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PubMed1995

[Antibiotic resistance--an ambivalence of attitudes. As of now, the bacteria are in advantage].

The value of the precious medical asset that antibiotics constitute is contimualby being eroded by the spread of resistance. For some time that bacterial world has been adapting itself to contend with the toxic assault of man-made poisons, antibiotics, by developing resistance in a very rapid process of evolutionary changes occurring before our very eyes. This evolutionary adaptation is an example of natural genetic engineering entailing an interchange between bacteria of genes conferring antibiotic resistance. Trimethoprim resistance is an example where numerous genes of unknown origin (some closely interrelated), expressing drug-resistant dihydrofolate reductases, move among human commensals and pathogens. They have been shown to move as gene cassettes in and out of the recently characterised integron structure occurring in many pathogens. They are also carried by various transposons such as Tn7, or Tn5393 originally observed in a plant pathogen, Erwinia amylovora. Betalactam resistance is another example of natural genetic engineering, where new betalactamases are continually emerging, and individual enzyme substrate specificity is modified by point mutation. At present, betalactamase mutants resistant to all commercially available betalactams, including clavulanic acid used in combination with betalactam antibiotics, are to be found in clinical isolates. Thus, currently bacteria seem to be triumphing in the running battle between the pharmaceutical industry and the bacterial world, the former introducing one new antibiotic variant after another, to which bacteria promptly develop resistance by manipulating their own genomes.

Animals↗
PubMed1998

[Bacterial resistance to antibiotics, an exemplary model of directed molecular evolution].

The simplest conceivable event that can occur at the gene level can result in the development of efficacious resistance tot antibiotics. The bacterial world behaves as an enormous organism whose cells can exchange their genes very easily. Accordingly, opportunities for the exchange of genetic material in nature are probably unlimited. This knowledge cannot be ignored. It leads to the important conclusion that the antibiotics are societal drugs. A resistance gene which has appeared somewhere in the world can travel far and fast.

Anti-Bacterial Agents↗
PubMed2005

Microbial succession associated with organic matter decomposition during thermophilic composting of organic waste.

Using dog food as a model of the organic waste, thermophilic composting was carried out for 14 days at a fixed temperature of 60 degrees C. The relationship between organic matter decomposition measured by CO2 evolution during the bio-stabilization process and microbial succession expressed as the changes over time in the restriction fragment length polymorphism (RFLP) patterns of 16S rDNA sequences, of micro-organisms associated with the composting material was also examined. The CO2 evolution rate peaked on day 3 and gradually decreased until it became extremely small after day 9 of composting, indicating that vigorous organic matter decomposition ceased around this time. On the other hand, the RFLP pattern changed drastically from day 0 to day 4 or 5, then remained stable until day 7 or 8, reaching its final configuration, with little variations, after day 9 of composting. RFLP analysis therefore indicates that microbial succession continued into the later stage of composting. Nevertheless, by day 9, the rate of organic matter decomposition was so low that its influence on microbial populations could be hardly recognized by conventional methods of dilution plating. Moreover, the compost produced by day 9 showed no inhibitory effect on the growth of Komatsuna (Brassica campestris L. var. rapiferafroug), indicating that the maturity of compost is sufficient for plant growth when the rate of organic matter decomposition has become extremely low and the RFLP patterns become stable.

Bacteria↗
PubMed2004

Effect of gas velocity and influent concentration on biofiltration of gasoline off-gas from soil vapor extraction.

