Marine Metagenomics From high-throughput data to ecogenomic interpretation

  • The field of marine ecological genomics is evolving at an unprecedented pace. The increasingly cheaper and faster sequencing technologies present new posibilities but also new challegnes. The sheer amound of sequencing data requires elegant solutions for storing, querying and exchanging it. Additonally. sequences alone are not enough to understand the complex interactions between microorganism and the marine environment. Comprehensive environmental and contextual metadata are needed to put the sequences into context. However, the integration of sequence and metadata is not a trivial task. The aim of this thesis was to enhance the field of marine ecological genomics by fulfilling two tasks. Firstly, the technology necessary for data integration, visualization and analysis was set up. Secondly, this technological platform was used to support three ecological analysis of marine microbes. The first task was addressed by improving the existing portal for marine ecological genomics ( The main goal of is to integrate sequences and their metadata based on geographic location. The focus lies on environmental parameters such as temperature, salinity and nutrients. As a result of this thesis, pofits from a new data model, a net web interface, improved and analysis tools. For the second task, the integrated resources offered by were used. The effect of environmental stability on the transcription factors content of microbial comunities was quantified using interpolated environmental data. In a second study, interpolations were used to give environmental context to new hypothesis for domains of unknown function in the marine metagenomes. Last but not least, a study of the community structures of high and low DNA content marine microbes was complemented with integrated metadata. The extended technological platform was sucessfully used to gain new insights into the ecology of marine microbes.

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Publishing Institution:IRC-Library, Information Resource Center der Jacobs University Bremen
Granting Institution:Jacobs Univ.
Author:Ivaylo Kostadinov
Referee:Frank Oliver Glöckner, Matthias Ullrich, Bernhard Fuchs
Advisor:Frank Oliver Glöckner
Persistent Identifier (URN):urn:nbn:de:101:1-2013052812242
Document Type:PhD Thesis
Date of Successful Oral Defense:2011/05/06
Date of First Publication:2011/05/24
PhD Degree:Bioinformatics
School:SES School of Engineering and Science
Other Organisations Involved:Max-Planck-Institut für Marine Mikrobiologie (marmic)
Library of Congress Classification:Q Science / QH Natural history - Biology / QH301-705.5 Biology (General) / QH324 Methods of research. Technique. Experimental biology / QH324.2 Data processing. Bioinformatics
Call No:Thesis 2011/17

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