Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “microbial evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,729 records · Page 96Linked to original sources
PubMedDate not supplied

Frontiers in genomics: insights into protist evolutionary biology, University of Iowa, May 19-21, 2004.

Protists constitute the bulk of eukaryotic diversity yet their genomes remain relatively unexplored. To address this issue, a workshop entitled, "Frontiers in Genomics: Insights into Protist Evolutionary Biology", was convened at the University of Iowa on June 19-21, 2004. The specific aims of the workshop were to define the role of genomics in the eukaryotic tree of life, to identify challenges in characterizing protist (i.e. microbial eukaryote) genomes, and in proposing specific solutions to these challenges. The findings of the workshop are presented here and in a white paper that provide a set of guidelines for organizing the protist community and for planning and executing a protist genome project.

Animals↗
PubMed1989

[Appearance and evolution of bacterial resistance to antibiotics].

Concomitant with antibiotic use has been the appearance of resistance bacteria which seem able to emerge as rapidly as new antibiotics are introduced. Although initially encountered in hospitals, resistant bacteria are now being detected as causes of human and animal infections and as colonizers of the gut. Moreover, resistant bacteria are isolated from the environment.

Animals↗
PubMed1999

Advances in antimicrobial therapy.

Despite several decades of improved therapy and prevention of infectious diseases, infectious pathogens remain major causes of morbidity and mortality in humans worldwide. Among the most complex and daunting problems facing medical science is the evolution of antibiotic resistance among many common and once easily-treated infectious agents. This review summarizes the status of newer antimicrobial agents that have utility against pathogens infecting the central nervous system.

Anti-Bacterial Agents↗
PubMed2005

Interaction network containing conserved and essential protein complexes in Escherichia coli.

Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.

Alleles↗
PubMed2025

Rapid replacement of blaKPC variant in ST11 carbapenem-resistant and hypervirulent Klebsiella pneumoniae contributed to ceftazidime/avibactam resistance during severe in vivo infection.

OBJECTIVES: Hypervirulent ceftazidime/avibactam (CAZ/AVI)-resistant Klebsiella pneumoniae (Kp) has emerged; however, its dynamic within-host evolution and competitive features are uncharacterized. This study aimed to clarify the systematic microevolution characteristics of the rapid transformation of blaKPC variants during long-term infection. METHODS: Thirty-nine Kp strains were isolated from a single patient with severe recurrent osteomyelitis during a 2-year period. Whole-genome sequencing and in vitro evolution assay was performed. Microbiological characteristics were examined through antimicrobial susceptibility testing, plasmid stability, growth curve, in vitro competition and Galleria mellonella larvae lethality assays. RESULTS: Among all the clinical Kp isolates, 37 were carbapenem-resistant Kp (CRKP), including 25 CAZ-/AVI-resistant Kp. All isolates belonged to the ST11-K47. During in vivo evolution, the blaKPC variant and its amplification emerged. Twenty-four isolates (24/39, 61.5%) harboured a novel blaKPC variant, blaKPC-144. All five Kp isolates carried blaKPC-2 in 2021. Surprisingly, 24 blaKPC-144-harbouring isolates (70.6%, 24/34) and 10 blaKPC-2-harboring isolates were identified in 2023, indicating rapid changing of blaKPC. Kp4 carried two copies of blaKPC-2, and Kp10-1 exhibited a 1.94-fold increase in the blaKPC-144 copy number. Similarly, in vitro, the blaKPC copy number increased upon exposure to low CAZ/AVI concentrations. However, at higher concentrations (4/1 mg/L), the blaKPC copy number increased significantly, and blaKPC mutations emerged simultaneously. The competition assay indicated that the blaKPC-144-harboring isolates exhibited a superior competitive capacity. CONCLUSIONS: The blaKPC amplification and mutation emerged simultaneously or sequentially during in vivo and in vitro evolution. Kp isolates harbouring blaKPC-144, conferring resistance to CAZ/AVI, exhibited a competitive advantage, promoting the rapid replacement of blaKPC-2.

