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At least 1,315 records · Page 73Linked to original sources
PubMed1983

Self-transmissible plasmids in staphylococci that encode resistance to aminoglycosides.

High-level resistance to gentamicin, tobramycin, and kanamycin was transferred between staphylococci of the same and different species by filter mating. Resistance and transfer proficiency were mediated by plasmids ranging from 38 to 54 kilobases in size. All of the plasmids encoded intermediate resistance to amikacin and netilmicin and resistance to ethidium bromide; some encoded beta-lactamase production. None of these plasmids carried resistance to other antibiotics or heavy metals. Transfer of antibiotic resistance occurred by a mechanism similar to that of conjugation, because it was DNase resistant, required cell-to-cell contact, and did not appear to involve phage. The participation of phage in transfer appeared to be unlikely because mijtomicin C-induced lysates of donor isolates did not mediate transfer, filter mating transfer proceeded at high frequency between nonlysogenic donor and recipient cells, and transfer of the aminoglycoside resistance plasmid mobilized the transfer of as many as five additional plasmids. All 17 gentamicin-resistant Staphylococcus aureus and all 6 Staphylococcus epidermidis isolates obtained from an outbreak of staphylococcal infections in a newborn nursery contained conjugative plasmids, as did all 6 gentamicin-resistant S. aureus isolates from bacteremic adults. However, only 3 of 10 gentamicin-resistant S. epidermidis isolates from colonized cardiac surgery patients and 1 of 2 S. epidermidis isolates from patients with prosthetic valve endocarditis transferred gentamicin resistance by filter mating. The recent increase in nosocomial infections caused by gentamicin-resistant staphylococci may be partially explained by the evolution of self-transmissible plasmids in these isolates.

Aminoglycosides↗
PubMed1979

Estimation of biodegradation potential of xenobiotic organic chemicals.

A method is described to estimate the biodegradation potential of soluble, insoluble, and unknown organic chemicals. The method consists of two stages: (i) generation of a microbial inoculum in a bench scale semicontinuous activated sludge system during which microorganisms are acclimated to test material and the removal of dissolved organic carbon is monitored and (ii) biodegradability testing (CO(2) evolution) in a defined minimal medium containing the test material as the sole carbon and energy source and a dilute bacterial inoculum obtained from the supernatant of homogenized activated sludge generated in the semicontinuous activated sludge system. Removal and biodegradation are measured using nonspecific methods, at initial concentrations of 5 to 10 mg of dissolved organic carbon per liter. Biodegradability data are accurately described by a nonlinear computer model which allows the rate and extent of biodegradation for different compounds to be compared and statistically examined. The evaluation of data generated in the combined removability-biodegradability system allows the biodegradation potential of a variety of xenobiotic organic chemicals to be estimated.

Journal Article↗
PubMed1971

Minor threonine dehydratase encoded within the threonine synthetic region of Bacillus subtilis.

Challenging auxotrophs on metabolites that are precursors of a biosynthetic step involving a mutated enzyme has revealed a new class of suppressor mutations which act by derepressing a minor enzyme activity not normally detected in the wild-type strain. These indirect, partial suppressor mutations which allow isoleucine auxotrophs to grow on homoserine or threonine have been analyzed to determine their effect on enzymes involved in the biosynthesis of these amino acids. It has been found that one class of these suppressor mutations (sprA) leads to the derepression of homoserine kinase, homoserine dehydrogenase, and a minor threonine dehydratase that is not sufficiently active to be detected in the wild-type strain. The gene encoding this second threonine dehydratase activity has been found to be located between the structural genes for homoserine kinase and homoserine dehydrogenase. The results of these experiments indicate that plating of auxotrophs on precursors of a biosynthetic step involving mutated enzymes could prove to be a valuable method for the detection of regulatory mutants as well as a possible tool in studying the evolution of biochemical pathways.

Bacillus subtilis↗
PubMed1984

[The microcomputer in bacteriology. Value in the automated performance of antibiograms in hospitals].

