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At least 289 records · Page 16Linked to original sources
PubMed2001

Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes.

The compositions of bacterial genomes can be changed rapidly and dramatically through a variety of processes including horizontal gene transfer. This form of change is key to bacterial evolution, as it leads to 'evolution in quantum leaps'. Horizontal gene transfer entails the incorporation of genetic elements transferred from another organism-perhaps in an earlier generation-directly into the genome, where they form 'genomic islands', i.e. blocks of DNA with signatures of mobile genetic elements. Genomic islands whose functions increase bacterial fitness, either directly or indirectly, have most likely been positively selected and can be termed 'fitness islands'. Fitness islands can be divided into several subtypes: 'ecological islands' in environmental bacteria and 'saprophytic islands', 'symbiosis islands' or 'pathogenicity islands' (PAIs) in microorganisms that interact with living hosts. Here we discuss ways in which PAIs contribute to the pathogenic potency of bacteria, and the idea that genetic entities similar to genomic islands may also be present in the genomes of eukaryotes.

Bacteria↗
PubMedDate not supplied

Emergence of Salmonella epidemics: the problems related to Salmonella enterica serotype Enteritidis and multiple antibiotic resistance in other major serotypes.

Two major changes in the epidemiology of salmonellosis occurred in the second half of the 20th century: the emergence of food-borne human infections caused by S. Enteritidis and by multiple-antibiotic resistant strains of Salmonella. This review updates information on the S. Enteritidis pandemic and focuses on the emergence of Salmonella, carrying the SGI1 antibiotic resistance gene cluster, resistant to extended-spectrum cephalosporins, or resistant to fluoroquinolones. The factors responsible for the emergence of these Salmonella strains could be either of human origin or related to bacterial genome evolution. However, our increasing understanding of the molecular fluidity of the genome shows that any attempt to counteract bacteria results in further bacterial evolution or adaptation of other bacteria to take place in the new free ecological niche. In these conditions, we can ask who is faster: humans who want to eliminate bacterial pathogens or bacteria that continuously evolve to gain new niches.

Animals↗
PubMed1997

Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon.

Mercury and its compounds are distributed widely across the earth. Many of the chemical forms of mercury are toxic to all living organisms. However, bacteria have evolved mechanisms of resistance to several of these different chemical forms, and play a major role in the global cycling of mercury in the natural environment. Five mechanisms of resistance to mercury compounds have been identified, of which resistance to inorganic mercury (HgR) is the best understood, both in terms of the mechanisms of resistance to mercury and of resistance to heavy metals in general. Resistance to inorganic mercury is encoded by the genes of the mer operon, and can be located on transposons, plasmids and the bacterial chromosome. Such systems have a worldwide geographical distribution, and furthermore, are found across a wide range of both Gram-negative and Gram-positive bacteria from both natural and clinical environments. The presence of mer genes in bacteria from sediment cores suggest that mer is an ancient system. Analysis of DNA sequences from mer operons and genes has revealed genetic variation both in operon structure and between individual genes from different mer operons, whilst analysis of bacteria which are sensitive to inorganic mercury has identified a number of vestigial non-functional operons. It is hypothesised that mer, due to its ubiquity with respect to geographical location, environment and species range, is an ancient system, and that ancient bacteria carried genes conferring resistance to mercury in response to increased levels of mercury in natural environments, perhaps resulting from volcanic activity. Models for the evolution of both a basic mer operon and for the Tn21-related family of mer operons and transposons are suggested. The study of evolution in bacteria has recently become dominated by the generation of phylogenies based on 16S rRNA genes. However, it is important not to underestimate the roles of horizontal gene transfer and recombinational events in evolution. In this respect mer is a suitable system for evaluating phylogenetic methods which incorporate the effects of horizontal gene transfer. In addition, the mer operon provides a model system in the study of environmental microbiology which is useful both as an example of a genotype which is responsive to environmental pressures and as a generic tool for the development of new methodology for the analysis of bacterial communities in natural environments.

Biological Evolution↗
PubMed2003

Evolution of the bacterial community during granules formation in denitrifying reactors followed by molecular, culture-independent techniques.

The microbial community in two acetate-fed denitrifying reactors, inoculated with methanogenic sludge, was monitored by 16S rDNA-based methods (SSCP and FISH). Both reactors converged to similar, stable communities. The predominant organisms belonged to the genera Thauera, Paracoccus and Denitrobacter, detected both by molecular and culture-based methods.

Bacteria↗
PubMed1982

[Evolution of bacteria in hospital (author's transl)].

This study reports the evolution of bacterial ecology during twelve years in a general hospital : prevalence of the different species isolated and their resistance to antibiotics. It appears, in the etiology of serious infections, a great stability in the repartition of bacterial groups responsible. Likewise, the evolution of bacterial resistance during this period did not show a gradual increase. A certain balance seems to occur in function of local conditions, among which a controlled use of antibiotics is certainly an important factor.

