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At least 37 records · Page 2Linked to original sources
PubMed2006

Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples.

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host-specific markers. Here we describe the application of a genome fragment enrichment (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities.

Animals↗
PubMed2000

The microbial genetics of antibiotic cycling.

Cycling of currently available antibiotics to reduce resistance is an attractive concept. For cycling strategies to be successful, their implementation must have a demonstrable impact on the prevalence of resistance determinants already dispersed throughout the hospital and associated healthcare facilities. While antibiotic use in hospitals clearly constitutes a stimulus for the emergence of resistance, it is by no means the only important factor. The incorporation of resistance determinants into potentially stable genetic structures, including bacteriophages, plasmids, transposons, and the more newly discovered movable elements termed integrons and gene cassettes, forces some degree of skepticism about the potential for such strategies in institutions where resistance determinants are already prevalent. In particular, the expanding role of integrons may pose an ultimate threat to formulary manipulations such as cycling. Despite these concerns, the crisis posed by antimicrobial resistance warrants investigation of any strategy with the potential for reducing the prevalence of resistance. Over the next decade, new studies with carefully designed outcomes should determine the utility of antibiotic cycling as one control measure for nosocomial resistance.

Anti-Bacterial Agents↗
PubMed2005

Utilizing the power of microbial genetics to bridge the gap between the promise and the application of marine natural products.

Marine organisms are a rich source of secondary metabolites. They have yielded thousands of compounds with a broad range of biomedical applications. Thus far, samples required for preclinical and clinical studies have been obtained by collection from the wild, by mariculture, and by total chemical synthesis. However, for a number of complex marine metabolites, none of these options is feasible for either economic or environmental reasons. In order to proceed with the development of many of these promising therapeutic compounds, a reliable and renewable source must be found. Over the last twenty years, the study of microbial secondary metabolites has greatly advanced our understanding of how nature utilizes simple starting materials to yield complex small molecules. Much of this work has focused on polyketides and nonribosomal peptides, two classes of molecules that are prevalent in marine micro- and macroorganisms. The lessons learned from the study of terrestrial metabolite biosynthesis are now being applied to the marine world. As techniques for cloning and heterologous expression of biosynthetic pathways continue to improve, they may provide our greatest hope for bridging the gap between the promise and application of many marine natural products.

Animals↗
PubMed1987

Two different approaches to computer-aided teaching of microbial genetics.

Two computer packages have been developed to teach bacterial genetics on an introductory genetics course for undergraduate students in biology. The first package, 'CONJUGACION', is designed to teach bacterial conjugation and its genetic outcomes. It includes four main parts. Firstly, a tutorial part presents a theoretical framework using screens of text and animated graphics. Secondly, an interactive concept application section requires students to carry out experiments for the determination of the correct sex and genotype of 10 bacterial strains. The third part uses the previously obtained data for simulating interrupted mating experiments and mapping the bacterial genome. Finally, an evaluation section allows the students to test their understanding through a series of multiple choice questions. The second package, 'LURIDEL', is intended for teaching the preadaptative character of mutation in bacterial populations on the basis of the fluctuation test of Luria and Delbrück. It simulates, graphically, the appearance of mutations in microbial cultures and gives results of simulated fluctuation experiments. Programs were written under the PCOS operating system in MBASIC extended to graphics for running on Olivetti M20 microcomputers.

Computer-Assisted Instruction↗
PubMed1979

Lack of microbial genetic response to 2.45-GHz CW and 8.5- to 9.6-GHz pulsed microwaves.

Strain D4 of the yeast Saccharomyces cerevisiae, and strains TA-1535, TA-100 and TA-98 of the bacterium Salmonella typhimurium, were exposed to 2.45-GHz continuous wave or 8.5- to 9.6-GHz pulsed electromagnetic radiation (EMR) at various power densities from 1 to 45 mW/cm2. The temperature during radiation was maintained at 30 degrees C for yeast cultures and at 37 degrees C for bacterial cultures. The studies revealed no increase in mutations or of mitotic gene conversions when cells were radiated for two hours or less. Decreased viability of cells was noted in all cultures tested after radiation at power densities of 30 mW/cm2 or more; however, no reliable changes in genetic events occurred.

Electromagnetic Fields↗
PubMed2001

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiological research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made.

Bacteria↗
PubMed2005

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data.

The inference of population recombination (rho), population mutation (Theta), and adaptive selection is of great interest in microbial population genetics. These parameters can be efficiently estimated using explicit statistical frameworks (evolutionary models) that describe their effect on gene sequences. Within this framework, we estimated rho and Theta using a coalescent approach, and adaptive (or destabilizing) selection under heterogeneous codon-based and amino acid property models in microbial sequences from MLST databases. We analyzed a total of 91 different housekeeping gene regions (loci) corresponding to one fungal and sixteen bacterial pathogens. Our results show that these three population parameters vary extensively across species and loci, but they do not seem to be correlated. For the most part, estimated recombination rates among species agree well with previous studies. Over all taxa, the rho/Theta ratio suggests that each factor contributes similarly to the emergence of variant alleles. Comparisons of Theta estimated under finite- and infinite-site models indicate that recurrent mutation (i.e., multiple mutations at some sites) can increase Theta by up to 39%. Significant evidence of molecular adaptation was detected in 28 loci from 13 pathogens. Three of these loci showed concordant patterns of adaptive selection in two to four different species.

