Folker Meyer

Publications of Folker Meyer

• From genomics to metagenomics.

  Authors: Narayan Desai, Dion Antonopoulos, Jack A Gilbert, Elizabeth M Glass, Folker Meyer

  Current opinion in biotechnology. 02/2012; 23(1):72-6.

  Next-generation sequencing has changed metagenomics. However, sequencing DNA is no longer the bottleneck, rather, the bottleneck is computational analysis and also interpretation. Computational costNext-generation sequencing has changed metagenomics. However, sequencing DNA is no longer the bottleneck, rather, the bottleneck is computational analysis and also interpretation. Computational cost is the obvious issue, as is tool limitations, considering most of the tools we routinely use have been built for clonal genomics or are being adapted to microbial communities. The current trend in metagenomics analysis is toward reducing computational costs through improved algorithms and through analysis strategies. Data sharing and interoperability between tools are critical, since computation for metagenomic datasets is very high.

• Metagenomics - a guide from sampling to data analysis.

  Authors: Torsten Thomas, Jack Gilbert, Folker Meyer

  Microbial informatics and experimentation. 01/2012; 2(1):3.

  ABSTRACT: Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has beenABSTRACT: Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.

• Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010.

  Authors: Sarah L O'Brien, Elizabeth M Glass, Jennifer M Brulc, Jack A Gilbert, Dionysios A Antonopoulos, Folker Meyer

  Standards in genomic sciences. 11/2011; 5(2):198-202.

  This report summarizes the proceedings of the 2(nd) Annual Argonne Soils Workshop held at Argonne National Laboratory October 6-8, 2010. The workshop assembled a diverse group of soil ecologists,This report summarizes the proceedings of the 2(nd) Annual Argonne Soils Workshop held at Argonne National Laboratory October 6-8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, molecular biologists, and computational scientists to discuss the challenges and opportunities related to implementation of metagenomics approaches in soil microbial ecology. The overarching theme of the workshop was "designing ecologically meaningful soil metagenomics research", which encouraged presentations on both ecological and computational topics. The workshop fostered valuable cross-discipline communication and delivered the message that soil metagenomics research must be based on an iterative process between biological inquiry and bioinformatics tools.

• 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.

• BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae).

  Authors: Steffen Lemke, Dionysios A Antonopoulos, Folker Meyer, Marc H Domanus, Urs Schmidt-Ott

  BMC genomics. 05/2011; 12:278.

  In animals, signaling of Bone Morphogenetic Proteins (BMPs) is essential for dorsoventral (DV) patterning of the embryo, but how BMP signaling evolved with changes in embryonic DV differentiation isIn animals, signaling of Bone Morphogenetic Proteins (BMPs) is essential for dorsoventral (DV) patterning of the embryo, but how BMP signaling evolved with changes in embryonic DV differentiation is largely unclear. Based on the extensive knowledge of BMP signaling in Drosophila melanogaster, the morphological diversity of extraembryonic tissues in different fly species provides a comparative system to address this question. The closest relatives of D. melanogaster with clearly distinct DV differentiation are hover flies (Diptera: Syrphidae). The syrphid Episyrphus balteatus is a commercial bio-agent against aphids and has been established as a model organism for developmental studies and chemical ecology. The dorsal blastoderm of E. balteatus gives rise to two extraembryonic tissues (serosa and amnion), whereas in D. melanogaster, the dorsal blastoderm differentiates into a single extraembryonic epithelium (amnioserosa). Recent studies indicate that several BMP signaling components of D. melanogaster, including the BMP ligand Screw (Scw) and other extracellular regulators, evolved in the dipteran lineage through gene duplication and functional divergence. These findings raise the question of whether the complement of BMP signaling components changed with the origin of the amnioserosa. To search for BMP signaling components in E. balteatus, we generated and analyzed transcriptomes of freshly laid eggs (0-30 minutes) and late blastoderm to early germband extension stages (3-6 hours) using Roche/454 sequencing. We identified putative E. balteatus orthologues of 43% of all annotated D. melanogaster genes, including the genes of all BMP ligands and other BMP signaling components. The diversification of several BMP signaling components in the dipteran linage of D. melanogaster preceded the origin of the amnioserosa.[Transcriptome sequence data from this study have been deposited at the NCBI Sequence Read Archive (SRP005289); individually assembled sequences have been deposited at GenBank (JN006969-JN006986).].