Klebsiella pneumoniae↗
PubMed1996

Development of a mechanistic model of intake and chewing activities of sheep.

A mechanistic model of intake and chewing activities was developed using data from confined sheep in order to integrate the relationships between feeding behavior and digestive processes. The model consists of two interconnected submodels. The ruminal digestion submodel describes flows of nutrients and is based on differential equations to simulate the dynamic evolution of particulate matter and volatile fatty acids (VFA) in the reticulorumen. The diet is characterized by cell wall content and its potential digestibility, by the proportion of large particles (LP) retained on a 1-mm mesh sieve, and by an index of palatability. Particle comminution occurs during eating and ruminating. Intake is determined from attributes of the diet, animal live weight, and satiety status. Particulate outflow is calculated from a description of the activity of the reticulo-omasal orifice. Microbial digestion rates vary with lag phase, chemical fraction, size of particles, and ruminal pH. The VFA are aggregated into one compartment. The feeding decision submodel distinguishes among eating, ruminating, and resting. The choice among these activities is decided at each minute of simulation according to the relative values of functions of intake motivation (FMI) and of satiety (FSAT). The FMI function is based on diet palatability, energy balance, and the diurnal cycle. The FSAT function is determined by rumen load signals and energy balance. When the animal does not eat, the decision between ruminating and resting is related to the proportion of long particles in the rumen. Sensitivity analysis and validations indicate that the overall behavior of the model is adequate.

Animals↗
PubMed2000

Role of mycoplasma in male infertility.

We trace the evidence-based evolution of ureaplasmal male infertility as an established clinical entity. We review epidemiology data, possible pathogenic mechanisms of Ureaplasma urealyticum in infertility, and the results of isolation studies and therapeutic trials. Future developments are outlined.

Anti-Bacterial Agents↗
PubMed1987

Skin lesions caused by Mycobacterium scrofulaceum.

A 32-year-old man with systemic lupus erythematosus controlled by steroid therapy developed multifocal cutaneous abscesses caused by Mycobacterium scrofulaceum. The distribution and evolution of the lesions suggested hematogenous dissemination, but he exhibited no pulmonary or other visceral manifestations of systemic mycobacterial disease. The patient completed nine months of therapy with isoniazid and rifampin, and the lesions resolved within five months of presentation.

Abscess↗
PubMed1986

The predominant cultivable microbial population of adult periodontitis.

An extensive characterization of the cultivable microbial population, present in gingival pockets of a selected group of eight patients with periodontal disease, has been performed. The result obtained, from samples collected from six different periodontal sites in each patient, indicate a great prevalence of anaerobic bacteria. It is likely that the presence inside the gingival pockets of anaerobic cocci, to which the rods are capable of a selective coaggregation mechanism, creates conditions favorable to the proliferation of the latter type of bacteria. These findings suggest that the evolution of adult periodontitis is based on a chronic inflammatory stimulus and the necrosis of gingival epithelium caused by the proliferation of the anaerobic rods.

Adult↗
PubMedDate not supplied

[Staphylococcus aureus septicemia in children: bacterial tolerance to vancomycin and serum bactericidal activity].

PURPOSE: To evaluate the susceptibility and of strains of Staphylococcus aureus isolated from children with septicemia, and to evaluate the importance of the serum bactericidal test. METHODS: Seventeen children with Staphylococcus aureus septicemia admitted to the Semi Intensive Care Unit of the Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo were studied. Twenty nine tests in the pico and 23 in the nadir of the antibiotics were made. RESULTS: Strains of Staphylococcus aureus from hospital origin were resistant to all the antibiotics but vancomycin and pefloxacin. The phenomenon of tolerance was seen in 5 (50%) of the strains that were tested for vancomycin, and 4 of the children had a bad evolution. The serum bactericidal tests showed titles in the pico > or = 1/8 in 55.5% of the observations; in this group the evolution was better. CONCLUSION: Strain of Staphylococcus aureus from hospital origin are multiresistant. The phenomenon of antimicrobial tolerance, as well as the serum bactericidal test may be related to a bad therapeutic evolution. The increasing value of the serum bactericidal test as a way to evaluate the therapeutic evolution in severe infections, and the role of the tolerance of the Staphylococcus aureus to vancomycin more studies.

