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Search Results: 1 - 10 of 723 matches for " Nikos Kyrpides "
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Microbial co-habitation and lateral gene transfer: what transposases can tell us
Sean D Hooper, Konstantinos Mavromatis, Nikos C Kyrpides
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-4-r45
Abstract: All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections.We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.Microbes dominate the planet, inhabiting a wide range of environments, including many previously thought to be too extreme or inhospitable for life. Identifying the habitat(s) occupied by a particular microbial organism is not a straightforward task. Often the initial habitat assignment stems from where the organism was first isolated, which may not be its only, or even its preferred, habitat. This is an increasingly frequent occurrence as more microbial species are being identified from metagenomic samples such as soil [1]. Furthermore, given the anthropocentric perspective of microbiology, it is not surprising that many bacteria have been associated with their location in the human body, even if this pathogenic phase constitutes only one part of their life cycle. For example, highly versatile, opportunistic pathogens in the Pseudomonas family are found in a wide range of habitats (for example, [2]), not only in humans or other hosts. Add to this the wide disper
Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System
Konstantinos Mavromatis,Ken Chu,Natalia Ivanova,Sean D. Hooper,Victor M. Markowitz,Nikos C. Kyrpides
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007979
Abstract: Computational methods for determining the function of genes in newly sequenced genomes have been traditionally based on sequence similarity to genes whose function has been identified experimentally. Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes. Context analysis is based on the observation that functionally related genes are often having similar gene context and relies on the identification of such events across phylogenetically diverse collection of genomes. We have used the data management system of the Integrated Microbial Genomes (IMG) as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations. Visualization and search tools to facilitate gene context analysis have been developed and applied across all publicly available archaeal and bacterial genomes in IMG. These computations are now maintained as part of IMG's regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov.
Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria
Iain Anderson, Birte Abt, Athanasios Lykidis, Hans-Peter Klenk, Nikos Kyrpides, Natalia Ivanova
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039331
Abstract: Cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. Anaerobes including Clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. In contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. Numerous actinobacterial genomes have become available through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. We identified putative cellulose-degrading enzymes belonging to families GH5, GH6, GH8, GH9, GH12, GH48, and GH51 in the genomes of eleven members of the actinobacteria. The eleven organisms were tested in several assays for cellulose degradation, and eight of the organisms showed evidence of cellulase activity. The three with the highest cellulase activity were Actinosynnema mirum, Cellulomonas flavigena, and Xylanimonas cellulosilytica. Cellobiose is known to induce cellulolytic enzymes in the model organism Thermobifida fusca, but only Nocardiopsis dassonvillei showed higher cellulolytic activity in the presence of cellobiose. In T. fusca, cellulases and a putative cellobiose ABC transporter are regulated by the transcriptional regulator CelR. Nine organisms appear to use the CelR site or a closely related binding site to regulate an ABC transporter. In some, CelR also regulates cellulases, while cellulases are controlled by different regulatory sites in three organisms. Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms.
Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample
Chengwei Luo, Despina Tsementzi, Nikos Kyrpides, Timothy Read, Konstantinos T. Konstantinidis
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030087
Abstract: Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R2>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides, Philip Hugenholtz
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-209
Abstract: CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats.In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(n) in space and O(nm/l) in time.Repetitive sequences are abundant in bacteria and archaea, accounting for close to 5% of the genome size in many organisms [1,2]. These repetitive sequences come in various forms/sizes and may be found dispersed throughout a genome, clustered in close proximity or arranged contiguously. The identification of repeats has proven to be of significance, as they provide insight into the functional and evolutionary roles of various organisms [3-7].This study centers on a recently recognized family of repeats known as Clustered Regularly Interspaced Palindromic Repeats (CRISPRs). Since their description by Mojica et al. [8], CRISPRs have attracted a great deal of interest [9-16]. CRISPRs have been found only in the genomes of prokaryotes and are composed of short direct repeats currently known to range in sizes from 21 – 47 base pairs. This family of repeats is unique in that they are interspaced by non-repeating sequences of similar size. CRISPRs
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
Andreas Wilke, Travis Harrison, Jared Wilkening, Dawn Field, Elizabeth M Glass, Nikos Kyrpides, Konstantinos Mavrommatis, Folker Meyer
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-141
Abstract: We introduce a mechanism for automatically maintaining a comprehensive, non-redundant protein database and for creating a quarterly release of this resource. In addition, we present tools for translating similarity searches into many annotation namespaces, e.g. KEGG or NCBI's GenBank.The data and tools we present allow the creation of multiple result sets using a single computation, permitting computational results to be shared between groups for large sequence data sets.
Improving Microbial Genome Annotations in an Integrated Database Context
I-Min A. Chen, Victor M. Markowitz, Ken Chu, Iain Anderson, Konstantinos Mavromatis, Nikos C. Kyrpides, Natalia N. Ivanova
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0054859
Abstract: Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.
Functional Genomics of Novel Secondary Metabolites from Diverse Cyanobacteria Using Untargeted Metabolomics
Richard Baran,Natalia N. Ivanova,Nick Jose,Ferran Garcia-Pichel,Nikos C. Kyrpides,Muriel Gugger,Trent R. Northen
Marine Drugs , 2013, DOI: 10.3390/md11103617
Abstract: Mass spectrometry-based metabolomics has become a powerful tool for the detection of metabolites in complex biological systems and for the identification of novel metabolites. We previously identified a number of unexpected metabolites in the cyanobacterium Synechococcus sp. PCC 7002, such as histidine betaine, its derivatives and several unusual oligosaccharides. To test for the presence of these compounds and to assess the diversity of small polar metabolites in other cyanobacteria, we profiled cell extracts of nine strains representing much of the morphological and evolutionary diversification of this phylum. Spectral features in raw metabolite profiles obtained by normal phase liquid chromatography coupled to mass spectrometry (MS) were manually curated so that chemical formulae of metabolites could be assigned. For putative identification, retention times and MS/MS spectra were cross-referenced with those of standards or available sprectral library records. Overall, we detected 264 distinct metabolites. These included indeed different betaines, oligosaccharides as well as additional unidentified metabolites with chemical formulae not present in databases of metabolism. Some of these metabolites were detected only in a single strain, but some were present in more than one. Genomic interrogation of the strains revealed that generally, presence of a given metabolite corresponded well with the presence of its biosynthetic genes, if known. Our results show the potential of combining metabolite profiling and genomics for the identification of novel biosynthetic genes.
Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes
Iain Anderson,Carmen Scheuner,Markus G?ker,Kostas Mavromatis,Sean D. Hooper,Iris Porat,Hans-Peter Klenk,Natalia Ivanova,Nikos Kyrpides
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0020237
Abstract: The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis.
Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii
Konstantinos Mavromatis, Natalia Ivanova, Iain Anderson, Athanasios Lykidis, Sean D. Hooper, Hui Sun, Victor Kunin, Alla Lapidus, Philip Hugenholtz, Bharat Patel, Nikos C. Kyrpides
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0004192
Abstract: Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.
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