Adult↗
PubMedDate not supplied

[Concept of a bacterial species and the evolution of the prokaryotic genome].

The present concepts of evolution and species delineation in prokaryotes are considered. Recently a considerable extension of knowledge on the processes of microevolution of medically significant bacteria was noted alongside with the importance of horizontal and lateral transfer of genes. The phylophenetic concept of species was considered in detail. The inclusion of the ecological criterion into a phylophenetic concept of a species is supposed to facilitate the development of more adequate notion on the evolution of bacteria, the improvement of species delineation in prokaryotes, their classification and nomenclature.

Bacteria↗
PubMed2003

Gastrointestinal disorders of the critically ill. Systemic consequences of ileus.

Ileus refers to the partial or complete blockage of the small and/or large intestine either by functional (adynamic or paralytic ileus) or mechanical bowel obstruction. The diffuse gastrointestinal dysmotility during functional and mechanical ileus may result in intestinal dilatation, increased luminal pressure and gut wall ischaemia which may lead to increased intra-abdominal pressure (IAP). Any type of ileus may promote abdominal fluid sequestration with severe systemic hypovolaemia, intestinal bacterial overgrowth with the evolution of bacterial translocation and systemic invasive infections and inflammation of the intestinal wall with concomitant release of cytokines and the development of the systemic inflammatory response syndrome. The most serious complications of ileus are mediated by an increase in IAP. Intra-abdominal hypertension has been found in up to 20% of critically ill patients and may lead to a broad pattern of systemic consequences with multiple organ dysfunction, including cardiovascular, hepatic, pulmonary, renal and neurological function. The abdominal compartment syndrome is an emergency condition which is defined as elevation of IAP above 20 to 25 mmHg and the presence of systemic consequences. Therapeutic considerations include the maintenance of adequate hydration status, avoidance of drugs known to impair intestinal perfusion, stimulation of gastric and intestinal motility and various nutritional aspects. Colonic tube placement after decompressive colonoscopy may be effective in reducing intestinal dilatation. In the abdominal compartment syndrome the 'open abdominal approach' with decompressive laparotomy by opening the peritoneal cavity and temporary abdominal closure is the therapy of choice.

Critical Illness↗
PubMed2004

A bacterial selection for the directed evolution of pyruvate aldolases.

A novel bacterial in vivo selection for pyruvate aldolase activity is described. Pyruvate kinase deficient cells, which lack the ability to biosynthetically generate pyruvate, require supplementation of exogenous pyruvate when grown on ribose. Supplementation with pyruvate concentrations as low as 50 microM rescues cell growth. A known substrate of the KDPG aldolases, 2-keto-4-hydroxy-4-(2'-pyridyl)butyrate (KHPB), also rescues cell growth, consistent with retroaldol cleavage by KDPG aldolase and rescue through pyruvate release. An initial round of selection against 2-keto-4-hydroxyoctonate (KHO), a nonsubstrate for wild-type aldolase, produced three mutants with intriguing alterations in protein sequence. This selection system allows rapid screening of mutant enzyme libraries and facilitates the discovery of enzymes with novel substrate specificities.

Aldehyde-Lyases↗
PubMed2001

Evolutionary genomics of pathogenic bacteria.

Complete genome sequences are now available for multiple strains of several bacterial pathogens and comparative analysis of these sequences is providing important insights into the evolution of bacterial virulence. Recently, DNA microarray analysis of many strains of several pathogenic species has contributed to our understanding of bacterial diversity, evolution and pathogenesis. Comparative genomics has shown that pathogens such as Escherichia coli, Helicobacter pylori and Staphylococcus aureus contain extensive variation in gene content whereas Mycobacterium tuberculosis nucleotide divergence is very limited. Overall, these approaches are proving to be a powerful means of exploring bacterial diversity, and are providing an important framework for the analysis of the evolution of pathogenesis and the development of novel antimicrobial agents.

Bacteria↗
PubMed2001

Whole genome plasticity in pathogenic bacteria.

The exploitation of bacterial genome sequences has so far provided a wealth of new general information about the genetic diversity of bacteria, such as that of many pathogens. Comparative genomics uncovered many genome variations in closely related bacteria and revealed basic principles involved in bacterial diversification, improving our knowledge of the evolution of bacterial pathogens. A correlation between metabolic versatility and genome size has become evident. The degenerated life styles of obligate intracellular pathogens correlate with significantly reduced genome sizes, a phenomenon that has been termed "evolution by reduction". These mechanisms can permanently alter bacterial genotypes and result in adaptation to their environment by genome optimization. In this review, we summarize the recent results of genome-wide approaches to studying the genetic diversity of pathogenic bacteria that indicate that the acquisition of DNA and the loss of genetic information are two important mechanisms that contribute to strain-specific differences in genome content.

Bacteria↗
PubMed2001

Ongoing evolution of strand composition in bacterial genomes.