In microbiology, most computerization is carried out by means of important centralized computers. On the contrary, our work is based upon the use of inexpensive microcomputers. We have developed general programs for the acquisition of data, their correction, and retrieval of lists arranged according to desired parameters (hospital department, germ, or sample) and various statistics, especially with respect to germ sensitivity. This system has been used on a routine basis since April 1982 in the Bacteriology Laboratory of Nancy University Hospital. It could easily be adapted to other laboratories and could provide a wide range of essential epidemiological data on the resistance of bacterial strains to antibiotics and their evolution with time.

Computers↗
PubMed2005

Environments shape the nucleotide composition of genomes.

To test the impact of environments on genome evolution, we analysed the relative abundance of the nucleotides guanine and cytosine ('GC content') of large numbers of sequences from four distinct environmental samples (ocean surface water, farm soil, an acidophilic mine drainage biofilm and deep-sea whale carcasses). We show that the GC content of complex microbial communities seems to be globally and actively influenced by the environment. The observed nucleotide compositions cannot be easily explained by distinct phylogenetic origins of the species in the environments; the genomic GC content may change faster than was previously thought, and is also reflected in the amino-acid composition of the proteins in these habitats.

Amino Acids↗
PubMed2004

Review of the knowledge of microbial contamination of the Russian manned spacecraft.

The 15-year experience of orbital station Mir service demonstrated that specifically modified space vehicle environments allows for the consideration of spaceship habitats as a certain ecological niche of microbial community development and functioning, which was formed from the organisms of different physiological and taxonomical groups. The base unit of the orbital station (OS) Mir was launched on February 20, 1986, and on March 13 the first crew arrived to it. From that moment a unique microbiocenosis started forming in the closed environment of the space station, and vital activity of the microorganisms continued for the next 15 years in a specifically changed environment, in conditions of continuous influence of a set of factors intrinsic to space flight. A total of 234 species of bacteria and fungi were found onboard orbital station Mir, among which microorganisms capable of resident colonization of the environment of space objects as a unique anthropotechnological niche were revealed. In such conditions the evolution of microflora is followed by the rise of medical and technical risks that can affect both sanitary-microbiological conditions of the environment and the safety and reliability characteristics of space equipment. The latter is caused by progressing biological damage to the structural materials. The microbial loading dynamic does not have linearly progressing character, but it is a wavy process of alternation of the microflora activation and stabilization phases; on this background there is a change of the dominating species by quantity and prevalence. The accumulated data is evidence of the necessity of the constant control of the microbial environmental factors to maintain their sanitary and microbiological optimum condition and to prevent the processes of constructional materials biodestruction.

Air Microbiology↗
PubMed1987

Microbial degradation of synthetic recalcitrant compounds.

Synthetic compounds, particularly highly chlorinated aromatics, comprise the bulk of the environmental pollutants that somehow must be removed from the environment. Microbial degradation of such compounds is usually very slow, making them highly persistent in nature. Some synthetic compounds, with a lower degree of chlorination are, however, biodegradable; biochemical, genetic, and molecular studies demonstrate the evolution of new plasmid-encoded enzymatic activities specifically designed for the chlorinated substrates. Nucleotide sequences of many of the genes encoding such enzymatic activities demonstrate considerable homology either near the active sites or throughout the molecules with the chromosomal genes encoding enzymes catalyzing analogous reactions. In some cases, unique repeated sequences, reminiscent of prokaryotic insertion sequence elements, are present at or near the newly evolved genes. This suggests gene duplication and divergence as well as recombinational events mediated by transposable type elements as key ingredients in the evolution of new degradative functions. An understanding of such evolutionary processes is an essential feature for the development of genetically-improved bacteria capable of utilizing and thereby removing highly chlorinated environmental pollutants from our environment.

Journal Article↗
PubMed2001

Characterization of bioreaction processes: aerobic Escherichia coli cultures.

