ORCID Profile
0000-0003-1112-2284
Current Organisation
Universität Duisburg-Essen
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Publisher: Springer Science and Business Media LLC
Date: 19-06-2020
Publisher: American Society for Microbiology
Date: 15-02-2008
DOI: 10.1128/AEM.01844-07
Abstract: Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas , in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.
Publisher: Oxford University Press (OUP)
Date: 25-09-2005
DOI: 10.1093/NAR/GKI866
Publisher: Springer Science and Business Media LLC
Date: 19-09-2008
Publisher: Public Library of Science (PLoS)
Date: 11-12-2009
Publisher: Elsevier BV
Date: 10-2011
DOI: 10.1016/J.BBAGEN.2011.03.010
Abstract: The development of next generation sequencing technology is rapidly changing the face of the genome annotation and analysis field. One of the primary uses for genome sequence data is to improve our understanding and prediction of phenotypes for microbes and microbial communities, but the technologies for predicting phenotypes must keep pace with the new sequences emerging. This review presents an integrated view of the methods and technologies used in the inference of phenotypes for microbes and microbial communities based on genomic and metagenomic data. Given the breadth of this topic, we place special focus on the resources available within the SEED Project. We discuss the two steps involved in connecting genotype to phenotype: sequence annotation, and phenotype inference, and we highlight the challenges in each of these steps when dealing with both single genome and metagenome data. This integrated view of the genotype-to-phenotype problem highlights the importance of a controlled ontology in the annotation of genomic data, as this benefits subsequent phenotype inference and metagenome annotation. We also note the importance of expanding the set of reference genomes to improve the annotation of all sequence data, and we highlight metagenome assembly as a potential new source for complete genomes. Finally, we find that phenotype inference, particularly from metabolic models, generates predictions that can be validated and reconciled to improve annotations. This review presents the first look at the challenges and opportunities associated with the inference of phenotype from genotype during the next generation sequencing revolution. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.
Publisher: Springer Science and Business Media LLC
Date: 06-2012
DOI: 10.1038/NBT.2235
Publisher: Oxford University Press (OUP)
Date: 15-07-2006
DOI: 10.1093/BIOINFORMATICS/BTL247
Abstract: Motivation: Novel sequencing techniques can give access to organisms that are difficult to cultivate using conventional methods. When applied to environmental s les, the data generated has some drawbacks, e.g. short length of assembled contigs, in-frame stop codons and frame shifts. Unfortunately, current gene finders cannot circumvent these difficulties. At the same time, the automated prediction of genes is a prerequisite for the increasing amount of genomic sequences to ensure progress in metagenomics. Results: We introduce a novel gene finding algorithm that incorporates features overcoming the short length of the assembled contigs from environmental data, in-frame stop codons as well as frame shifts contained in bacterial sequences. The results show that by searching for sequence similarities in an environmental s le our algorithm is capable of detecting a high fraction of its gene content, depending on the species composition and the overall size of the s le. The method is valuable for hunting novel unknown genes that may be specific for the habitat where the s le is taken. Finally, we show that our algorithm can even exploit the limited information contained in the short reads generated by 454 technology for the prediction of protein coding genes. Availability: The program is freely available upon request. Contact: Lutz.Krause@CeBiTec.Uni-Bielefeld.DE
Publisher: Springer Science and Business Media LLC
Date: 08-02-2008
Abstract: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.
Publisher: Oxford University Press (OUP)
Date: 03-01-2007
DOI: 10.1093/NAR/GKL947
No related grants have been discovered for Folker Meyer.