W Ludwig

Ribocon GmbH, Bremen, Bremen, Germany

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Publications (247)837.6 Total impact

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    ABSTRACT: Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.
    Nature Reviews Microbiology 08/2014; 12(9):635-45. · 22.49 Impact Factor
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    ABSTRACT: Nitrite oxidizing bacteria are an integral part of the nitrogen cycle in marine waters, but the knowledge about their diversity is limited. Recently, a high abundance of Nitrospina-like 16S rRNA gene sequences has been detected in oceanic habitats with low oxygen content by molecular methods. Here, we describe a new strain of Nitrospina, which was sampled in 100m depth from the Black Sea. It coexisted with a not-yet cultivated chemoorganotrophic gammaproteobacterium and could be purified by classical isolation methods including Percoll density gradient centrifugation. The new Nitrospina-like bacterium grew lithoautotrophically at 28°C in diluted seawater supplemented with inorganic salts and nitrite. Gram-negative rods were characterized morphologically, physiologically and partly biochemically. The 16S rRNA gene of the new strain of Nitrospina is 97.9% similar to the described species N. gracilis and DNA/DNA hybridization experiments revealed a relatedness of 30.0%. The data from both Nitrospina species and environmental clones were used for an extensive 16S rRNA based phylogenetic study applying high quality filtering. Treeing analyses confirm the newly defined phylum status for "Nitrospinae" [18]. The results of phylogenetic and genotypic analyses support the proposal of a novel species Nitrospina watsonii sp. nov. (type strain 347(T), LMG 27401(T), NCIMB 14887(T)).
    Systematic and Applied Microbiology 02/2014; · 3.29 Impact Factor
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    ABSTRACT: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.
    Nucleic Acids Research 11/2013; · 8.81 Impact Factor
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    ABSTRACT: High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
    Systematic and Applied Microbiology 02/2013; 36(1):69-73. · 3.29 Impact Factor
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    ABSTRACT: 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 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.
    Nature Biotechnology 05/2011; 29(5):415-20. · 32.44 Impact Factor
  • 05/2011: pages 399 - 406; , ISBN: 9781118010518
  • Systematic and Applied Microbiology 05/2011; 34(3):169-70. · 3.29 Impact Factor
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    Wolfgang Ludwig, Jean Euzéby, William B. Whitman
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    ABSTRACT: This revised road map updates previous outlines of Garrity and Holt (2001) and Garrity et al. (2005) with the description of additional taxa and new phylogenetic analyses. While the outline/road map seeks to be complete for all taxa validated prior to July 1, 2006, some taxa described after that date are included.
    02/2011: pages 1-24;
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    01/2011: pages 1-13;
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    ABSTRACT: 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 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.
    Systematic and Applied Microbiology 10/2010; 33(6):291-9. · 3.29 Impact Factor
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    ABSTRACT: The order Rickettsiales (Alphaproteobacteria) is a well-known group containing obligate endocellular prokaryotes. The order encompasses three families (Rickettsiaceae, Anaplasmataceae, and Holosporaceae) and a fourth, family-level cluster, which includes only one candidate species, "Candidatus Midichloria mitochondrii," as well as several unnamed bacterial symbionts. The broad host range exhibited by the members of the "Candidatus Midichloria" clade suggests their eventual relevance for a better understanding of the evolution of symbiosis and host specificity of Rickettsiales. In this paper, two new bacteria belonging to the "Candidatus Midichloria" clade, hosted by two different strains of the ciliate protist Euplotes harpa, are described on the basis of ultrastructural observations, comparative 16S rRNA gene sequence analysis, and an estimation of the percentage of infection. Ultrastructure of these bacteria shows some unusual features: one has an electron-dense cytoplasm, and the other one lacks a symbiosomal membrane. The latter was up to now considered an exclusive feature of bacteria belonging to the family Rickettsiaceae. 16S rRNA gene phylogenetic analysis unambiguously places the new bacteria in the "Candidatus Midichloria" clade, although their phylogenetic relationships with other members of the clade are not clearly resolved. This is the first report of a ciliate-borne bacterium belonging to the "Candidatus Midichloria" clade. On the basis of the data obtained, the two bacteria are proposed as two new candidate genera and species, "Candidatus Anadelfobacter veles" and "Candidatus Cyrtobacter comes."
    Applied and Environmental Microbiology 06/2010; 76(12):4047-54. · 3.95 Impact Factor
