Frank Oliver Glöckner

Publications of Frank Oliver Glöckner

• Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom.

  Authors: Hanno Teeling, Bernhard M Fuchs, Dörte Becher, Christine Klockow, Antje Gardebrecht, Christin M Bennke, Mariette Kassabgy, Sixing Huang, Alexander J Mann, Jost Waldmann [......] Michael Hecker, Jörg Peplies, Frank D Bockelmann, Ulrich Callies, Gunnar Gerdts, Antje Wichels, Karen H Wiltshire, Frank Oliver Glöckner, Thomas Schweder, Rudolf Amann

  Science (New York, N.Y.). 05/2012; 336(6081):608-11.

  Phytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession ofPhytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession of populations at genus-level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes (transporters; in particular, TonB-dependent transporters) and phosphate acquisition strategies were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria are specialized for successive decomposition of algal-derived organic matter. Our results suggest that algal substrate availability provided a series of ecological niches in which specialized populations could bloom. This reveals how planktonic species, despite their seemingly homogeneous habitat, can evade extinction by direct competition.

• SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes.

  Authors: Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner

  Bioinformatics (Oxford, England). 05/2012;

  MOTIVATION: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNAMOTIVATION: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. RESULTS: Here we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA employs a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands.SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAli- Base III benchmark MSAs could be reproduced with 99.3%, 97.6% and 96.1% accuracy. A larger benchmark MSA comprising 38,772 sequences could be reproduced with 98.9% and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. AVAILABILITY: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref data-sets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license. CONTACT: epruesse@mpi-bremen.de.

• Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

  Authors: Hanno Teeling, Bernhard M. Fuchs, Dörte Becher, Christine Klockow, Antje Gardebrecht, Christin M. Bennke, Mariette Kassabgy, Sixing Huang, Alexander J. Mann, Jost Waldmann [......] Michael Hecker, Jörg Peplies, Frank D. Bockelmann, Ulrich Callies, Gunnar Gerdts, Antje Wichels, Karen H. Wiltshire, Frank Oliver Glöckner, Thomas Schweder, Rudolf Amann

  Science. 05/2012; 336(6081-4):608-611.

  Phytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession ofPhytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession of populations at genus-level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes (transporters; in particular, TonB-dependent transporters) and phosphate acquisition strategies were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria are specialized for successive decomposition of algal-derived organic matter. Our results suggest that algal substrate availability provided a series of ecological niches in which specialized populations could bloom. This reveals how planktonic species, despite their seemingly homogeneous habitat, can evade extinction by direct competition.

• Ecological structuring of bacterial and archaeal taxa in surface ocean waters.

  Authors: Pelin Yilmaz, Morten H Iversen, Wolfgang Hankeln, Renzo Kottmann, Christian Quast, Frank Oliver Glöckner

  FEMS microbiology ecology. 03/2012;

  The Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific and Indian Oceans. ThisThe Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific and Indian Oceans. This study makes use of the wide range of environmental conditions and habitats encompassed within the GOS sampling sites in order to investigate the ecological structuring of bacterial and archaeal taxon ranks. Community structures based on taxonomically classified 16S ribosomal RNA (rRNA) gene fragments at phylum, class, order, family, and genus rank levels were examined using multivariate statistical analysis and the results were inspected in the context of oceanographic environmental variables, and structured habitat classifications. At all taxon rank levels, community structures of neritic, oceanic, estuarine biomes, as well as other exotic biomes (salt marsh, lake, mangrove) were readily distinguishable from each other. A strong structuring of the communities with chlorophyll a concentration and a weaker yet significant structuring with temperature and salinity was observed. Furthermore, there were significant correlations between community structures and habitat classification. These results were used for further investigation of one-to-one relationships between taxa and environment, and provided indications for ecological preferences shaped by primary production for both cultured and uncultured bacterial and archaeal clades. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

• Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study.

  Authors: Manuel Ferrer, Johannes Werner, Tatyana N Chernikova, Rafael Bargiela, Lucía Fernández, Violetta La Cono, Jost Waldmann, Hanno Teeling, Olga V Golyshina, Frank Oliver Glöckner, Michail M Yakimov, Peter N Golyshin

  Environmental microbiology. 01/2012; 14(1):268-81.