This study was conducted to evaluate the effects of gas inlet concentration and velocity on the biofiltration of gasoline vapor. Gasoline vapor was treated using a compost biofilter operated in an upflow mode for about 3 months. The inlet concentration of gasoline total petroleum hydrocarbon (TPH) ranged from about 300 to 7000 mgm(-3) and gas was injected at velocities of 6 and 15 mh(-1) (empty bed residence time (EBRT)=10 and 4 min, respectively). The maximum elimination capacities of TPH at 6 and 15 mh(-1) found in this research were over 24 and 19 gm(-3) of filling material h(-1), respectively. TPH removal data was fit using a first-order kinetic relationship. In the low concentration range of 300-3000 mg m(-3), the first-order kinetic constants varied between about 0.10 and 0.29 min(-1) regardless of gas velocities. At TPH concentrations greater than 3000 mgm(-3), the first-order kinetic constants were about 0.09 and 0.07 min(-1) at gas velocities of 6 mh(-1) and 15 mh(-1), respectively. To evaluate microbial dynamics, dehydrogenase activity, CO2 generation and microbial species diversity were analyzed. Dehydrogenase activity could be used as an indicator of microbial activity. TPH removal corresponded well with CO2 evolution. The average CO2 recovery efficiency for the entire biofilter ranged between 60% and 70%. When the gas velocity was 6 mh(-1), most of the microbial activity and TPH removal occurred in the first quarter of the biofilter. However, when the gas velocity was 15 mh(-1), the entire column contributed to removal. Spatial and temporal variations in the biofilter microbial population were also observed. Nearly 60% of the colonies isolated from the compost media prior to biofiltration were Bacillus. After 90 days of biofiltration, the predominant species in the lower portion (0-50 cm) of the filter were Rhodococcus, while Pseudomonas and Acinetobacter dominated the upper portion (75-100 cm).

Bacteria↗
PubMed2003

Structure of the micronuclear alpha-tubulin gene in the phyllopharyngean ciliate Chilodonella uncinata: implications for the evolution of chromosomal processing.

Ciliates are a group of microbial eukaryotes defined by the presence of dimorphic nuclei-each cell contains both a transcriptionally active macronucleus and a germline micronucleus. During the development of the macronucleus, germline chromosomes are rearranged through extensive fragmentation, removal of internally excised sequences (IESs) and DNA amplification. We have characterized three IESs in the gene that encodes alpha-tubulin in the phyllopharyngean ciliate Chilodonella uncinata. The IESs are located within the coding domain, range in size from 81 to 107 bp, and are flanked by direct repeats that vary in length from 6 to 8 bp. All three IESs are moderately AT-rich and each contains two copies of a conserved sequence motif. These data provide evidence for the existence of IESs in phyllopharyngean ciliates and suggest that IES processing in C. uncinata may rely on a novel cis-acting sequence. Comparisons of the IESs in C. uncinata with those of 'model' ciliates-Paramecium, Tetrahymena, Euplotes, Oxytricha and Stylonychia-reveal considerable variation in chromosomal processing among ciliates.

Animals↗
PubMed2004

Genome diversity in microbial eukaryotes.

The genomic peculiarities among microbial eukaryotes challenge the conventional wisdom of genome evolution. Currently, many studies and textbooks explore principles of genome evolution from a limited number of eukaryotic lineages, focusing often on only a few representative species of plants, animals and fungi. Increasing emphasis on studies of genomes in microbial eukaryotes has and will continue to uncover features that are either not present in the representative species (e.g. hypervariable karyotypes or highly fragmented mitochondrial genomes) or are exaggerated in microbial groups (e.g. chromosomal processing between germline and somatic nuclei). Data for microbial eukaryotes have emerged from recent genome sequencing projects, enabling comparisons of the genomes from diverse lineages across the eukaryotic phylogenetic tree. Some of these features, including amplified rDNAs, subtelomeric rDNAs and reduced genomes, appear to have evolved multiple times within eukaryotes, whereas other features, such as absolute strand polarity, are found only within single lineages.

Journal Article↗
PubMed2005

Diversity, dynamics and activity of bacterial populations in 'Registered Designation of Origin' Salers cheese by single-strand conformation polymorphism analysis of 16S rRNA genes.

AIMS: The aim of this work was to measure the dynamic global metabolic activities of the microbial community during ripening of RDO Salers cheese by using a direct molecular approach. METHODS AND RESULTS: A culture-independent approach including PCR, reverse transcriptase PCR (RT-PCR) and single strand conformation polymorphism (SSCP) analysis of 16S rRNA genes was applied on 'Registered Designation of Origin' Salers cheese samples collected in three farms. The evolution of the global structure of the microbial community in terms of structure or global activities was assessed using ecological indices. The diversity of the global population was higher on RNA patterns than on DNA patterns, because of less dominance and greater richness. Comparison of the SSCP patterns derived from RNA and DNA analysis indicated that the dominant population was not necessarily the most active. The metabolic activities of each bacterial group changed significantly during ripening. Besides lactic acid bacteria that were dominant on both DNA and RNA patterns, the dynamics of the presence and activity of microbial groups rarely studied in the core of cheese, such as corynebacteria, or of unidentified peaks were reported. CONCLUSIONS: By using SSCP RNA analysis, we were able to obtain information about the activity of bacterial population in cheese, which varied a lot between cheeses and was changing perpetually during ripening. SIGNIFICANCE AND IMPACT OF THE STUDY: Double DNA-RNA SSCP analysis opens up future prospects in the microbial ecology of cheeses. It will have many applications for controlling of microbial community during cheese processing.

