Genomics and microbiology. Microbial forensics--"cross-examining pathogens".
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Animals↗
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Results for “Genome, Microbial”
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The microbial pan-genome.
A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed. Experimental data have shown that in some species new genes are discovered even after sequencing the genomes of several strains. Mathematical modeling predicts that new genes will be discovered even after sequencing hundreds of genomes per species. Therefore, a bacterial species can be described by its pan-genome, which is composed of a "core genome" containing genes present in all strains, and a "dispensable genome" containing genes present in two or more strains and genes unique to single strains. Given that the number of unique genes is vast, the pan-genome of a bacterial species might be orders of magnitude larger than any single genome.
Animals↗
Towards microbial systems science: integrating microbial perspective, from genomes to biomes.
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Biological Science Disciplines↗
Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters.
[This corrects the article on p. 4101 in vol. 59.].
Journal Article↗
Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation.
Genomic markers for anaerobic microbial processes in marine sediments-sulfate reduction, methanogenesis, and anaerobic methane oxidation-reveal the structure of sulfate-reducing, methanogenic, and methane-oxidizing microbial communities (including uncultured members); they allow inferences about the evolution of these ancient microbial pathways; and they open genomic windows into extreme microbial habitats, such as deep subsurface sediments and hydrothermal vents, that are analogs for the early Earth and for extraterrestrial microbiota.
Bacteria, Anaerobic↗
In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats.
Genome sequences of two Synechococcus ecotypes inhabiting the Octopus Spring microbial mat in Yellowstone National Park revealed the presence of all genes required for nitrogenase biosynthesis. We demonstrate that nif genes of the Synechococcus ecotypes are expressed in situ in a region of the mat that varies in temperature from 53.5 degrees C to 63.4 degrees C (average 60 degrees C); transcripts are only detected at the end of the day when the mat becomes anoxic. Nitrogenase activity in mat samples was also detected in the evening. Hitherto, N2 fixation in hot spring mats was attributed either to filamentous cyanobacteria (not present at >50 degrees C in these mats) or to heterotrophic bacteria. To explore how energy-generating processes of the Synechococcus ecotypes track natural light and O2 conditions, we evaluated accumulation of transcripts encoding proteins involved in photosynthesis, respiration, and fermentation. Transcripts from photosynthesis (cpcF, cpcE, psaB, and psbB) and respiration (coxA and cydA) genes declined in the evening. In contrast, transcripts encoding enzymes that may participate in fermentation fell into two categories; some (ldh, pdhB, ald, and ackA) decreased in the evening, whereas others (pflB, pflA, adhE, and acs) increased at the end of the day and remained high into the night. Energy required for N2 fixation during the night may be derived from fermentation pathways that become prominent as the mat becomes anoxic. In a broader context, our data suggest that there are critical regulatory switches in situ that are linked to the diel cycle and that these switches alter many metabolic processes within the microbial mat.
Energy Metabolism↗
Bioinformatics and the discovery of novel anti-microbial targets.
Genomic research is playing a critical role in the discovery of new anti-microbial drugs. The rapid increase in bacterial and eukaryotic genome sequences allows for new and innovative ways for obtaining antimicrobial protein targets. Here, we describe a two level strategy for target identification and validation using computers (in silico). First, large scale comparative analyses of genome sequences were used to identify highly conserved genes which might be essential for in vitro and/or in vivo survival of bacterial pathogens. Lab-based experiments provided confirmation or validation of the hypothesis of in silico essentiality for over 350 individual genes. Over 200 validated, broad spectrum; yet highly specific gene targets, were identified in community infection pathogens. The second part of the target discovery strategy is an in-depth evolutionary, structural and cellular analysis of key drug targets. As an example, phylogenetic and structural analyses suggest that sequence and binding-pocket conservation in FabH (beta-ketoacyl-ACP synthase III) would allow for the development of small molecule inhibitors not only effective against a broad species spectrum of community bacterial pathogens but also as potential new therapies for tuberculosis and malaria.
Animals↗
Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.
Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.
DNA, Ribosomal↗
Gene transfer, speciation, and the evolution of bacterial genomes.
Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.
Bacteria↗
An experimental metagenome data management and analysis system.
The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m.
Bacterial Physiological Phenomena↗
NIAID takes next genome step.
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Genetics, Microbial↗
New mutations in pncA of in vitro selected pyrazinamide-resistant strains of Mycobacterium tuberculosis.
Mutations within the pncA gene can cause pyrazinamide (PZA) resistance in Mycobacterium tuberculosis. To study further the mutational events leading to PZA resistance, a H37Rv PZA-susceptible strain was used to derive PZA-resistant mutants in vitro. This parental strain was grown at gradually increased concentrations of PZA (from 200 up to 500 microg/ml). A total of eight variant strains were selected for further study. PZA resistance was selected at 250 microg/ml or higher. Seven of them lost PZase activity and hence were PZA resistant. The remaining strain has shown a functional PZase and hence was sensitive to PZA after being exposed to 200 microg/ml PZA. Sequence analysis shows different novel mutations within the pncA gene of these variants. Two silent mutations at nucleotide 6 (G --> A) and 300 (C --> T) were found in the PZA-sensitive variant. Among the seven PZA-resistant variants, there were three deletion mutations found at nucleotide 78 (G), 79 (A), and 143 (A), all resulting in a frameshift, and one nonsense mutation at nucleotide 102 (C --> G), creating a stop codon TAG. It was observed that the mutations found in the pncA gene of these PZA-resistant mutants show a distinctive pattern: mutation positions moved toward the beginning of the open reading frame correlating with the increase in PZA concentration, suggesting a possible relationship between the increase of PZA concentration and the early occurrence of mutations on the pncA gene.