  So far only little is known about the microbial ecology of Mediterranean deep-sea hypersaline anoxic lakes (DHALs). These brine lakes were formed by evaporite dissolution/brine seeps and areSo far only little is known about the microbial ecology of Mediterranean deep-sea hypersaline anoxic lakes (DHALs). These brine lakes were formed by evaporite dissolution/brine seeps and are important model environments to provide insights into possible metabolisms and distributions of microorganisms on the early Earth. Our study on the Lake Thetis, a new thalassohaline DHAL located South-East of the Medriff Corridor, has revealed microbial communities of contrasting compositions with a high number of novel prokaryotic candidate divisions. The major finding of our present work is co-occurrence of at least three autotrophic carbon dioxide fixation pathways in the brine-seawater interface that are likely fuelled by an active ramified sulphur cycle. Genes for the reductive acetyl-CoA and reductive TCA pathways were also found in the brine suggesting that these pathways are operational even at extremely elevated salinities and that autotrophy is more important in hypersaline environments than previously assumed. Surprisingly, genes coding for RuBisCo were found in the highly reduced brine. Three types of sulphide oxidation pathways were found in the interface. The first involves a multienzyme Sox complex catalysing the complete oxidation of reduced sulphur compounds to sulphate, the second type recruits SQR sulphide:quinone reductase for oxidation of sulphide to elemental sulphur, which, in the presence of sulphide, could further be reduced by polysulphide reductases in the third pathway. The presence of the latter two allows a maximal energy yield from the oxidation of sulphide and at the same time prevents the acidification and the accumulation of S(0) deposits. Amino acid composition analysis of deduced proteins revealed a significant overrepresentation of acidic residues in the brine compared with the interface. This trait is typical for halophilic organisms as an adaptation to the brine's extreme hypersalinity. This work presents the first metagenomic survey of the microbial communities of the recently discovered Lake Thetis whose brine constitutes one of saltiest water bodies ever reported.

• Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean.

  Authors: Paola R Gómez-Pereira, Margarete Schüler, Bernhard M Fuchs, Christin Bennke, Hanno Teeling, Jost Waldmann, Michael Richter, Valérie Barbe, Elodie Bataille, Frank Oliver Glöckner, Rudolf Amann

  Environmental microbiology. 09/2011; 14(1):52-66.

  Bacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolyticBacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean, the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as phylogenetic marker, and their comparison to complete Bacteroidetes genomes. Almost all of the 16S rRNA harbouring fosmids belonged to clades that we previously identified in BPLR and NAST. The majority of sequenced fosmids could be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also present novel genomic information on the classes Cytophagia and Sphingobacteria, suggesting a capability of the latter for attachment to algal surfaces. In our fosmid set we identified a larger potential for polysaccharide degradation and cell surface attachment in the phytoplankton-rich BPLR. Particularly, two flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a whole armoury of enzymes that likely function in degradation of sulfated polysaccharides known to be major constituents of phytoplankton cell walls. Genes involved in protein and peptidoglycan degradation, although present in both fosmid sets, seemed to have a slight preponderance in NAST. This study provides support for the hypothesis of a distinct specialization among marine Bacteroidetes for the degradation of certain types of polymers.

• Analysis of 23S rRNA genes in metagenomes - a case study from the Global Ocean Sampling Expedition.

  Authors: Pelin Yilmaz, Renzo Kottmann, Elmar Pruesse, Christian Quast, Frank Oliver Glöckner

  Systematic and applied microbiology. 06/2011; 34(6):462-9.

  As an evolutionary marker, 23S ribosomal RNA (rRNA) offers more diagnostic sequence stretches and greater sequence variation than 16S rRNA. However, 23S rRNA is still not as widely used. Based on 80As an evolutionary marker, 23S ribosomal RNA (rRNA) offers more diagnostic sequence stretches and greater sequence variation than 16S rRNA. However, 23S rRNA is still not as widely used. Based on 80 metagenome samples from the Global Ocean Sampling (GOS) Expedition, the usefulness and taxonomic resolution of 23S rRNA were compared to those of 16S rRNA. Since 23S rRNA is approximately twice as large as 16S rRNA, twice as many 23S rRNA gene fragments were retrieved from the GOS reads than 16S rRNA gene fragments, with 23S rRNA gene fragments being generally about 100bp longer. Datasets for 16S and 23S rRNA sequences revealed similar relative abundances for major marine bacterial and archaeal taxa. However, 16S rRNA sequences had a better taxonomic resolution due to their significantly larger reference database. Reevaluation of the specificity of previously published PCR amplification primers and group specific fluorescence in situ hybridization probes on this metagenomic set of non-amplified 23S rRNA sequences revealed that out of 16 primers investigated, only two had more than 90% target group coverage. Evaluations of two probes, BET42a and GAM42a, were in accordance with previous evaluations, with a discrepancy in the target group coverage of the GAM42a probe when evaluated against the GOS metagenomic dataset.

• From genomics to microevolution and ecology: the case of Salinibacter ruber

  Authors: Arantxa Peña, Hanno Teeling, Jaime Huerta-Cepas, Fernando Santos, Inmaculada Meseguer, Marianna Lucio, Philippe Schmitt-Kopplin, Joaquín Dopazo, Ramon Rosselló-Mora, Margarete Schüler, Frank Oliver Glöckner, Rudolf Amann, Toni Gabaldón, Josefa Antón

  06/2011: pages 109-122;

  ISBN: ISBN 978-3-642-20197-4

• The Genomic Standards Consortium.