We tried to identify the substitutions involved in the establishment of replication strand bias, which has been recognized as an important evolutionary factor in the evolution of bacterial genomes. First, we analyzed the composition asymmetry of 28 complete bacterial genomes and used it to test the possibility that asymmetric deamination of cytosine might be at the origin of the bias. The model showed significant correlation to the data but left unexplained a significant portion of the variance and indicated a systematic underestimation of GC skews in comparison with TA skews. Second, we analyzed the substitutions acting on the genes from five fully sequenced Chlamydia genomes that had not suffered strand switch since speciation. This analysis showed that substitutions were not at equilibrium in Chlamydia trachomatis or in C. muridarum and that strand bias is still an on-going process in these genes. Third, we identified substitutions involved in the adaptation of genes that had switched strands after speciation. These genes adapted quickly to the skewed composition of the new strand, mostly due to C-->T, A-->G, and C-->G asymmetric substitutions. This observation was reinforced by the analysis of genes that switched strands after divergence between Bacillus subtilis and B. halodurans. Finally, we propose a more extended model based on the analysis of the substitution asymmetries of CHLAMYDIA: This model fits well with the data provided by bacterial genomes presenting strong strand bias.

Bacteria↗
PubMed1993

Evolution of histidine decarboxylase bacterial groups during the ripening of Spanish semi-preserved anchovies.

We have studied the count evolutions of total aerobic mesophilic microorganisms, psychotrophic microorganisms, enterobacteria, faecal coliforms, sulphite-reducing bacteria and vibrio in spanish semi-preserved anchovies. These microorganisms are a sanitary index of the product and may produce high concentrations of histamine in both fresh and processed fish. The influence of NaCl concentration, redox potential, oxygen concentration and pH on bacterial growth have also been studied. With the exception of the sulphite-reducers and vibrio, the counts of the different bacterial groups decreased during the first two weeks of ripening, but later stabilized. The faecal coliforms did not appear in the culture media after these first two weeks, and the enterobacteria, what initially did not appear after first two weeks too, are detected at final phases probably for the final manipulation of elaboration processes. The count of the sulfite-reducers remained unchanged during the whole ripening process. Vibrio were not detected in any of the samples studied. NaCl and oxygen concentrations were the main factors influencing the decreasing bacterial counts. According to our results, the accumulation of high histamine concentrations in salted fish could be due to poor quality of the raw material, to inadequate handling or to other causes during its shelf life. The relationship with the histamine activity is probably due more to the presence of the halophilic or halotolerant microorganisms.

Animals↗
PubMed2005

Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities.

Bacterial dehalogenases catalyse the cleavage of carbon-halogen bonds, which is a key step in aerobic mineralization pathways of many halogenated compounds that occur as environmental pollutants. There is a broad range of dehalogenases, which can be classified in different protein superfamilies and have fundamentally different catalytic mechanisms. Identical dehalogenases have repeatedly been detected in organisms that were isolated at different geographical locations, indicating that only a restricted number of sequences are used for a certain dehalogenation reaction in organohalogen-utilizing organisms. At the same time, massive random sequencing of environmental DNA, and microbial genome sequencing projects have shown that there is a large diversity of dehalogenase sequences that is not employed by known catabolic pathways. The corresponding proteins may have novel functions and selectivities that could be valuable for biotransformations in the future. Apparently, traditional enrichment and metagenome approaches explore different segments of sequence space. This is also observed with alkane hydroxylases, a category of proteins that can be detected on basis of conserved sequence motifs and for which a large number of sequences has been found in isolated bacterial cultures and genomic databases. It is likely that ongoing genetic adaptation, with the recruitment of silent sequences into functional catabolic routes and evolution of substrate range by mutations in structural genes, will further enhance the catabolic potential of bacteria toward synthetic organohalogens and ultimately contribute to cleansing the environment of these toxic and recalcitrant chemicals.

Amino Acid Sequence↗
PubMed2006

The fate of laterally transferred genes: life in the fast lane to adaptation or death.

Large-scale genome arrangement plays an important role in bacterial genome evolution. A substantial number of genes can be inserted into, deleted from, or rearranged within genomes during evolution. Detecting or inferring gene insertions/deletions is of interest because such information provides insights into bacterial genome evolution and speciation. However, efficient inference of genome events is difficult because genome comparisons alone do not generally supply enough information to distinguish insertions, deletions, and other rearrangements. In this study, homologous genes from the complete genomes of 13 closely related bacteria were examined. The presence or absence of genes from each genome was cataloged, and a maximum likelihood method was used to infer insertion/deletion rates according to the phylogenetic history of the taxa. It was found that whole gene insertions/deletions in genomes occur at rates comparable to or greater than the rate of nucleotide substitution and that higher insertion/deletion rates are often inferred to be present at the tips of the phylogeny with lower rates on more ancient interior branches. Recently transferred genes are under faster and relaxed evolution compared with more ancient genes. Together, this implies that many of the lineage-specific insertions are lost quickly during evolution and that perhaps a few of the genes inserted by lateral transfer are niche specific.

Adaptation, Physiological↗