• 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.

• Meeting report of the RNA Ontology Consortium January 8-9, 2011.

  Authors: Amanda Birmingham, Jose C Clemente, Narayan Desai, Jack Gilbert, Antonio Gonzalez, Nikos Kyrpides, Folker Meyer, Eric Nawrocki, Peter Sterk, Jesse Stombaugh, Zasha Weinberg, Doug Wendel, Neocles B Leontis, Craig Zirbel, Rob Knight, Alain Laederach

  Standards in genomic sciences. 04/2011; 4(2):252-6.

  This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop toThis report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop to facilitate collaborations among those researchers formalizing concepts in RNA, those developing RNA-related software, and those performing genome annotation and standardization. The workshop included three software presentations, extended round-table discussions, and the constitution of two new working groups, the first to address the need for better software integration and the second to discuss standardization and benchmarking of existing RNA annotation pipelines. These working groups have subsequently pursued concrete implementation of actions suggested during the discussion. Further information about the ROC and its activities can be found at http://roc.bgsu.edu/.

• Connecting genotype to phenotype in the era of high-throughput sequencing.

  Authors: Christopher S Henry, Ross Overbeek, Fangfang Xia, Aaron A Best, Elizabeth Glass, Jack Gilbert, Peter Larsen, Rob Edwards, Terry Disz, Folker Meyer [......] Matthew Dejongh, Daniela Bartels, Narayan Desai, Mark D'Souza, Scott Devoid, Kevin P Keegan, Robert Olson, Andreas Wilke, Jared Wilkening, Rick L Stevens

  Biochimica et biophysica acta. 03/2011; 1810(10):967-77.

  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 ourThe 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.

• Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset.

  Authors: Peter E Larsen, Frank R Collart, Dawn Field, Folker Meyer, Kevin P Keegan, Christopher S Henry, John McGrath, John Quinn, Jack A Gilbert

  Microbial informatics and experimentation. 01/2011; 1(1):4.

  ABSTRACT: The world's oceans are home to a diverse array of microbial life whose metabolic activity helps to drive the earth's biogeochemical cycles. Metagenomic analysis has revolutionized ourABSTRACT: The world's oceans are home to a diverse array of microbial life whose metabolic activity helps to drive the earth's biogeochemical cycles. Metagenomic analysis has revolutionized our access to these communities, providing a system-scale perspective of microbial community interactions. However, while metagenome sequencing can provide useful estimates of the relative change in abundance of specific genes and taxa between environments or over time, this does not investigate the relative changes in the production or consumption of different metabolites. We propose a methodology, Predicted Relative Metabolic Turnover (PRMT) that defines and enables exploration of metabolite-space inferred from the metagenome. Our analysis of metagenomic data from a time-series study in the Western English Channel demonstrated considerable correlations between predicted relative metabolic turnover and seasonal changes in abundance of measured environmental parameters as well as with observed seasonal changes in bacterial population structure. The PRMT method was successfully applied to metagenomic data to explore the Western English Channel microbial metabalome to generate specific, biologically testable hypotheses. Generated hypotheses linked organic phosphate utilization to Gammaproteobactaria, Plantcomycetes, and Betaproteobacteria, chitin degradation to Actinomycetes, and potential small molecule biosynthesis pathways for Lentisphaerae, Chlamydiae, and Crenarchaeota. The PRMT method can be applied as a general tool for the analysis of additional metagenomic or transcriptomic datasets.

• Predicted Relative Metabolomic Turnover - Predicting Changes in the Environmental Metabolome from the Metagenome.

  Authors: Peter E. Larsen, Frank Collart, Folker Meyer, Jack A. Gilbert

  BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Rome, Italy, 26-29 January, 2011; 01/2011

• Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

  Authors: Suparna Mitra, Paul Rupek, Daniel Richter, Tim Urich, Jack Gilbert, Folker Meyer, Andreas Wilke, Daniel Huson

  BMC Bioinformatics. 01/2011;

