Projects

Investigations in molecular biology have transitioned from single experiments to high-throughput endeavours spearheaded by genomic science. Although the genomic revolution is rooted in medicine and biotechnology, environmental studies, most notably those of marine ecosystems, currently deliver the highest quantity of data. New sequencing technologies are providing an increasingly powerful resource to investigate microbial diversity and function at the gene level.
The Microbial Genomics and Bioinformatics Research Group aims to transform the wealth of sequence and contextual (meta)data into biological knowledge. To accomplish this, we focus on the development of enabling technologies and products. In particular, we are developing components and standards for an integrative bioinformatic workbench to bring together organism diversity and abundance data, functional data (genomic data), and the environmental data contextualising them. The workbench will allow the persistent and dynamic study of relationships between organisms, their genomic repertoire, and their environment.

This integrated view will serve as a foundation for ecosystem-level statistical analysis and modelling of microbial communities and metabolisms. Such approaches will reveal key genes involved in central ecosystem processes and deepen understanding of their functions in a natural setting. An ecosystem context will also provide new insight into the role of genes with no known function. These results will not only promote a better understanding of the marine environment and its impact on human welfare in times of global climate change, but also deliver new targets for medical and biotechnological applications.

Environmental genomics at MPI-Bremen has been introduced in the year 2000 by selecting three environmentally relevant marine bacteria for whole genome sequencing, annotation and functional analysis. At this time the organisms of interest were two sulfate reducing bacteria (Desulfotalea psychrophila and Desulfobacterium autotrophicum) and one Planctomycete (Rhodopirellula baltica SH1 T, formerly Pirellula sp. strain 1). The REGX (Real Environmental GenomiX) project, as it was named, got a six year funding by the Federal Ministry of Education and Research (BMBF).
Within the project we focussed on technology development and competence building by setting up a bioinformatic analysis pipeline for whole genomes. This includes gene-finding, automatic annotation, metabolic reconstruction, genome linguistics and comparative genomics. Furthermore, to cope with the increasing amount of data coming from annotation and functional analysis (transcriptomics/proteomics) the development of new software solutions for visualisation and data integration was started.
The REGX project just marked the starting point. In 2005 we got partners of the Network of Excellence "Marine Genomics Europe". Since then we have processed many genomes from environmental organisms funded by Genoscope, the Moore-foundation and the Max Planck Society.
In order to investigate genes vital for environmental adaptation of environmentally relevant marine microorganisms, for many years Rhodopirellula baltica SH 1T was under continuous investigation. Based on its high quality genome sequence, whole genome microarrays as well as mRNA (cDNA) tag sequencing were set up to perform adaptation experiments. From 2012 on all work related to Planctomycetes will be transferred and continued by Christian Jogler at the DSMZ.

Standards Development
The group is an active member of the Genomic Standards Consortium (GSC) to internationally coordinate the standardisation of contextual (meta)data from the point of data acquisition to publication and data submission to INSDC (EMBL-EBI, GenBank and DDBJ). Widely adopted data standards are a prerequisite for any kind of small- to large-scale data comparison and integration. MIMARKS and MIxS are recent developments of the GSC.

Metagenomics
With the competence gained by the complete genome analysis of cultivated bacteria we were able to start the analysis of genomic fragments from uncultured microorganisms - called metagenomics. Currently, we are involved in several in house and external co-operations.
In October 2008 we started the MIMAS (Microbial Interactions in MArine Systems) project, funded by the BMBF, to investigate the diversity and function of the microbial community in the North Sea at Helgoland Roads. Besides metagenomics, metatranscriptomics using next generation sequencing technology is now conducted.
Since July 2009 we are partners of the MAMBA (Marine Metagenomics for new Biotechnological Applications) project funded by the EU. We will provide the bioinformatic backbone for sequence data analysis and screening for new enzymes for biotechnological applications.

