Leibniz Institute DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH.
Leibniz Institute DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH.
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: PHC-07-2014 | Award Amount: 20.85M | Year: 2014
COMPARE aims to harness the rapid advances in molecular technology to improve identification and mitigation of emerging infectious diseases and foodborne outbreaks. To this purpose COMPARE will establish a One serves all analytical framework and data exchange platform that will allow real time analysis and interpretation of sequence-based pathogen data in combination with associated data (e.g. clinical, epidemiological data) in an integrated inter-sectorial, interdisciplinary, international, one health approach. The framework will link research, clinical and public health organisations active in human health, animal health, and food safety in Europe and beyond, to develop (i) integrated risk assessment and risk based collection of samples and data, (ii) harmonised workflows for generating comparable sequence and associated data, (iii) state-of-the-art analytical workflows and tools for generating actionable information for support of patient diagnosis, treatment, outbreak detection and -investigation and (iv) risk communication tools. The analytical workflows will be linked to a flexible, scalable and open-source data- and information platform supporting rapid sharing, interrogation and analysis of sequence-based pathogen data in combination with other associated data. The system will be linked to existing and future complementary systems, networks and databases such as those used by ECDC, NCBI and EFSA. The functionalities of the system will be tested and fine tuned through underpinning research studies on priority pathogens covering healthcare-associated infections, food-borne disease, and (zoonotic) (re-) emerging diseases with epidemic or pandemic potential. Throughout the project, extensive consultations with future users, studies into the barriers to open data sharing, dissemination and training activities and studies on the cost-effectiveness of the system will support future sustainable user uptake.
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.90M | Year: 2013
Marine sponges harbour extremely diverse populations of microbes, and are world record holders for the production of a plethora of bioactive molecules. Previous studies, however, aiming at the growth of sponges or their associated microbes for the production of bioactive compounds to supply biological material for clinical trials, have been largely unsuccessful. BLUEPHARMTRAIN is a multi-disciplinary alliance of 20 academic and industrial partners that will excel in research and training through integration of complementary expertise in cell biology, microbiology, natural product chemistry, genomics & transcriptomics (omics) and socio-economics. We will adopt cutting-edge omics technologies to give a new boost to the more traditional disciplines: microbial isolation, cell culture and natural product chemistry to go beyond the current scientific frontiers. For example, metagenomic and transcriptomic data will be applied to identify the metabolic potential and restrictions of -yet- uncultured microbes and will serve for the design of tailor-made cultivation conditions. In addition, heterologous expression of bioactive gene clusters and enzymes able to perform unusual modifications will serve as an alternative strategy to unlock the bioactive potential of sponges. Thus we aim to develop an extensive technology platform that is applicable for obtaining a wide variety of bioactive compounds from distinct sponges and their microbes. BLUEPHARMTRAIN will provide a complementary set of experimental and conceptual local and network-wide training modules and workshops to 15 young researchers. The recruited fellows will work towards personalized training plans to meet individual needs and interests, generating a critical mass of young researchers in the emerging field of blue biotechnology. The presence of a large consortium of versatile biotechnology, pharmaceutical and consultancy firms ensures a good balance between academic and transferable skills acquired by the fellows.
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: INFRADEV-4-2014-2015 | Award Amount: 9.04M | Year: 2015
Marine (blue) biotechnology is the key to unlocking the huge economic potential of the unique biodiversity of marine organisms. This potential remains largely underexploited due to lack of connectivity between research services, practical and cultural difficulties in connecting science with industry, and high fragmentation of regional research, development and innovation (RDI) policies. To overcome these barriers, EMBRIC (European Marine Biological Resource Infrastructure Cluster) will link biological and social science research infrastructures (EMBRC, MIRRI, EU-OPENSCREEN, ELIXIR, AQUAEXCEL, RISIS) and will build inter-connectivity along three dimensions: science, industry and regions. The objectives of EMBRIC are to: (1) develop integrated workflows of high quality services for access to biological, analytical and data resources, and deploy common underpinning technologies and practices; (2) strengthen the connection of science with industry by engaging companies and by federating technology transfer (TT) services; (3) defragment RDI policies and involve maritime regions with the construction of EMBRIC. Acceleration of the pace of scientific discovery and innovation from marine bioresources will be achieved through: (i) establishment of multidisciplinary service-oriented technological workflows; (ii) joint development activities focusing on bioprospection for novel marine natural products, and marker-assisted selection in aquaculture; (iii) training and knowledge transfer; (iv) pilot transnational access to cluster facilities and services. EMBRIC will also connect TT officers from contrasted maritime regions to promote greater cohesion in TT practices. It will engage with policy-makers with the aim of consolidating a perennial pan-European virtual infrastructure cluster rooted in the maritime regions of Europe and underpinning the blue bioeconomy.