  Abstract Background Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods areAbstract Background Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the number and scope of metagenome projects. While metagenomics provides information on the gene content, metatranscriptomics aims at understanding gene expression patterns in microbial communities. The initial computational analysis of a metagenome or metatranscriptome addresses three questions: (1) Who is out there? (2) What are they doing? and (3) How do different datasets compare? There is a need for new computational tools to answer these questions. In 2007, the program MEGAN (MEtaGenome ANalyzer) was released, as a standalone interactive tool for analyzing the taxonomic content of a single metagenome dataset. The program has subsequently been extended to support comparative analyses of multiple datasets. Results The focus of this paper is to report on new features of MEGAN that allow the functional analysis of multiple metagenomes (and metatranscriptomes) based on the SEED hierarchy and KEGG pathways. We have compared our results with the MG-RAST service for different datasets. Conclusions The MEGAN program now allows the interactive analysis and comparison of the taxonomical and functional content of multiple datasets. As a stand-alone tool, MEGAN provides an alternative to web portals for scientists that have concerns about uploading their unpublished data to a website.

• An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud.

  Authors: Andreas Wilke, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer

  Concurrency and Computation: Practice and Experience. 01/2011; 23:2250-2257.

• Proposal for Open Discussion - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments.

  Authors: Folker Meyer, Nikos Kyrpides

  BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Rome, Italy, 26-29 January, 2011; 01/2011

• Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.

  Authors: Suparna Mitra, Paul Rupek, Daniel C Richter, Tim Urich, Jack A Gilbert, Folker Meyer, Andreas Wilke, Daniel H Huson

  BMC bioinformatics. 01/2011; 12 Suppl 1:S21.

  Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods are fueling a rapid increaseMetagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the number and scope of metagenome projects. While metagenomics provides information on the gene content, metatranscriptomics aims at understanding gene expression patterns in microbial communities. The initial computational analysis of a metagenome or metatranscriptome addresses three questions: (1) Who is out there? (2) What are they doing? and (3) How do different datasets compare? There is a need for new computational tools to answer these questions. In 2007, the program MEGAN (MEtaGenome ANalyzer) was released, as a standalone interactive tool for analyzing the taxonomic content of a single metagenome dataset. The program has subsequently been extended to support comparative analyses of multiple datasets. The focus of this paper is to report on new features of MEGAN that allow the functional analysis of multiple metagenomes (and metatranscriptomes) based on the SEED hierarchy and KEGG pathways. We have compared our results with the MG-RAST service for different datasets. The MEGAN program now allows the interactive analysis and comparison of the taxonomical and functional content of multiple datasets. As a stand-alone tool, MEGAN provides an alternative to web portals for scientists that have concerns about uploading their unpublished data to a website.

• The future of microbial metagenomics (or is ignorance bliss?).

  Authors: Jack A Gilbert, Folker Meyer, Mark J Bailey

  The ISME journal. 11/2010; 5(5):777-9.

• Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.

  Authors: Yunwei Wang, Dionysios A Antonopoulos, Xiaorong Zhu, Laura Harrell, Ira Hanan, John C Alverdy, Folker Meyer, Mark W Musch, Vincent B Young, Eugene B Chang

  Applied microbiology and biotechnology. 10/2010; 88(6):1333-42.

  Metagenomic analysis of colonic mucosa-associated microbes has been complicated by technical challenges that disrupt or alter community structure and function. In the present study, we determined theMetagenomic analysis of colonic mucosa-associated microbes has been complicated by technical challenges that disrupt or alter community structure and function. In the present study, we determined the feasibility of laser capture microdissection (LCM) of intact regional human colonic mucosa-associated microbes followed by phi29 multiple displacement amplification (MDA) and massively parallel sequencing for metagenomic analysis. Samples were obtained from the healthy human subject without bowel preparation and frozen sections immediately prepared. Regional mucosa-associated microbes were successfully dissected using LCM with minimal contamination by host cells, their DNA extracted and subjected to phi29 MDA with a high fidelity, prior to shotgun sequencing using the GS-FLX DNA sequencer. Metagenomic analysis of approximately 67 million base pairs of DNA sequences from two samples revealed that the metabolic functional profiles in mucosa-associated microbes were as diverse as those reported in feces, specifically the representation of functional genes associated with carbohydrate, protein, and nucleic acid utilization. In summary, these studies demonstrate the feasibility of the approach to study the structure and metagenomic profiles of human intestinal mucosa-associated microbial communities at small spatial scales.

• Maternal activation of gap genes in the hover fly Episyrphus.

  Authors: Steffen Lemke, Stephanie E Busch, Dionysios A Antonopoulos, Folker Meyer, Marc H Domanus, Urs Schmidt-Ott

  Development (Cambridge, England). 05/2010; 137(10):1709-19.

