approaches for the immobilisation, culture and isolation of marine extremophiles

Prof. Gwenaelle LeBlay (Laboratory of Microbiology of Extreme Environments, University of East Brittany, Brest, France) is a Professor at the University of Brest (UBO), France. During the 16 years she spent in different laboratories in Europe (Switzerland, Germany, France) and Canada, she has acquired strong expertise in microbial physiology and ecology in different ecosystems. She recently directed her research to work on the culture of microorganisms from marine extreme environments. She is currently working on the development of immobilized microbial communities from deep sea ecosystems to study microbial population dynamics during continuous cultures in bioreactors.


A new hypothesis on the nature of microbial "uncultivability" 

Prof. Slava Epstein (Northeastern University, College of Science, Boston, USA) is Professor at the Northeastern University in Boston, whose lab team, for the past 15 years, has been working on one of the most intriguing biological phenomena: why 99% of microbial diversity has gone missing from the lab. The basic and applied potential of this microbial “dark matter” is unprecedented, and so his lab has focused on, developed, and continues to practice innovative approaches to sample and study this pool of unexplored species. These approaches led to the new ideas about why uncultivated species remain uncultivated.


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