Alleles↗
PubMed2000

Comparison of genetically engineered microbial and plant phytase for young broilers.

This study was conducted to compare the efficacy of genetically engineered microbial (Natuphos) and plant (Phytaseed) phytase for enhancing the utilization of phytate P in corn-soybean meal-based diets fed to young broilers and to evaluate the safety of Phytaseed phytase. Three levels of each of the two sources of phytase (250, 500, and 2,500 U/kg of diet) were added to a corn-soybean meal basal diet containing 0.46% total P, 0.21% nonphytate P, and 0.92% Ca. There were eight cages per treatment (eight birds per cage for Weeks 2 to 3 and seven birds for Weeks 4 to 5), except for the basal diet without added phytase that had 16 cages. Cage BW and feed consumption were recorded weekly. During Week 5, cage excreta samples were collected for determination of apparent retention coefficients of DM, Ca, and P. At the end of Week 5, all birds were killed, and the left and right toes were removed for determination of toe ash weight and percentage. Forty birds (one per cage from the diet without added phytase and diets with 500 or 2,500 U phytase/kg from both sources) were randomly selected for gross necropsy and histologic evaluation of liver, kidney, and bone tissues. Addition of both sources of phytase resulted in similar increases (P < 0.05) of BW gain; feed intake; gain:feed; apparent retention of DM, P and Ca; and toe measurements. Phosphorus excretion decreased as phytase addition increased. No significant abnormalities were seen in any of the 40 broilers necropsied. Further, the fit of a nonlinear function revealed that most measurements reached a plateau at 2,500 U/kg. Based on performance, bone characteristics, and retention of P, Ca, and DM of young broilers, the efficacy of Phytaseed phytase was similar to that of Natuphos phytase for enhancing the utilization of phytate P in corn-soybean meal-based diets. General necropsy and histologic examination of liver, kidney, and tibial tissues revealed no adverse effects of phytase source or level.

6-Phytase↗
PubMed2006

Current concept on the pathogenesis of inflammatory bowel disease-crosstalk between genetic and microbial factors: pathogenic bacteria and altered bacterial sensing or changes in mucosal integrity take "toll" ?

The pathogenesis of inflammatory bowel disease (IBD) is only partially understood. Various environmental and host (e.g. genetic-, epithelial-, immune and non-immune) factors are involved. It is a multifactorial polygenic disease with probable genetic heterogeneity. Some genes are associated with IBD itself, while others increase the risk of ulcerative colitis (UC) or Crohn's disease (CD) or are associated with disease location and/or behaviour. This review addresses recent advances in the genetics of IBD. The article discusses the current information on the crosstalk between microbial and genetic factors (e.g. NOD2/CARD15, SLC22A46A5 and DLG5). The genetic data acquired in recent years help in understanding the pathogenesis of IBD and can identify a number of potential targets for therapeutic intervention. In the future, genetics may help more accurately diagnose and predict disease course in IBD.

Adaptor Proteins, Signal Transducing↗
PubMed2000

Genetic variation: molecular mechanisms and impact on microbial evolution.

On the basis of established knowledge of microbial genetics one can distinguish three major natural strategies in the spontaneous generation of genetic variations in bacteria. These strategies are: (1) small local changes in the nucleotide sequence of the genome, (2) intragenomic reshuffling of segments of genomic sequences and (3) the acquisition of DNA sequences from another organism. The three general strategies differ in the quality of their contribution to microbial evolution. Besides a number of non-genetic factors, various specific gene products are involved in the generation of genetic variation and in the modulation of the frequency of genetic variation. The underlying genes are called evolution genes. They act for the benefit of the biological evolution of populations as opposed to the action of housekeeping genes and accessory genes which are for the benefit of individuals. Examples of evolution genes acting as variation generators are found in the transposition of mobile genetic elements and in so-called site-specific recombination systems. DNA repair systems and restriction-modification systems are examples of modulators of the frequency of genetic variation. The involvement of bacterial viruses and of plasmids in DNA reshuffling and in horizontal gene transfer is a hint for their evolutionary functions. Evolution genes are thought to undergo biological evolution themselves, but natural selection for their functions is indirect, at the level of populations, and is called second-order selection. In spite of an involvement of gene products in the generation of genetic variations, evolution genes do not programmatically direct evolution towards a specific goal. Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction.

Bacteria↗