  The metameric organization of the insect body plan is initiated with the activation of gap genes, a set of transcription-factor-encoding genes that are zygotically expressed in broad and partiallyThe metameric organization of the insect body plan is initiated with the activation of gap genes, a set of transcription-factor-encoding genes that are zygotically expressed in broad and partially overlapping domains along the anteroposterior (AP) axis of the early embryo. The spatial pattern of gap gene expression domains along the AP axis is generally conserved, but the maternal genes that regulate their expression are not. Building on the comprehensive knowledge of maternal gap gene activation in Drosophila, we used loss- and gain-of-function experiments in the hover fly Episyrphus balteatus (Syrphidae) to address the question of how the maternal regulation of gap genes evolved. We find that, in Episyrphus, a highly diverged bicoid ortholog is solely responsible for the AP polarity of the embryo. Episyrphus bicoid represses anterior zygotic expression of caudal and activates the anterior and central gap genes orthodenticle, hunchback and Krüppel. In bicoid-deficient Episyrphus embryos, nanos is insufficient to generate morphological asymmetry along the AP axis. Furthermore, we find that torso transiently regulates anterior repression of caudal and is required for the activation of orthodenticle, whereas all posterior gap gene domains of knirps, giant, hunchback, tailless and huckebein depend on caudal. We conclude that all maternal coordinate genes have altered their specific functions during the radiation of higher flies (Cyclorrhapha).

• Metagenomics: A foundling finds its feet.

  Authors: Jack A Gilbert, Folker Meyer, Dawn Field, Lynn M Schriml, George M Garrity

  Standards in genomic sciences. 01/2010; 3(2):212-3.

• The United States of America and scientific research.

  Authors: Gregory J Hather, Winston Haynes, Roger Higdon, Natali Kolker, Elizabeth A Stewart, Peter Arzberger, Patrick Chain, Dawn Field, B Robert Franza, Biaoyang Lin, Folker Meyer, Vural Ozdemir, Charles V Smith, Gerald van Belle, John Wooley, Eugene Kolker

  PloS one. 01/2010; 5(8):e12203.

  To gauge the current commitment to scientific research in the United States of America (US), we compared federal research funding (FRF) with the US gross domestic product (GDP) and industry researchTo gauge the current commitment to scientific research in the United States of America (US), we compared federal research funding (FRF) with the US gross domestic product (GDP) and industry research spending during the past six decades. In order to address the recent globalization of scientific research, we also focused on four key indicators of research activities: research and development (R&D) funding, total science and engineering doctoral degrees, patents, and scientific publications. We compared these indicators across three major population and economic regions: the US, the European Union (EU) and the People's Republic of China (China) over the past decade. We discovered a number of interesting trends with direct relevance for science policy. The level of US FRF has varied between 0.2% and 0.6% of the GDP during the last six decades. Since the 1960s, the US FRF contribution has fallen from twice that of industrial research funding to roughly equal. Also, in the last two decades, the portion of the US government R&D spending devoted to research has increased. Although well below the US and the EU in overall funding, the current growth rate for R&D funding in China greatly exceeds that of both. Finally, the EU currently produces more science and engineering doctoral graduates and scientific publications than the US in absolute terms, but not per capita. This study's aim is to facilitate a serious discussion of key questions by the research community and federal policy makers. In particular, our results raise two questions with respect to: a) the increasing globalization of science: "What role is the US playing now, and what role will it play in the future of international science?"; and b) the ability to produce beneficial innovations for society: "How will the US continue to foster its strengths?"

• Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010.

  Authors: Jack A Gilbert, Folker Meyer, Rob Knight, Dawn Field, Nikos Kyrpides, Pelin Yilmaz, John Wooley

  Standards in genomic sciences. 01/2010; 3(3):235-9.

  This report summarizes the proceedings of the Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructure (M5) Roundtable at the 13th International Society for Microbial Ecology Meeting inThis report summarizes the proceedings of the Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructure (M5) Roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, USA August 22-27, 2010. The Genomic Standards Consortium (GSC) hosted this meeting as a community engagement exercise to describe the GSC to the microbial ecology community during this important international meeting. The roundtable included five talks given by members of the GSC, and was followed by audience participation in the form of a roundtable discussion. This report summarizes this event. Further information on the GSC and its range of activities can be found at http://www.gensc.org.