Anti-Bacterial Agents↗
PubMed2005

The role of potassium as an ionic signal in the regulation of cyanobacterium Nostoc muscorum response to salinity and osmotic stress.

Spontaneously occurring thallium-resistant (Tl+ -R) mutant of diazotrophic, heterocystous cyanobacterium Nostoc muscorum is described in which Tl+ -R phenotype is the cause of defective salinity-inducible K+ uptake activity and proline uptake activity. The results indicate that mutant strain is more sensitive to salinity and osmotic stresses than its parent. The mutational inactivation of salinity-inducible proline uptake was found associated with increased sensitivity of the cyanobacterial photosynthetic O2 evolution and nitrogenase activity under salinity and osmotic stresses. It is suggested that in the cyanobacterium Nostoc muscorum K+ functions as a primary osmolyte which is associated with salinity-inducible proline uptake leading to the acquisition of salt tolerance in the cyanobacterium.

Adaptation, Physiological↗
PubMed2003

Molecular identification of bacteria and Eukarya inhabiting an Antarctic cryoconite hole.

Inhabitants of a cryoconite hole formed in the Canada Glacier in the McMurdo Dry Valley region of Antarctica have been isolated and identified by small subunit (16S/18S) rDNA amplification, cloning, and sequencing. The sequences obtained revealed the presence of members of eight bacterial lineages (Acidobacterium, Actinobacteria, Cyanobacteria, Cytophagales, Gemmimonas, Planctomycetes, Proteobacteria, and Verrucomicrobia) and metazoan (nematode, tardigrade, and rotifer), truffle (Choiromyces), ciliate (Spathidium), and green algal (Pleurastrium) Eukarya. Bacterial recovery was approximately 20-fold higher at 4 degrees C and 15 degrees C than at 22 degrees C, and obligately psychrophilic bacteria were identified and isolated. Several of the rDNA molecules amplified from isolates and directly from cryoconite DNA preparations had sequences similar to rDNA molecules of species present in adjacent lake ice and microbial mat environments. This cryoconite hole community was therefore most likely seeded by particulates from these local environments. Cryoconite holes may serve as biological refuges that, on glacial melting, can repopulate the local environments.

Antarctic Regions↗
PubMed2003

Annotation of bacterial genomes using improved phylogenomic profiles.

MOTIVATION: Phylogenomic profiling is a large-scale comparative genomic method used to infer protein function from evolutionary information first described in a binary form by Pellegrini et al. (1999). Here, we propose improvements of this approach including the use of normalized Blastp bit scores, a normalization of the matrix of profiles to take into account the evolutionary distances between bacteria, the definition of a phylogenomic neighborhood based on continuous pairwise distances between genes and an original annotation procedure including the computation of a p-value for each functional assignment. RESULTS: The method presented here increases the number of Ecocyc enzymes identified as being evolutionarily related by about 25% with respect to the original binary form (absent/present) method. The fraction of 'false' positives is shown to be smaller than 20%. Based on their phylogenomic relationships, genes of unknown function can then be automatically related to annotated genes. Each gene annotation predicted is associated with a p-value, i.e. its probability to be obtained by chance. The validity of this method was extensively tested on a large set of genes of known function using the MultiFun database. We find that 50% of 3122 function attributions that can be made at a p-value level of 10(-11) correspond to the actual gene annotation. The method can be readily applied to any newly sequenced microbial genome. In contrast to earlier work on the same topic, our approach avoids the use of arbitrary cut-off values, and provides a reliability estimate of the functional predictions in form of p-values.

Algorithms↗
PubMed2000

Metronidazole activation is mutagenic and causes DNA fragmentation in Helicobacter pylori and in Escherichia coli containing a cloned H. pylori RdxA(+) (Nitroreductase) gene.