Cheese↗
PubMed1987

[Erythrocyte sedimentation rate and serum immunoglobulins in rheumatic pelvispondylitis].

Blood sedimentation rate and balanced titration of immunoglobulins were studied in 59 patients presenting a ankylosing pelvispondylitis: in 30 of them, these examinations were repeated at an interval of 3-6 months. The sedimentation rate (Sed. rate) and the level of immunoglobulins G and A increased in the course of the disease, but an elective increase of the level of immunoglobulins A was not demonstrated. Neither the Sed. rate, nor the level of IgA are correlated to evolution criteria of the disease; a positive correlation is only found with the platelets number, in a vertical study of 59 patients. Nevertheless, the variations of the immunoglobulins A is positively correlated with alterations of the clinical condition as demonstrated in the longitudinal study carried out in 30 patients. This finding supports physiopathological hypothesis which incriminates microbial intestinal infections at the origin of evolutive bouts of ankylosing pelvispondylitis.

Arthritis, Rheumatoid↗
PubMedDate not supplied

Antibiotic resistance and maxillofacial pathogens: emerging treatment issues.

The practice of using antibiotics to treat and control microbial infections is a little more than 50 years old. Widespread administration of multiple classes of antibiotics over the years has had the unfortunate secondary effect of inducing the emergence of an increasing array of drug-resistant microbial strains. This article will discuss the evolution of certain forms of antibiotic resistance, as well as the mechanisms by which bacteria render numerous antimicrobials ineffective. Special emphasis is placed on emerging issues relating to organisms making up portions of the normal oral microflora.

Bacteria, Anaerobic↗
PubMed2000

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

Amino Acid Motifs↗
PubMed2003

Effect of glyphosate on the microbial activity of two Brazilian soils.

Glyphosate [N-(phosphonomethyl)-glycine] is a broad-spectrum, non-selective, post-emergence herbicide that is widely used in agricultural. We studied, in vitro, changes in the microbial activity of typical Hapludult and Hapludox Brazilian soils, with and without applied glyphosate. Glyphosate was applied at a rate of 2.16 mg glyphosate kg(-1) of soil and microbial activity was measured by soil respiration (evolution of CO(2)) and fluorescein diacetate (FDA) hydrolysis over a period of 32 days. We found an increase of 10-15% in the CO(2) evolved and a 9-19% increase in FDA hydrolyses in the presence of glyphosate compared with the same type of soil which had never received glyphosate. Soil which had been exposed to glyphosate for several years had the strongest response in microbial activity. Most probable number (MPN) counts showed that after 32 days incubation the number of actinomycetes and fungi had increased while the number of bacteria showed a slight reduction. After the incubation period, high pressure liquid chromatography (HPLC) detected the glyphosate metabolite aminomethyl phosphonic acid (AMPA), indicating glyphosate degradation by soil microorganisms.

Bacteria↗
PubMed2026

Cross-domain cooperation drives nutrient acquisition and metabolism in the bark beetle holobiont.

Microbial symbiosis underpins host adaptation, yet mechanisms of metabolic integration in holobionts remain unclear. Using metatranscriptomics, genomics, and metabolic assays, we investigated gut microbiome interactions in the European spruce bark beetle (Ips typographus). We observed metabolic complementarity among symbionts and host, forming cross-domain networks that support nutrient acquisition. Nitrogen recycling revealed strong interdependence: no single partner possessed a complete uric acid degradation pathway, but combined evidence supports a distributed pathway spanning beetle, Bacteria, and fungi. Additionally, bacterial nitrate reduction to ammonia indicates a potential nitrogen influx, making otherwise inaccessible inorganic nitrogen available to the host. Shaped by microbial interactions, symbionts also likely supply specific amino acids, while vitamin metabolism showed cross-domain co-metabolism, with Bacteria as main producers of B vitamins, while host and fungi modulated interconversion. Carbohydrate degradation was highly partitioned; bacteria target xylan and pectin, while fungi contribute to glucan breakdown. Crucially, our data provide indirect evidence that the beetle may contribute to complete cellulose degradation, highlighting an underappreciated host role in lignocellulose processing. In terms of enzymatic functional diversity, the bacteriome emerged as the most important microbiome component-an observation that contrasts with the traditional focus on fungi and underscores the need to consider bacterial contributions in insect symbioses. Despite life-stage variation, core metabolic functions remained stable. Overall, metabolic interdependence, rather than microbial composition alone, structures holobiont function. These results highlight functional redundancy and ecological resilience, emphasizing the importance of microbial cooperation and host-microbe metabolic evolution.