Amidohydrolases↗
Mapping regulatory networks in microbial cells.
Genome sequences are the blueprints of diverse life forms but they reveal little information about how cells make coherent responses to environmental changes. The combined use of gene fusions, gene chips, 2-D polyacrylamide gel electrophoresis, mass spectrometry and 'old-fashioned' microbial physiology will provide the means to reveal a cell's regulatory networks and how those networks are integrated.
Bacteria↗
Protein microarrays: from serodiagnosis to whole proteome scale analysis of the immune response against pathogenic microorganisms.
Microbial diseases remain the most common cause of global mortality and morbidity. Scientific and technical achievements have dramatically improved the possibilities of investigating the humoral immune response against the whole proteome of microbial organisms. A number of genomes of microbial organisms responsible for diseases of worldwide medical importance such as Plasmodium, Toxoplasma, Mycobacterium, Streptococcus, Neisseria, Salmonella, Borrelia, and Rickettsia species have already been sequenced or will be available in the very near future. High-throughput assays such as protein microarrays have been clinically validated in serum for detecting the presence of antibodies directed against microbial antigens. Computational technologies for processing large sets of data are rapidly being developed. Such a powerful combination of genomic information and assays now offers the opportunity to identify the microbial antigens that, either alone or in combination, function as targets of natural acquired immunity against infectious diseases. This information will prove invaluable for developing vaccines against a series of microorganisms of medical relevance that are urgently needed, e.g., malaria. Additional applications of these technologies include the development of a microbial antigen array for the early serodiagnosis of both common and rare infectious diseases. This review will focus on technical and scientific issues concerning the use of antigen microarrays for vaccine development and the serodiagnosis of infectious diseases.
Antigens↗
[Early diagnosis of colorectal anastomotic leakages by detection of bacterial genome].
BACKGROUND: Microbial infections and translocation of intestinal bacteria are thought to contribute to multiple system organ failure, but bacterial cultures are often negative in patients with this complication. The purpose of this study was to determine the sensitivity of PCR for detecting microbial DNA in the blood of animals after conducting an experimental model of anastomotic leakage. METHODS: Fourty rats were divided into three groups as follows: Control Group; simple laparotomy group, Anastomosis Group; colon resection and anastomosis group, and Leakage Group; group with colon resection and an anastomosis leaving a 5 mm opening. Blood was drawn form rats before the procedure, and postoperative 3rd and 6th days. DNAs were extracted from these samples and PCR techniques were used to amplify genes of Escherichia coli. Statistical analysis for the percentage of rats with microbial DNA in the blood for all groups was done by Fisher's exact chi- square test. The difference among groups was considered significant if the P value was less than 0.05. RESULTS: Most of the detected Escherichia coli genes were from the Leakage Group, and the detection rate was significant compared to other groups. CONCLUSION: We suggest that PCR could be a useful adjunct tool for immediate diagnosis of anastomotic leakages.
Anastomosis, Surgical↗
Environmental whole-genome amplification to access microbial populations in contaminated sediments.
Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using phi29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2% genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small-subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9% of the sequences had significant similarities to known proteins, and "clusters of orthologous groups" (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. Whole-genome amplification of metagenomic DNA from very minute microbial sources, while introducing an amplification bias, will allow access to genomic information that was not previously accessible. The reported SSU rRNA sequences and library clone end sequences are listed with their respective GenBank accession numbers, DQ 404590 to DQ 404652, DQ 404654 to DQ 404938, and DX 385314 to DX 389173.
Bacillus Phages↗
Genome-scale models of microbial cells: evaluating the consequences of constraints.
Microbial cells operate under governing constraints that limit their range of possible functions. With the availability of annotated genome sequences, it has become possible to reconstruct genome-scale biochemical reaction networks for microorganisms. The imposition of governing constraints on a reconstructed biochemical network leads to the definition of achievable cellular functions. In recent years, a substantial and growing toolbox of computational analysis methods has been developed to study the characteristics and capabilities of microorganisms using a constraint-based reconstruction and analysis (COBRA) approach. This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells.
Bacterial Physiological Phenomena↗
Microbial disease in humans: A genomic perspective.
The approach of whole-genome shotgun sequencing coupled with the availability of computational algorithms to facilitate the assembly, gene prediction, and functional annotation of entire genomes has sparked a revolution in our understanding of the biology of free-living organisms. More than 40 bacterial genomes have been sequenced to date, of which several are important human pathogens. The capacity to sequence and assemble entire genomes of bacteria, pathogenic protozoans, and fungi in a rapid and cost-effective way has energized every aspect of microbial science. Comparative genome analysis allows us to dissect the evolutionary forces at work and provides insights into adaptations of microbes to their unique ecological niches. Factors that shape host-pathogen interactions and their outcomes include genetic polymorphisms in the microbial pathogen and host, both of which can impact on microbial virulence or host immune responses to infection. The availability of the genome sequence of entire organisms, together with the use of high-throughput sequence-based genomic technologies to define microbial and host physiological states, provides the unparalleled opportunity to better define clinical outcomes in the field of infectious diseases. There is one overarching lesson: completion of the genomic sequence of any species answers many questions, while at the same time it invites totally new questions.
Animals↗