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2012.3.2-02 | Award Amount: 11.97M | Year: 2012
Marine microorganisms form an almost untapped resource of biotechnological potential. However, its use is hindered by the low success rate of isolation of novel microorganisms and often by poor growth efficiency. Hence, the vast majority of marine microorganisms has not been cultivated and is often considered as unculturable. MaCuMBA aims at improving the isolation rate and growth efficiency of marine microorganisms from conventional and extreme habitats, by applying innovative methods, and the use of automated high throughput procedures. The approaches include the co-cultivation of interdependent microorganisms, as well as gradient cultures and other methods mimicking the natural environment, and the exploitation of cell-to-cell communication. Signaling molecules produced by microorganisms may be necessary for stimulating growth of the same or other species, or may prevent their growth. Signaling molecules also represent an interesting and marketable product. MaCuMBA will make use of high throughput platforms such Cocagne, using gel micro-droplet technology, or MicroDish in which many thousands of cultures are grown simultaneously. Various single-cell isolation methods, such as optical tweezers, will aid the isolation of specific target cells. Isolated microorganisms as well as their genomes will be screened for a wide range of bioactive products and other properties of biotechnological interest, such as genetic transformability. Growth efficiency and expression of silent genes of selected strains will be increased also by using the clues obtained from genomic information. MaCuMBA is targeted to SMEs and industry and they make a significant part of the consortium, ensuring that the project focuses on the interests of these partners. Moreover, MaCuMBA has adopted a comprehensive and professional exploitation, dissemination, implementation, and education strategy, ensuring that MaCuMBAs results and products will be directed to end-users and stakeholders.
Agency: European Commission | Branch: FP7 | Program: CSA-CA | Phase: KBBE.2013.1.2-06 | Award Amount: 597.34K | Year: 2013
International trade is increasing tremendously in recent years with a lot of import and export material going in and out of the European Union. Within this context there is also the increasing risk of importing unwanted organisms via this trade. Organisms include plant pests and pathogens, some of which may be on the quarantine list of the European Union. Also climate change may increase the ability of plant pests to survive regions other than those of their origin. Within the field of Plant Health a decline in taxonomic and phytosanitary experience has become eminent in the last decade; also relevant phytosanitary collections are under pressure. This will affect all members of the EU and other nations as well. To regulate and control plant pathogens there is an increasing need for efficient and reliable identification and detection tools. For their development and validation, good and well maintained collections containing relevant species are indispensable. A significant number of plant pest collections are still present within Europe but they are dispersed, widespread and of very variable quality. NPPOs, mandated laboratories, universities and research institutes all have their own collections related to their specific work and scope. Many of these collections are connected to a single specialist. Within Europe there is a need to improve the infrastructure supporting phytosanitary important collections so as to more efficiently use the available infrastructure and improve collaboration in the field of phytosanitary infrastructure with regard to means, knowledge, expertise on taxonomy, development of detection methods and collections of phytosanitary important organisms. The main outputs to be disseminated from the project will include an inventory on characteristics of phytosanitary important collections within Europe and guidelines to improve quality standards and access and to design and build sustainable networks of reference collections.
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE-2007-3-2-07;KBBE-2007-3-2-08 | Award Amount: 7.53M | Year: 2009
The exponential increase in microbial genome and metagenome sequencing throughput has widened the gap between sequence and functional understanding. A clear picture of metabolic processes across the spectrum of bacterial species is essential to enable the exploitation of microbial genomics for the purposes of environmental biotechnology. The Microme project endeavors to extend the scope of microbial genome annotation from functional assignment at the gene level to the systematic generation of pathway assemblies and genome-scale metabolic models. A few key ideas and design principles will enable the Microme reconstruction pipeline to achieve this ambitious goal.A clear definition of a metabolic pathway as a collection of reaction sets, each of which convert the same defined inputs into the same outputs, will allow species-specific pathway variants to be identified, assembled into networks, compared across species, and used for downstream computations. A unique pathways projection, curation and assembly cycle, feeding directly into the flow of newly sequenced genomes, will allow a qualitative increase in the speed and reliability of the pathway generation process. Pathways and models produced the pipeline will be accessible to the scientific community as an integrated resource via the Microme portal. Finally, taking advantage of the availability of pathway assemblies from a large sample of genomes, methods for comparative and phylogenetic analyses and novel metabolic engineering strategies for environmental biotechnology goals will be developed, applied to proof-of-concept studies, and integrated to the resource as an analytical tool layer. Microme will be supported by a robust bioinformatics infrastructure, developed by integrating a set of established European databases and tools, integrated with reference protein annotation, metabolites and reactions databases, and interfaced with the annotation pipelines of the two main European sequencing centers.