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    ABSTRACT: A Gram-negative, oxidase- and catalase-positive, flagellated, rod-shaped bacterium, designated strain EM 1(T), was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belonged to the family Oxalobacteraceae within the class Betaproteobacteria; the closest phylogenetic relative was Undibacterium pigrum DSM 19792(T) (96.7 % gene sequence similarity). The new isolate could be distinguished from the type strain of U. pigrum DSM 19792(T) (=CCUG 49009(T)=CIP 109318(T)) and from strain CCUG 49012(T), which has been described as a second genomovar of this species, on the basis of genotypic data and several phenotypic properties. An S-layer was present in the cell envelope in U. pigrum DSM 19792(T), but was absent in strains EM 1(T) and CCUG 49012(T). Test conditions were established that enabled strain CCUG 49012(T) to be distinguished from U. pigrum DSM 19792(T). As found for U. pigrum, the main fatty acids of strains EM 1(T) and CCUG 49012(T) were summed feature 3 (including unsaturated C(16 : 1)ω7c), straight-chain C(16 : 0) and unsaturated C(18 : 1)ω7c (low percentage in strain CCUG 49012(T)), and C(10 : 0) 3-OH was the sole hydroxylated fatty acid. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamine profile was mainly composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. In contrast to U. pigrum and strain CCUG 49012(T), where ubiquinone Q8 was reported as the sole quinone component, the quinone system of strain EM 1(T) consisted of ubiquinone Q-8 (64 %) and Q-7 (36 %). The 16S rRNA gene sequence similarity, the polar lipid profile and the absence of C(12)-hydroxylated fatty acids all indicated that strain EM 1(T) was affiliated with the genus Undibacterium. 16S rRNA gene sequence similarity values lower than 97.0 % and several differentiating phenotypic traits demonstrated that strain EM 1(T) represents a novel species for which the name Undibacterium oligocarboniphilum sp. nov. is proposed (type strain EM 1(T)=DSM 21777(T)=CCUG 57265(T)). In addition, based on previously published results and this study, a separate species, Undibacterium parvum sp. nov., is proposed with strain CCUG 49012(T) (=DSM 23061(T)=CIP 109317(T)) as the type strain.
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 03/2010; 61(Pt 2):384-91. · 2.11 Impact Factor
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    ABSTRACT: The phylum Bacteroidetes is a phenotypically diverse group of Gram-stain-negative rods that do not form endospores. They are circumscribed for this volume on the basis of phylogenetic analysis of 16S rRNA gene sequences.
    01/2010;
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    ABSTRACT: Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.
    International journal of systematic and evolutionary microbiology 09/2009; 60(Pt 1):249-66. · 2.11 Impact Factor
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    ABSTRACT: Despite their widespread occurrence in soils, the ecology of Acidobacteria and their response to environmental perturbations due to human activities remain very poorly documented. This study was aimed at assessing changes in the diversity and abundance of Acidobacteria in soils contaminated with 2,4,6-trinitrotoluene (TNT) compared with nonpolluted soils. The analysis of Acidobacteria communities at two sites with long-term and short-term contamination revealed that TNT has a drastic impact on the relative abundance of Acidobacteria in soil bacterial 16S rRNA gene libraries. The disappearance of most Acidobacteria from these soils was concomitant with a shift in Acidobacteria community composition and a loss of diversity, although the extent of diversity erosion depended on the sampling site.
    FEMS Microbiology Letters 06/2009; 296(2):159-66. · 2.05 Impact Factor
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    ABSTRACT: Aerobic sewage granules are dense, spherical biofilms, regarded as a useful and promising tool in wastewater treatment processes. Recent studies revealed that fungi can be implemented in biofilm formation. This study attempts to uncover the fungal diversity in aerobic granules by sequence analysis of the 18S and 5.8S rRNA genes and the internal transcribed spacer regions. For this purpose, appropriate PCR and sequencing primer sets were selected and an improved DNA isolation protocol was used. The sequences of 41 isolates were assigned to the taxonomic groups Pleosporaceae, Xylariales, Theleobolaceae, Claviceps, Aureobasidium, Candida boleticola, and Tremellomycetes within the fungi. It turned out that the fungal community composition in granules depended on the wastewater type and the phase of granule development.
    FEMS Microbiology Ecology 06/2009; 68(2):246-54. · 3.56 Impact Factor
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    ABSTRACT: Few reports on in situ mRNA detection in bacteria have been published, even though a major aim in environmental microbiology is to link function/activity to the identity of the organisms. This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. Thus, the approach enabled us specifically to link in situ the information from the dinitrogen fixation activity of an organism to its identity. Unexpectedly, the signals derived from nifH mRNA hybridization showed a distinct uneven pattern within the cells. This indicated that the method used could even give insights about the localization of the detected mRNA within the cell, which is a potential use of mRNA fluorescence in situ hybridization (FISH) that has not been reported up to now for bacterial cells.
    Systematic and Applied Microbiology 03/2009; 32(3):186-92. · 3.29 Impact Factor
