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Wally N, Schneider M, Thannesberger J, Kastner MT, Bakonyi T, Indik S, Rattei T, Bedarf J, Hildebrand F, Law J, Jovel J, Steininger C. Plasmid DNA contaminant in molecular reagents. Sci Rep 2019; 9:1652. [PMID: 30733546 PMCID: PMC6367390 DOI: 10.1038/s41598-019-38733-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
Background noise in metagenomic studies is often of high importance and its removal requires extensive post-analytic, bioinformatics filtering. This is relevant as significant signals may be lost due to a low signal-to-noise ratio. The presence of plasmid residues, that are frequently present in reagents as contaminants, has not been investigated so far, but may pose a substantial bias. Here we show that plasmid sequences from different sources are omnipresent in molecular biology reagents. Using a metagenomic approach, we identified the presence of the (pol) of equine infectious anemia virus in human samples and traced it back to the expression plasmid used for generation of a commercial reverse transcriptase. We found fragments of multiple other expression plasmids in human samples as well as commercial polymerase preparations. Plasmid contamination sources included production chain of molecular biology reagents as well as contamination of reagents from environment or human handling of samples and reagents. Retrospective analyses of published metagenomic studies revealed an inaccurate signal-to-noise differentiation. Hence, the plasmid sequences that seem to be omnipresent in molecular biology reagents may misguide conclusions derived from genomic/metagenomics datasets and thus also clinical interpretations. Critical appraisal of metagenomic data sets for the possibility of plasmid background noise is required to identify reliable and significant signals.
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Affiliation(s)
- N Wally
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - M Schneider
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - J Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - M T Kastner
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - T Bakonyi
- University of Veterinary Medicine, Department of Virology, Vienna, Austria
| | - S Indik
- University of Veterinary Medicine, Department of Virology, Vienna, Austria
| | - T Rattei
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - J Bedarf
- German Centre for neurodegenerative disease research (DZNE), Department of Neurology, University of Bonn, Bonn, Germany
| | - F Hildebrand
- European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
| | - J Law
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - J Jovel
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - C Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria.
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2
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Vázquez-Castellanos JF, Serrano-Villar S, Jiménez-Hernández N, Soto Del Rio MD, Gayo S, Rojo D, Ferrer M, Barbas C, Moreno S, Estrada V, Rattei T, Latorre A, Moya A, Gosalbes MJ. Interplay between gut microbiota metabolism and inflammation in HIV infection. ISME J 2018; 12:1964-1976. [PMID: 29789624 PMCID: PMC6052150 DOI: 10.1038/s41396-018-0151-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/12/2018] [Accepted: 04/28/2018] [Indexed: 02/07/2023]
Abstract
HIV infection causes a disruption of gut-associated lymphoid tissue, driving a shift in the composition of gut microbiota. A deeper understanding of the metabolic changes and how they affect the interplay with the host is needed. Here, we assessed functional modifications of HIV-associated microbiota by combining metagenomic and metatranscriptomic analyses. The transcriptionally active microbiota was well-adapted to the inflamed environment, overexpressing pathways related to resistance to oxidative stress. Furthermore, gut inflammation was maintained by the Gram-negative nature of the HIV-associated microbiota and underexpression of anti-inflammatory processes, such as short chain fatty acid biosynthesis or indole production. We performed co-occurrence and metabolic network analyses that showed relevance in the microbiota structure of both taxonomic and metabolic HIV-associated biomarkers. The Bayesian network revealed the most determinant pathways for maintaining the structure stability of the bacterial community. In addition, we identified the taxa's contribution to metabolic activities and their interactions with host health.
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Affiliation(s)
- Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Nuria Jiménez-Hernández
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
| | - María Dolores Soto Del Rio
- Department of Agricultural, Forest and Food Sciences, Università degli Studi di Torino, Turin, Piedmont, Italy
| | - Sara Gayo
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
- CSIC, Institute of Catalysis, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - Tomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Amparo Latorre
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- Integrative Systems Biology Institute (I2SysBio), University of Valencia and Spanish Research Council (CSIC), Valencia, Spain
| | - Andrés Moya
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain.
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain.
- Integrative Systems Biology Institute (I2SysBio), University of Valencia and Spanish Research Council (CSIC), Valencia, Spain.
| | - María José Gosalbes
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain.
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain.
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3
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Felkel S, Vogl C, Rigler D, Jagannathan V, Leeb T, Fries R, Neuditschko M, Rieder S, Velie B, Lindgren G, Rubin CJ, Schlötterer C, Rattei T, Brem G, Wallner B. Asian horses deepen the MSY phylogeny. Anim Genet 2018; 49:90-93. [PMID: 29333704 DOI: 10.1111/age.12635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2017] [Indexed: 01/09/2023]
Abstract
Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.
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Affiliation(s)
- S Felkel
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - C Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - D Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - R Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - M Neuditschko
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - S Rieder
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - B Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - G Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C-J Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - C Schlötterer
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, Austria
| | - T Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - G Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - B Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
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Zihler A, Le Blay G, de Wouters T, Lacroix C, Braegger C, Lehner A, Tischler P, Rattei T, Hächler H, Stephan R. In vitroinhibition activity of different bacteriocin-producingEscherichia coliagainstSalmonellastrains isolated from clinical cases. Lett Appl Microbiol 2009; 49:31-8. [DOI: 10.1111/j.1472-765x.2009.02614.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KFX, Münsterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T. MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res 2007; 36:D196-201. [PMID: 18158298 PMCID: PMC2238900 DOI: 10.1093/nar/gkm980] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).
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Affiliation(s)
- H W Mewes
- Institute for Bioinformatics (MIPS), German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
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Mewes HW, Frishman D, Mayer KFX, Münsterkötter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stümpflen V. MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 2006; 34:D169-72. [PMID: 16381839 PMCID: PMC1347510 DOI: 10.1093/nar/gkj148] [Citation(s) in RCA: 281] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server ().
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Affiliation(s)
- H. W. Mewes
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
- Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food ScienceD-85350 Freising-Weihenstephan, Germany
- To whom correspondence should be addressed. Tel: +49 89 3187 3580; Fax: +49 89 3187 3585;
| | - D. Frishman
- Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food ScienceD-85350 Freising-Weihenstephan, Germany
| | - K. F. X. Mayer
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - M. Münsterkötter
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - O. Noubibou
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - P. Pagel
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - T. Rattei
- Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food ScienceD-85350 Freising-Weihenstephan, Germany
| | - M. Oesterheld
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - A. Ruepp
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - V. Stümpflen
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthIngolstädter Landstraße 1, D-85764 Neuherberg, Germany
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7
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Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, Stark M, Bauer M, Zibat A, Lombardot T, Becker I, Amann J, Gellner K, Teeling H, Leuschner WD, Glöckner FO, Lupas AN, Amann R, Klenk HP. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol 2004; 6:887-902. [PMID: 15305914 DOI: 10.1111/j.1462-2920.2004.00665.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C(4)-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a beta-oxidation complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and ncc. D. psychrophila encodes more than 30 two-component regulatory systems, including a new Ntr subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.
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Affiliation(s)
- R Rabus
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
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