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: INFRADEV-4-2014-2015 | Award Amount: 14.84M | Year: 2015
The social and economic challenges of ageing populations and chronic disease can only be met by translation of biomedical discoveries to new, innovative and cost effective treatments. The ESFRI Biological and Medical Research Infrastructures (BMS RI) underpin every step in this process; effectively joining scientific capabilities and shared services will transform the understanding of biological mechanisms and accelerate its translation into medical care. Biological and medical research that addresses the grand challenges of health and ageing span a broad range of scientific disciplines and user communities. The BMS RIs play a central, facilitating role in this groundbreaking research: inter-disciplinary biomedical and translational research requires resources from multiple research infrastructures such as biobank samples, and resources from multiple research infrastructures such as biobank samples, imaging facilities, molecular screening centres or animal models. Through a user-led approach CORBEL will develop the tools, services and data management required by cutting-edge European research projects: collectively the BMS RIs will establish a sustained foundation of collaborative scientific services for biomedical research in Europe and embed the combined infrastructure capabilities into the scientific workflow of advanced users. Furthermore CORBEL will enable the BMS RIs to support users throughout the execution of a scientific project: from planning and grant applications through to the long-term sustainable management and exploitation of research data. By harmonising user access, unifying data management, creating common ethical and legal services, and offering joint innovation support CORBEL will establish and support a new model for biological and medical research in Europe. The BMS RI joint platform will visibly reduce redundancy and simplify project management and transform the ability of users to deliver advanced, cross-disciplinary research.
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2008-1.1.2 | Award Amount: 5.65M | Year: 2009
EMbaRC will establish a self-sustainable community of European Microbial Resource Centres representing a large bio-diversity and offering a wide-range of not only bio-resources but also expert services. These services will enable the development of new partnerships with public institutes in the field of biodiversity and will facilitate revenue-generating partnerships with the economic sector (large food or biotech companies, research organisations, SMEs, NGOs etc) that will be defined in a set of validate business models for Biological Resource Centres. The objective is to enable not only the EMbaRC partners but also other European BRCs, especially those who are endangered or isolated, to find complementary sources of funding to ensure their future existence. Thus EMbaRC proposes an extensive training and outreach programme targeting these collections as well as the wider research community. Furthermore providing access to the partners expert services via the transnational access proposed will enable EMbaRC to improve, coordinate and validate its offer to the research community from within both public and private sectors. Through its networking and harmonisation activities EMbaRC will lay down the foundations of the future Global Biological Resource Centre Network ensuring that European expertise and research are at the forefront of the International scene. Through the EMbaRC joint research programme the partners will pool their resources and expertise to collaboratively improve strain and DNA storage and develop new identification methods for microorganisms for the benefit of the wider scientific community.
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2012-2.2.5. | Award Amount: 4.12M | Year: 2012
MIRRI will be a pan-European distributed RI providing microbiological services, thus facilitating access to high quality microorganisms, their derivatives and associated data for research, development and application. It will connect resource holders with researchers and policy makers to deliver the resources and services more effectively and efficiently to meet the needs of innovation in biotechnology. The RI builds upon 60 microbial domain resource centres (BRCs) in 26 European countries; collectively they provide access to more than 350,000 strains of microorganisms. Microorganisms provide essential raw material for biotechnology - but to date less than 1% of the estimated number of species are described and available to be harnessed by man. As new species are discovered, expertise is difficult to locate to ensure correct identification. Public sequence databases provide modern tools for identification but the information is often of poor quality and often not backed up by the biological material to enable validation of data. The current fragmented resource distributed across Europe needs to be coordinated and operated to common standards with facilitating policy to help focus activities to the big challenges in healthcare, food security, poverty alleviation and climate change. Lacking infrastructure, policy framework and governance structures will be defined in the preparatory phase, as will be the links to researchers and policy makers. Specialist clusters will address priority issues and output steering. BRCs should be placed on national road maps, ensuring the pan-European strategy can be implemented. Cross discipline interactions with other RIs will lead to new approaches. Linking the microbial strain information to other relevant data will allow their full exploitation. Appropriate data mining solutions will enable focussing acquisition and delivery strategies, thus bridging current gaps and improving user access.
Schumann P.,Leibniz Institute DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Methods in Microbiology | Year: 2011
Information on the peptidoglycan structure is an indispensable component for the description of new genera of Gram-positive bacteria. In certain genera, structural variations of the peptidoglycan support even the differentiation at the species level. The analysis of the peptidoglycan requires the isolation and purification of this three-dimensionally cross-linked polymer, a set of analytical techniques to identify and to quantify its components as well as specific knowledge on how to conclude structural information from the data. Though there are several review articles describing the rather cumbersome procedure of analyzing the peptidoglycan structure, the respective methods are not widely used, and many laboratories have to seek cooperation or service for peptidoglycan analyses. This chapter has the aim to provide taxonomists with detailed and feasible protocols including contemporary analytical approaches for the stepwise elucidation of the peptidoglycan structure and advice on how to evaluate the results. © 2011 Elsevier Ltd.