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    ABSTRACT: Phylogenetic analysis is currently used worldwide for taxonomic classification and identification of microorganisms. However, despite the countless trees that have been reconstructed and published in recent decades, so far, no user-friendly compilation of recommendations to standardize the data analysis and tree reconstruction process has been published. Consequently, this standard operating procedure for phylogenetic inference (SOPPI) offers a helping hand for working through the process from sampling in the field to phylogenetic tree reconstruction and publication. It is not meant to be authoritative or comprehensive, but should help to make phylogenetic inference and diversity analysis more reliable and comparable between different laboratories. It is mainly focused on using the ribosomal RNA as a universal phylogenetic marker, but the principles and recommendations can be applied to any valid marker gene. Feedback and suggestions from the scientific community are welcome in order to improve these guidelines further. Any updates will be made available on the SILVA webpage at http://www.arb-silva.de/projects/soppi.
    Systematic and Applied Microbiology 10/2008; 31(4):251-7. · 3.29 Impact Factor
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    ABSTRACT: Thirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of ribosomal RNA (rRNA) genes. Adopted by researchers worldwide, rRNA has become the "gold-standard" for molecular taxonomy, biodiversity analysis and the identification of microorganisms. The more than 700,000 rRNA sequences in public databases constitute an unprecedented hallmark of the richness of microbial biodiversity on earth. The International Workshop on Ribosomal RNA Technology convened on April 7-9, 2008 in Bremen, Germany (http://www.arb-silva.de/rrna-workshop) to summarize the current status of the field and strategize on the best ways of proceeding on both biological and technological fronts. In five sessions, 26 leading international speakers and approximately 120 participants representing diverse disciplines discussed new technological approaches to address three basic ecological questions: "Who is out there?" "How many are there?" and "What are they doing?".
    Systematic and Applied Microbiology 10/2008; 31(4):258-68. · 3.29 Impact Factor
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    ABSTRACT: The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project that has been conceived to provide a useful tool especially for the scientific microbial taxonomist community. The aim of what we have called "The All-Species Living Tree" is to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. This tree is to be regularly updated by adding the species with validly published names that appear monthly in the Validation and Notification lists of the International Journal of Systematic and Evolutionary Microbiology. For this purpose, the SAM executive editors, together with the responsible teams of the ARB, SILVA, and LPSN projects (www.arb-home.de, www.arb-silva.de, and www.bacterio.cict.fr, respectively), have prepared a 16S rRNA database containing over 6700 sequences, each of which represents a single type strain of a classified species up to 31 December 2007. The selection of sequences had to be undertaken manually due to a high error rate in the names and information fields provided for the publicly deposited entries. In addition, from among the often occurring multiple entries for a single type strain, the best-quality sequence was selected for the project. The living tree database that SAM now provides contains corrected entries and the best-quality sequences with a manually checked alignment. The tree reconstruction has been performed by using the maximum likelihood algorithm RAxML. The tree provided in the first release is a result of the calculation of a single dataset containing 9975 single entries, 6728 corresponding to type strain gene sequences, as well as 3247 additional high-fquality sequences to give robustness to the reconstruction. Trees are dynamic structures that change on the basis of the quality and availability of the data used for their calculation. Therefore, the addition of new type strain sequences in further subsequent releases may help to resolve certain branching orders that appear ambiguous in this first release. On the web sites: www.elsevier.de/syapm and www.arb-silva.de/living-tree, the All-Species Living Tree team will release a regularly updated database compatible with the ARB software environment containing the whole 16S rRNA dataset used to reconstruct "The All-Species Living Tree". As a result, the latest reconstructed phylogeny will be provided. In addition to the ARB file, a readable multi-FASTA universal sequence editor file with the complete alignment will be provided for those not using ARB. There is also a complete set of supplementary tables and figures illustrating the selection procedure and its outcome. It is expected that the All-Species Living Tree will help to improve future classification efforts by simplifying the selection of the correct type strain sequences. For queries, information updates, remarks on the dataset or tree reconstructions shown, a contact email address has been created (living-tree@arb-silva.de). This provides an entry point for anyone from the scientific community to provide additional input for the construction and improvement of the first tree compiling all sequenced type strains of all prokaryotic species for which names had been validly published.
    Systematic and Applied Microbiology 09/2008; 31(4):241-50. · 3.29 Impact Factor