  Authors: Dawn Field, Linda Amaral-Zettler, Guy Cochrane, James R Cole, Peter Dawyndt, George M Garrity, Jack Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Ilene Karsch-Mizrachi [......] Nikos Kyrpides, Folker Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M Schriml, Peter Sterk, Tatiana Tatusova, David W Ussery, Owen White, John Wooley

  PLoS biology. 06/2011; 9(6):e1001088.

  A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise itsA vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

• Phylogenetic characterisation of picoplanktonic populations with high and low nucleic acid content in the North Atlantic Ocean.

  Authors: Martha Schattenhofer, Jörg Wulf, Ivalyo Kostadinov, Frank Oliver Glöckner, Mikhail V Zubkov, Bernhard M Fuchs

  Systematic and applied microbiology. 05/2011; 34(6):470-5.

  In flow cytometric analyses of marine prokaryotic picoplankton often two populations with distinct differences in their apparent nucleic acid content are discernable, one with a high and one with aIn flow cytometric analyses of marine prokaryotic picoplankton often two populations with distinct differences in their apparent nucleic acid content are discernable, one with a high and one with a low nucleic acid content (HNA and LNA, respectively). In this study we determined the phylogenetic composition of flow cytometrically sorted HNA and LNA populations, collected at six stations along a transect across three oceanic provinces from Iceland to the Azores. Catalysed reporter deposition fluorescence in situ hybridisation (CARD-FISH) analysis of sorted cells revealed distinct differences in phylogenetic composition between the LNA and HNA populations with only little overlap. At all stations the LNA population was dominated by the alphaproteobacterial clade SAR11 (45-74%). Also, Betaproteobacteria were always present at 2-4%. While the LNA composition was rather stable, the HNA populations were composed of distinct phylogenetic clades in the different oceanic provinces of Arctic and Tropics. For example Cyanobacteria dominated the North Atlantic Gyre HNA population (29-44%) with Prochlorococcus as the major clade (34-44%), but were low in Arctic and Polar waters (1% and 5%, respectively). In contrast, Bacteroidetes accounted for the majority of HNA cells in the Polar and Arctic province (26% and 32%, respectively), but were low in the Gyre region (3-10%). The DNA content of the HNA population was about 3.5 times higher than that of the LNA populations. This reflects differences in the genome sizes of closely related cultured representatives of HNA clades (3-6Mbp) and LNA clades (1.3-1.5Mbp).

• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

  Authors: Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane [......] James M Tiedje, Doyle V Ward, George M Weinstock, Doug Wendel, Owen White, Andrew Whiteley, Andreas Wilke, Jennifer R Wortman, Tanya Yatsunenko, Frank Oliver Glöckner

  Nature biotechnology. 05/2011; 29(5):415-20.

  Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce aHere we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

• Release LTPs104 of the All-Species Living Tree.

  Authors: Raúl Munoz, Pablo Yarza, Wolfgang Ludwig, Jean Euzéby, Rudolf Amann, Karl-Heinz Schleifer, Frank Oliver Glöckner, Ramon Rosselló-Móra

  Systematic and applied microbiology. 05/2011; 34(3):169-70.

• Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard.

  Authors: Melissa Beth Duhaime, Renzo Kottmann, Dawn Field, Frank Oliver Glöckner

  Standards in genomic sciences. 04/2011; 4(2):271-85.

  In any sequencing project, the possible depth of comparative analysis is determined largely by the amount and quality of the accompanying contextual data. The structure, content, and storage of thisIn any sequencing project, the possible depth of comparative analysis is determined largely by the amount and quality of the accompanying contextual data. The structure, content, and storage of this contextual data should be standardized to ensure consistent coverage of all sequenced entities and facilitate comparisons. The Genomic Standards Consortium (GSC) has developed the "Minimum Information about Genome/Metagenome Sequences (MIGS/MIMS)" checklist for the description of genomes and here we annotate all 30 publicly available marine bacteriophage sequences to the MIGS standard. These annotations build on existing International Nucleotide Sequence Database Collaboration (INSDC) records, and confirm, as expected that current submissions lack most MIGS fields. MIGS fields were manually curated from the literature and placed in XML format as specified by the Genomic Contextual Data Markup Language (GCDML). These "machine-readable" reports were then analyzed to highlight patterns describing this collection of genomes. Completed reports are provided in GCDML. This work represents one step towards the annotation of our complete collection of genome sequences and shows the utility of capturing richer metadata along with raw sequences.

• Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

  Authors: Norman Morrison, David Hancock, Lynette Hirschman, Peter Dawyndt, Bert Verslyppe, Nikos Kyrpides, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner, Jeff Grethe, Tim Booth, Peter Sterk, Goran Nenadic, Dawn Field

  Standards in genomic sciences. 04/2011; 4(2):286-92.

  In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that mustIn the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources.

• The genomic standards consortium: bringing standards to life for microbial ecology.

  Authors: Pelin Yilmaz, Jack A Gilbert, Rob Knight, Linda Amaral-Zettler, Ilene Karsch-Mizrachi, Guy Cochrane, Yasukazu Nakamura, Susanna-Assunta Sansone, Frank Oliver Glöckner, Dawn Field

  The ISME journal. 04/2011; 5(10):1565-7.

• Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes.

  Authors: Ivaylo Kostadinov, Renzo Kottmann, Alban Ramette, Jost Waldmann, Pier Luigi Buttigieg, Frank Oliver Glöckner

  Microbial informatics and experimentation. 01/2011; 1(1):9.

  ABSTRACT: DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure onABSTRACT: DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine Synechococcus strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated. We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool. Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to in situ measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data.

• CDinFusion--submission-ready, on-line integration of sequence and contextual data.

  Authors: Wolfgang Hankeln, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner

  PloS one. 01/2011; 6(9):e24797.

  State of the art (DNA) sequencing methods applied in "Omics" studies grant insight into the 'blueprints' of organisms from all domains of life. Sequencing is carried out around the globe and the dataState of the art (DNA) sequencing methods applied in "Omics" studies grant insight into the 'blueprints' of organisms from all domains of life. Sequencing is carried out around the globe and the data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental data, as well as information about the environment are rarely submitted along with the sequence data. If these contextual or metadata are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence data collection and to promote the capturing, exchange and integration of sequence data with contextual data. In a recent community effort the GSC has developed a series of recommendations for contextual data that should be submitted along with sequence data. To support the scientific community to significantly enhance the quality and quantity of contextual data in the public sequence data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate contextual and sequence data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.

• Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1.

  Authors: Melissa Beth Duhaime, Antje Wichels, Jost Waldmann, Hanno Teeling, Frank Oliver Glöckner

  The ISME journal. 01/2011; 5(1):107-21.

  Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes areMarine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed 'ecogenomic' patterns of Pseudoalteromonas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intra-genomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most 'host'-adapted proteins also have the strongest bacterial tetra signature, whereas the least 'host'-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules. Finally, analysis of the structural proteome identified seven proteins that make up the mature virion, four of which were previously unknown. This integrated approach combines both novel and classical strategies and serves as a model to elucidate ecological inferences and evolutionary relationships from phage genomes that typically abound with unknown gene content.

• Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics.

  Authors: Marc Weber, Hanno Teeling, Sixing Huang, Jost Waldmann, Mariette Kassabgy, Bernhard M Fuchs, Anna Klindworth, Christine Klockow, Antje Wichels, Gunnar Gerdts, Rudolf Amann, Frank Oliver Glöckner

  The ISME journal. 12/2010; 5(5):918-28.

  Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifyingNext-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.

• Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses.

  Authors: Pablo Yarza, Wolfgang Ludwig, Jean Euzéby, Rudolf Amann, Karl-Heinz Schleifer, Frank Oliver Glöckner, Ramon Rosselló-Móra

  Systematic and applied microbiology. 10/2010; 33(6):291-9.

  The "All-Species Living Tree Project" (LTP) provides the scientific community with a useful taxonomic tool consisting of a curated database of type strain sequences, a universal and optimizedThe "All-Species Living Tree Project" (LTP) provides the scientific community with a useful taxonomic tool consisting of a curated database of type strain sequences, a universal and optimized alignment and a single phylogenetic tree harboring all the type strains of the hitherto classified species. On the website http://www.arb-silva.de/projects/living-tree an update has been regularly maintained by including the 1301 new descriptions that have appeared in the validation and notification lists of the IJSEM journal. The topology of the 16S rRNA-based tree was validated with a detailed comparison against a collection of taxa-specific and broad-range trees made using different approaches, subsets of sequences and alignments. Seven percent of the classified species is still missing, as their type strains do not have a good quality SSU sequence. In addition, a new database of type strains for which adequate 23S rRNA entries existed in public repositories was built. Among the 8602 species with validly published names until February 2010, we were able to find good quality LSU representatives for 792 type strains, whereas around 91% of the complete catalogue still remains unsequenced. Despite the scarce representation of some groups in LSU databases, we have devised a highly optimized alignment and a reliable LSU tree in order to set up a stable phylogenetic starting point for taxonomic purposes. The current release corresponds to the fourth update of the project (LTPs102), and contains additional features which increase usability and compatibility. Use the contact address living-tree@arb-silva.de to provide additional input for the development of this taxonomic tool.