Ecosystems Biology
After nearly one decade of marine molecular research it is now time to bridge the gap between marine diversity research, marine (meta)genomics and the environment. An integration of (i) data on diversity and spatio-temporal abundance of microorganisms with (ii) genomic data and (iii) further oceanographic information on the chemistry, physics, geology and biology of the habitat can be readily achieved based on geographic location and sampling time, see www.megx.net. This was started within the EU-project MetaFunctions coordinated by the Microbial Genomics Group. To archive these goals contextual data acquisition and standardisation is a prerequisite. Furthermore, since October 2009 we are partner of the EuroFleets project funded by the EU. We will provide expertise in bioinformatics for environmental data integration.

Coordinated by the Microbial Genomics and Bioinformatics Research Group the large-scale integrated 7FP EU project Micro B3 (Biodiversity, Bioinformatics, Biotechnology) will develop innovative bioinformatic approaches and a legal framework to make large-scale data on marine viral, bacterial, archaeal and protists genomes and metagenomes accessible for marine ecosystems biology and to define new targets for biotechnological applications. Micro B3 will build upon a highly interdisciplinary consortium of 32 academic and industrial partners comprising world-leading experts in bioinformatics, computer science, biology, ecology, oceanography, bioprospecting and biotechnology, as well as legal aspects. Micro B3 is based on a strong user- and data basis from ongoing European sampling campaigns to long-term ecological research sites.

Phylogenetic inference has a long tradition within the group. We use and develop the software package ARB for phylogenetic tree reconstruction based on ribosomal RNAs and functional genes.
To cope with the increasing amount of ribosomal RNA data we have set up the SILVA system for quality-checked, aligned small- and large subunit ribosomal RNA sequences. We are happy that the SILVA project and databases have become an internationally accepted resource with numerous citations and hits on the webpage.
As a spin-off from SILVA “The All-Species Living Tree” project provides a highly manual curated subset especially designed to serve the microbial taxonomist community. The aim of the project is to reconstruct a single 16S rRNA tree harbouring all sequenced type strains of the hitherto classified species of Archaea and Bacteria.
Furthermore, we offer international workshops and training courses on the theory and practical applications of phylogenetic tree reconstruction. To date more than 600 researchers have participated in these workshops held in Europe and the US. If you want to know more about it, please refer to the company Ribocon.

We have set up a complete bioinformatic pipeline for (meta)genome research. Starting from gene-finding, where we integrated several gene-finders in our metatool MORFind, we managed to install, maintain and adapt the annotation system GenDB. Based on this system we developed the MicHanThi tool for automatic annotation and JCoast for visualisation and manual annotation.
To cope with the deluge of data from Next Generation Sequencing, new software pipelines to store, normalize, cluster, classify and analyse the sequence data are currently under development. Tools to facilitate data analysis, visualisation and metabolic reconstructions have been implemented and are currently being extended.
The organization of small and large sequence fragments into bins of taxonomically related sequences (taxobins) is crucial to link the primarily uncultured functional diversity in the environment with the diversity and abundance of the organisms. Nevertheless, the bioinformatic organisation of these “data clouds” is a computationally demanding task, which is still only partially solved. For this task TaxoMeter is currently under development and TaxSOM has been recently deployed.

Taken together the new technological approaches and unprecedented capacities in environmental research will allow gaining new, unbiased insights into the genes involved in the processes driven by environmental organisms. On a long run, this will provide us the key to open the black box of microbial ecology. As technology developers and providers we generate tools, products and software pipelines to support the biologists coping with the flood of data in life sciences. Transferring data into biological knowledge is our primary goal.

Beginning of 2005 we founded the Ribocon GmbH as a spin-off of the Microbial Genomics and Bioinformatics Research Group for knowledge transfer and product development. Our competences focus on bioinformatic analysis of genes and genomes, phylogenetic inference, the software package ARB, as well as the SILVA databases. Currently, the management team consists of: Dr. Jörg Peplies (CEO), Arno Geerds (CFO) and Prof. Frank Oliver Glöckner.

This page was last updated in December 2011