Much of the normal high sensitivity of wild-type Helicobacter pylori to metronidazole (Mtz) depends on rdxA (HP0954), a gene encoding a novel nitroreductase that catalyzes the conversion of Mtz from a harmless prodrug to a bactericidal agent. Here we report that levels of Mtz that partially inhibit growth stimulate forward mutation to rifampin resistance in rdxA(+) (Mtz(s)) and also in rdxA (Mtz(r)) H. pylori strains, and that expression of rdxA in Escherichia coli results in equivalent Mtz-induced mutation. A reversion test using defined lac tester strains of E. coli carrying rdxA(+) indicated that CG-to-GC transversions and AT-to-GC transitions are induced more frequently than other base substitutions. Alkaline gel electrophoretic tests showed that Mtz concentrations near or higher than the MIC for growth also caused DNA breakage in H. pylori and in E. coli carrying rdxA(+), suggesting that this damage may account for most of the bactericidal action of Mtz. Coculture of Mtz(s) H. pylori with E. coli (highly resistant to Mtz) in the presence of Mtz did not stimulate forward mutation in E. coli, indicating that the mutagenic and bactericidal products of Mtz metabolism do not diffuse significantly to neighboring (bystander) cells. Our results suggest that the widespread use of Mtz against other pathogens in people chronically infected with H. pylori may stimulate mutation and recombination in H. pylori, thereby speeding host-specific adaptation, the evolution of virulence, and the emergence of resistance against Mtz and other clinically useful antimicrobials.

Amino Acid Substitution↗
PubMed1995

[Phenotypes of resistance to antibiotics of the most frequently isolated strains in five specialized hospital centers. Multicenter study].

Antibiotic susceptibility of 948 bacterial strains isolated from varied samples essentially proceeding from urinary infections in five Paris psychiatric Hospitals was determined by disk diffusion method. E. coli, P. mirabilis, Klebsiella spp., P. aeruginosa et S. aureus are the predominant bacteria. 40% of S. aureus are methicilline resistant. Enterobacteriaceae are progressively becoming resistant to aminopenicillines, but remain sensitive to third generation cephalosporines. They are still susceptible to first generation quinolones. At least, if no resistance of P. aeruginosa to imipeneme has been reported, 30% of strains are resistant to ciprofloxacine. Resistance phenotypes to antibiotics of the strains isolated in patients from psychiatric Hospitals are located between those observed in out patients and in patients from general Hospitals. However, we noticed a worrying evolution of resistance to those encontered in psychiatric Hospitals. Therefore, a multiresistant strains emergence monitoring must be carried out regulary.

4-Quinolones↗
PubMed2005

Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes.

Historically, the prokaryotic genome was assumed to consist of a single circular replicon. However, as more microbial genome sequencing projects are completed, it is becoming clear that multipartite genomes comprised of more than one chromosome are not unusual among prokaryotes. Chromosomes are distinguished from plasmids by the presence of essential genes as well as characteristic cell cycle-linked replication kinetics; unlike plasmids, chromosomes initiate replication once per cell cycle. The existence of multipartite prokaryotic genomes raises several questions regarding how multiple chromosomes are replicated and segregated during the cell cycle. These divided genomes also introduce questions regarding chromosome evolution and genome stability. In this review, we discuss these and other issues, with particular emphasis on the cholera pathogen Vibrio cholerae.

Bacteria↗
PubMed2006

New opportunities revealed by biotechnological explorations of extremophiles.

Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of potential applications for biotechnology. More recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for the biotechnological exploration of extremophiles.

Archaea↗
PubMed1998

A natural species concept for prokaryotes.

Direct molecular analyses of natural microbial populations reveal patterns that should compel microbiologists to adopt a more natural species concept that has been known to biologists for decades. The species debate can be exploited to address a larger issue - microbiologists need, in general, to take a more natural view of the organisms they study.

Bacteria↗