The simulation of a microbial transformation course is an important tool for the optimal design or characterization of industrial processes. Usually, models are developed to describe a specific part of the culture such as microbial growth and most of the time ignore the influence of physical and chemical environment on growth dynamics of the microorganism. In this work we propose a method which combines the description of the evolution of components involved in the bioprocess including biomass and the physical environment generated mainly by the bioreactor characteristics and operational conditions. Stoichiometric, kinetic, fluid dynamics and mass transfer models are linked to predict the course of the Escherichia coli culture under the influence of different experimental conditions and types of bioreactors. A set of 22 kinetic and physical parameters obtained from independent experiments and from literature are used in order to predict glucose, biomass, acetate, dissolved oxygen and CO(2) concentrations in airlift and stirred tank bioreactors.

Acetates↗
PubMed2004

General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli.

Microbial cells under growth-limiting stress can generate mutations by mechanisms distinct from those in rapidly growing cells. These mechanisms might be specific stress responses that increase mutation rates, potentially altering rates of evolution, or might reflect non-stress-specific processes in rare growing cells. In an Escherichia coli model system, both frameshift reversion mutations and gene amplifications occur as apparent starvation-induced mutations. Whereas frameshift reversion ("point mutation") requires recombination proteins, the SOS response, and error-prone DNA polymerase IV (DinB), amplification requires neither SOS nor pol IV. We report that both point mutation and amplification require the stationary-phase and general stress response transcription factor RpoS (sigmaS). Growth-dependent mutation does not. Alternative interpretations are excluded. The results imply, first, that point mutation and amplification are stress responses that occur in differentiated stationary-phase (not rare growing) cells and, second, that transient genetic instability, producing both point mutation and genome rearrangement, may be a previously unrecognized component of the RpoS-dependent general stress response.

Adaptation, Biological↗
PubMed2026

Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa.

Microbial populations strongly shape their environment, which can re-route adaptation toward organism-generated fitness optima. However, the conditions that promote these eco-evolutionary feedbacks are unclear. Here, we used experimental evolution to test whether high population density, by strengthening niche construction, drives eco-evolutionary feedbacks in the bacterial pathogen Pseudomonas aeruginosa (Pa) MPAO1. We tested for adaptation to organism-modified environments by measuring the relative performance of ancestral and endpoint populations in filtrate generated by each evolutionary line sampled across generations. Contrary to expectations, we found that endpoint populations had higher performance than the ancestral strain in filtrate across nearly all evolutionary lines regardless of population density. This was caused by the emergence of hyperactive filamentous bacterio(phage) mutants during experimental passaging that inhibited the ancestral strain but not endpoint populations in modified media. Hyperactive phages emerged from one of two avirulent prophages in MPAO1's genome (Pf4 or Pf6). Hyperactive phages drove the evolution of phage resistance in bacterial populations via mutations in the type IV pilus (TIVP), the phage's binding receptor. In a follow-up experiment, we showed that these TIVP mutations pleiotropically reduced motility and conferred resistance to a TIVP-targeting virulent phage, both of which are important traits for Pa infection and treatment. Overall, this work suggests that filamentous phage evolution can drive eco-evolutionary feedbacks in bacterial populations, causing phenotypic and genetic changes that would not be anticipated from adaptation to the extrinsic environment alone.

Pseudomonas aeruginosa↗
PubMed2006

Toll-like receptors are part of the innate immune defense system of sponges (demospongiae: Porifera).

