[A system for comparative analysis of microbial genomes].
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Algorithms↗
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Results for “Genome, Microbial”
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[Development of a microbial genome database for comparative analysis].
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Computer Communication Networks↗
Correlation of PAS domains with electron transport-associated proteins in completely sequenced microbial genomes.
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Archaeal Proteins↗
[Studies on microbial genome].
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Escherichia coli↗
Comparative genomics and understanding of microbial biology.
The sequences of close to 30 microbial genomes have been completed during the past 5 years, and the sequences of more than 100 genomes should be completed in the next 2 to 4 years. Soon, completed microbial genome sequences will represent a collection of >200,000 predicted coding sequences. While analysis of a single genome provides tremendous biological insights on any given organism, comparative analysis of multiple genomes provides substantially more information on the physiology and evolution of microbial species and expands our ability to better assign putative function to predicted coding sequences.
Bacteria↗
Microbial pathogen genomes--new strategies for identifying therapeutics and vaccine targets.
Advances in high-throughput DNA-sequencing techniques have given us the unprecedented ability to rapidly determine the nucleotide sequences of entire bacterial genomes. The application of these methods to the genomes of microbial pathogens, combined with efficient analytical tools and genome-scale approaches for studying gene expression, is revolutionizing our approach to the selection of targets for drug screening and vaccine development. This is bringing new life to this important, but long-neglected, field of research.
Animals↗
Impact of genomics on microbial food safety.
Genome sequences are now available for many of the microbes that cause food-borne diseases. The information contained in pathogen genome sequences, together with the development of themed and whole-genome DNA microarrays and improved proteomics techniques, might provide tools for the rapid detection and identification of such organisms, for assessing their biological diversity and for understanding their ability to respond to stress. The genomic information also provides insight into the metabolic capacity and versatility of microbes; for example, specific metabolic pathways might contribute to the growth and survival of pathogens in a range of niches, such as food-processing environments and the human host. New concepts are emerging about how pathogens function, both within foods and in interactions with the host. The future should bring the first practical benefits of genome sequencing to the field of microbial food safety, including strategies and tools for the identification and control of emerging pathogens.
Biofilms↗
Evidence of a large novel gene pool associated with prokaryotic genomic islands.
Microbial genes that are "novel" (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome) in 63 prokaryotic genomes, and then characterized the distribution of novel genes and other features. All but a few of the genomes examined contained significantly higher proportions of novel genes in their predicted genomic islands compared with the rest of their genome (Paired t test = 4.43E-14 to 1.27E-18, depending on method). Moreover, the reverse observation (i.e., higher proportions of novel genes outside of islands) never reached statistical significance in any organism examined. We show that this higher proportion of novel genes in predicted genomic islands is not due to less accurate gene prediction in genomic island regions, but likely reflects a genuine increase in novel genes in these regions for both bacteria and archaea. This represents the first comprehensive analysis of novel genes in prokaryotic genomic islands and provides clues regarding the origin of novel genes. Our collective results imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. Moreover, there are more novel genes within the gene pool associated with genomic islands. Since genomic islands are frequently associated with a particular microbial adaptation, such as antibiotic resistance, pathogen virulence, or metal resistance, this suggests that microbes may have access to a larger "arsenal" of novel genes for adaptation than previously thought.
Bacteriophages↗
Megx.net--database resources for marine ecological genomics.
Marine microbial genomics and metagenomics is an emerging field in environmental research. Since the completion of the first marine bacterial genome in 2003, the number of fully sequenced marine bacteria has grown rapidly. Concurrently, marine metagenomics studies are performed on a regular basis, and the resulting number of sequences is growing exponentially. To address environmentally relevant questions like organismal adaptations to oceanic provinces and regional differences in the microbial cycling of nutrients, it is necessary to couple sequence data with geographical information and supplement them with contextual information like physical, chemical and biological data. Therefore, new specialized databases are needed to organize and standardize data storage as well as centralize data access and interpretation. We introduce Megx.net, a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts. Megx.net includes (i) a geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; (ii) an environmental genome browser with fast search functionalities; (iii) a database with precomputed analyses for selected complete genomes; and (iv) a database and tool to classify metagenomic fragments based on oligonucleotide signatures. These integrative databases and webserver will help researchers to generate a better understanding of the functioning of marine ecosystems. All resources are freely accessible at http://www.megx.net.
Databases, Genetic↗
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups.