Publication Stats

19k Citations
837.60 Total Impact Points

Institutions

  • 2008–2013
    • Ribocon GmbH
      Bremen, Bremen, Germany
  • 2011
    • Jacobs University
      Bremen, Bremen, Germany
  • 1998–2011
    • Max Planck Institute for Marine Microbiology
      • Department of Molecular Ecology
      Bremen, Bremen, Germany
  • 1983–2011
    • University of Technology Munich
      • • Chair of Technical Microbiology
      • • Department of Microbiology
      München, Bavaria, Germany
  • 2005–2010
    • Università di Pisa
      • Department of Biology
      Pisa, Tuscany, Italy
    • Asklepios Klinikum Bad Abbach
      Abach, Bavaria, Germany
  • 2003–2007
    • University of Innsbruck
      • • Institute of Ecology
      • • Institut für Zoologie
      Innsbruck, Tyrol, Austria
  • 2000–2002
    • University of Valencia
      • Departamento de Microbiología y Ecología
      Valencia, Valencia, Spain
    • University of Bayreuth
      • Chair of Microbiology
      Bayreuth, Bavaria, Germany
  • 1995–2002
    • Universität Konstanz
      • Department of Biology
      Konstanz, Baden-Wuerttemberg, Germany
    • The University of Waikato
      • Department of Biological Sciences
      Hamilton City, Waikato, New Zealand
  • 1988–2000
    • Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
      Brunswyck, Lower Saxony, Germany
  • 1992–1998
    • Deutsches Herzzentrum München
      München, Bavaria, Germany
    • Wageningen University
      • Laboratory of Microbiology
      Wageningen, Provincie Gelderland, Netherlands
    • ETH Zurich
      • Institute of Microbiology
      Zürich, ZH, Switzerland
  • 1997
    • University of Duisburg-Essen
      Essen, North Rhine-Westphalia, Germany
  • 1993–1994
    • Ghent University
      • Laboratory of Microbiology
      Gand, Flanders, Belgium
    • Carl von Ossietzky Universität Oldenburg
      Oldenburg, Lower Saxony, Germany
  • 1985–1991
    • Christian-Albrechts-Universität zu Kiel
      • Institute for General Microbiology
      Kiel, Schleswig-Holstein, Germany
    • University of Illinois, Urbana-Champaign
      • Department of Microbiology
      Urbana, Illinois, United States