During evolution and with the emergence of multicellular animals, the need arose to ward off foreign organisms that threaten the integrity of the animal body. Among many different receptors that participate in the recognition of microbial invaders, toll-like receptors (TLRs) play an essential role in mediating the innate immune response. After binding distinct microbial components, TLRs activate intracellular signaling cascades that result in an induced expression of diverse antimicrobial molecules. Because sponges (phylum Porifera) are filter feeders, they are abundantly exposed to microorganisms that represent a potential threat. Here, we describe the identification, cloning, and deduced protein sequence from 3 major elements of the poriferan innate response (to bacterial lipopeptides): the TLR, the IL-1 receptor-associated kinase-4-like protein (IRAK-4l), and a novel effector caspase from the demosponge Suberites domuncula. Each molecule shares significant sequence similarity with its homologues in higher Metazoa. Sequence homologies were found in particular within the family-specific domains toll/interleukin-1 receptor/resistance (TLR family), Ser/Thr/Tyr kinase domain (IRAK family), and CASc (caspase family). In addition, in situ hybridization and immunohistological analyses revealed an abundance of SDTLR (TLR) transcripts in epithelial layers of the sponge surface (exopinacoderm and endopinacoderm). Furthermore, it is shown that both SDTLR and SDIRAK-4 like (IRAK) are expressed constitutively, regardless of treatment with synthetic triacyl lipopeptide Pam(3)Cys-Ser-(Lys)(4). In contrast, SDCASL (caspase) expression is highly Pam(3)Cys-Ser-(Lys)(4) inducible. However, blocking of the lipopeptide with recombinant TLR prior to its application completely prevented the induced expression of this poriferan caspase. These results underscore that the phylogenetically oldest extant metazoan phylum is provided already with the signaling pathways of the antimicrobial host-defense system of Metazoa.

Amino Acid Sequence↗
PubMed2006

Role of the envelope genetic context in the development of enfuvirtide resistance in human immunodeficiency virus type 1-infected patients.

Acquired human immunodeficiency virus type 1(HIV-1) resistance to the fusion inhibitor enfuvirtide (ENF) is primarily associated with mutations within the highly conserved first heptad repeat (HR1) region of gp41. Viral env sequences, however, are remarkably variable, and the envelope genetic background could have an important impact on optimal expression of HR1 mutations. We have examined the genetic evolution of env sequences, ENF susceptibility, and Env replicative capacity in patients failing ENF treatment. Sequential plasma-derived virus populations, obtained from six patients initiating ENF treatment as part of a salvage therapy, were studied using a recombinant phenotypic assay evaluating the entire gp120 and the gp41 ectodomains. Regardless of major differences in the baseline ENF susceptibilities, viral populations with similar phenotypic ENF resistance (50% inhibitory concentration, >3,000 ng/ml) were selected under treatment in four of six patients. As expected, in all patients ENF-resistant viruses harbored one or more HR1 mutations (positions 36, 38, and 43). Interestingly, in five patients the emergence of resistance mutations was not associated with reduced Env replicative capacity. Phylogenetic analysis of env sequences in sequential samples from two patients showed that the HR1 mutations had emerged in the context of env quasi-species that were different from those prevalent at baseline. Thus, the envelope genetic context appears to play a critical role in the selection of HR1 mutations and the expression of ENF resistance, thereby conditioning the evolution of HIV-1 under fusion inhibitor selective pressure.

Amino Acid Sequence↗
PubMed1998

Phylogenetic mapping of bacterial morphology.

The availability of a meaningful molecular phylogeny for bacteria provides a context for examining the historical significance of various developments in bacterial evolution. Herein, the classical morphological descriptions of selected members of the domain Bacteria are mapped upon the genealogical ancestry deduced from comparison of small-subunit rRNA sequences. For the species examined in this study, a distinct pattern emerges which indicates that the coccus shape has arisen and accumulated independently multiple times in separate lineages and typically survived as a persistent end-state morphology. At least two other morphologies persist but have evolved only once. This study demonstrates that although bacterial morphology is not useful in defining bacterial phylogeny, it is remarkably consistent with that phylogeny once it is known. An examination of the experimental evidence available for morphogenesis as well as microbial fossil evidence corroborates these findings. It is proposed that the accumulation of persistent morphologies is a result of the biophysical properties of peptidoglycan and their genetic control, and that an evolved body-plan strategy based on peptidoglycan may have been a fate-sealing step in the evolution of Bacteria. More generally, this study illustrates that significant evolutionary insights can be obtained by examining biological and biochemical data in the context of a reliable phylogenetic structure.

Bacteria↗
PubMed2005

Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community.

The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that (13)C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of alpha-, beta-, and gamma-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food chains.

Alphaproteobacteria↗