The microbial genome database for comparative analysis (MBGD) is a comprehensive platform for microbial comparative genomics. The central function of MBGD is to create orthologous groups among multiple genomes from precomputed all-against-all similarity relationships using the DomClust algorithm. The database now contains >300 published genomes and the number continues to grow. For researchers who are interested in ongoing genome projects, we have now started a new service called 'My MBGD,' which allows users to add their own genome sequences to MBGD for the purpose of identifying orthologs among both the new and the existing genomes. Furthermore, in order to make available the rapidly accumulating information on closely related genome sequences, we enhanced the interface for pairwise genome comparisons using the CGAT interface, which allows users to see nucleotide sequence alignments of non-coding as well as coding regions. MBGD is available at http://mbgd.genome.ad.jp/.
Algorithms↗
An automated system for genome analysis to support microbial whole-genome shotgun sequencing.
We developed a semi-automated genome analysis system called GAMBLER in order to support the current whole-genome sequencing project focusing on alkaliphilic Bacillus halodurans C-125. GAMBLER was designed to reduce the human intervention required and to reduce the complications in annotating thousands of ORFs in the microbial genome. GAMBLER automates three major routines: analyzing assembly results provided by genome assembler software, assigning ORFs, and homology searching. GAMBLER is equipped with an interface for convenience of annotation. All processes and options are manipulatable through a WWW browser that enables scientists to share their genome analysis results without choosing computer platforms.
Automation↗
Microbial pathogenesis: genomics and beyond.
The growing number of complete microbial genome sequences provides a powerful tool for studying the biology of microorganisms. In combination with assays for function, genomic-based approaches can facilitate efficient and directed research strategies to elucidate mechanisms of bacterial pathogenicity. As genomic information accrues, the challenge remains to construct a picture of the biology that accurately reflects how individual genes collaborate to create the complex world of microbial specialization.
Animals↗
Microbial community genomics in the ocean.
Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.
Bacteria↗
Genomics and marine microbial ecology.
Genomics has brought about a revolution in all fields of biology. Before the development of microbial ecology in the 1970s, microbes were not even considered in marine ecological studies. Today we know that half of the total primary production of the planet must be credited to microorganisms. This and other discoveries have changed dramatically the perspective and the focus of marine microbial ecology. The application of genomics-based approaches has provided new challenges and has allowed the discovery of novel functions, an appreciation of the great diversity of microorganisms, and the introduction of controversial ideas regarding the concepts of species, genome, and niche. Nevertheless, thorough knowledge of the traditional disciplines of biology is necessary to explore the possibilities arising from these new insights. This work reviews the different genomic techniques that can be applied to marine microbial ecology, including both sequencing of the complete genomes of microorganisms and metagenomics, which, in turn, can be complemented with the study of mRNAs (transcriptomics) and proteins (proteomics). The example of proteorhodopsin illustrates the type of information that can be gained from these approaches. A genomics perspective constitutes a map that will allow microbiologists to focus their research on potentially more productive aspects.
Bacteria↗
Low-pass sequencing for microbial comparative genomics.
BACKGROUND: We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile Haloarcula marismortui; (2) the non-pigmented Natrialba asiatica; (3) the psychrophile Halorubrum lacusprofundi and (4) the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe. RESULTS: As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI) for their predicted proteins. Multiple insertion sequence (IS) elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP) and transcription factor IIB (TFB) homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi. CONCLUSION: Despite the diverse habitats of these species, all five halophiles share (1) high GC content and (2) low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the IS-element rich genome of H. sp. NRC-1. Identification of multiple TBP and TFB homologs in these four halophiles are consistent with the hypothesis that different types of complex transcriptional regulation may occur through multiple TBP-TFB combinations in response to rapidly changing environmental conditions. Low-pass shotgun sequence analyses of genomes permit extensive and diverse analyses, and should be generally useful for comparative microbial genomics.
Archaea↗
Genomic analyses of microbial virulence.
Genomic sequencing of bacterial pathogens is providing an increasing wealth of new data. It is, however, still unclear how this information can be used to develop new experimental approaches. Here, we describe recent efforts to complement existing bacterial genetics with genomic methods for the study of pathogenesis.
Bacteria↗
Comparative genomics of microbial drug efflux systems.
The complete genome sequences of 36 microorganisms have now been published and this wealth of genome data has enabled the development of comparative genomic and functional genomic approaches to investigate the biology of these organisms. Comparative genomic analyses of membrane transport systems have revealed that transporter substrate specificities correlate with an organism's lifestyle. The types and numbers of predicted drug efflux systems vary dramatically amongst sequenced organisms. Microarray and gene knockout studies to date have suggested that predicted drug efflux genes often appear to be a) non-essential and b) expressed at detectable levels under standard laboratory growth conditions.
Bacteria↗
Microbial population genomics and ecology.
The origins of biological complexity in microbial ecosystems are encoded within the collective genomes of the community. Cultivation-independent genomic studies provide direct access to the genomes of naturally occurring microbes, cultivated or not. Genome-enabled approaches are now significantly advancing current knowledge of genome content, diversity, population biology and evolution in natural microbial populations.
Ecology↗