Bark beetle↗
PubMed1999

Antibiotic resistance and maxillofacial pathogens: emerging treatment issues.

The practice of using antibiotics to treat and control microbial infections is a little more than 50 years old. Widespread administration of multiple classes of antibiotics over the years has had the unfortunate secondary effect of inducing the emergence of an increasing array of drug-resistant microbial strains. This article will discuss the evolution of certain forms of antibiotic resistance, as well as the mechanisms by which bacteria render numerous antimicrobials ineffective. Special emphasis is placed on emerging issues relating to organisms making up portions of the normal oral microflora.

Anti-Bacterial Agents↗
PubMedDate not supplied

Real-time determination of microbial activity of pasteurized fluid milk using a novel microrespirometer method.

The effectiveness of the rapid CO2 evolution rate (CER) method was evaluated by using a novel noninstrumental microrespirometer to determine the microbial activity of pasteurized milk and comparing it with traditional culturing methods in homogeneous milk samples. Three different kinds of milk (skim, 1% fat, and whole) stored at 2 temperatures (4 degrees and 7 degrees C) were measured daily for CER, aerobic plate count (APC), and psychrotrophic bacterial count. The mean initial rates of CO2 evolution for all 3 samples stored at the 2 temperatures ranged from 3.42 to 3.71 microL/h/mL and increased to 29 microL/h/mL and above on the final day of the experiment. Regression analysis showed a high correlation (R = 0.98-0.99) between the APC and CER results in combined milk samples. A cut-off value of CER (25 microL/h/mL) for milk spoilage at refrigeration temperatures was identified. The real-time CER method shows promise as a potential alternative to the traditional culture method.

Animals↗
PubMed2006

Microbial Baeyer-Villiger oxidation: stereopreference and substrate acceptance of cyclohexanone monooxygenase mutants prepared by directed evolution.

[reaction: see text] An array of random mutants of cyclohexanone monooxygenase (CHMO) from Acinetobacter sp. NCIMB 9871 was screened against a library of structurally diverse ketones for modifications in the substrate acceptance profile and stereopreference of the enzymatic Baeyer-Villiger biooxidation. While the set of mutant biocatalysts was initially evolved for the enantiocomplementary oxidation of 4-hydroxycyclohexanone, improved and/or divergent stereoselectivities were observed for several substrates. In addition, expanded substrate acceptance to facilitate biotransformation of sterically demanding ketones was found.

Acinetobacter↗
PubMed2003

Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes.

BACKGROUND: Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH), to evaluate and compare the patterns and rates of lateral gene transfer (LGT) in prokaryotes and eukaryotes. RESULTS: We extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists). CONCLUSION: LGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution.

Algal Proteins↗
PubMed2003

Infection control: its evolution to the current standard precautions.

BACKGROUND: The use of appropriate infection control precautions to protect against transmission of bloodborne and other occupational microbial pathogens has become a routine component of health care provision. Evolution and revision of recommendations continues to be based on updated scientific information, as well as documented and inferred clinical applications of new knowledge. In addition, surveillance of occupational risks in medical treatment settings often has served as a basis for subsequent disease prevention recommendations for dental care. TYPES OF STUDIES REVIEWED: Guidelines designed to protect dental professionals and their patients have focused on bloodborne pathogens since the first published American Dental Association recommendations in the 1970s. Subsequent statements developed by the Centers for Disease Control and Prevention, the ADA and other organizations during the past 30 years also have addressed prevention of other infections, transmitted by either direct or indirect contact with a variety of potentially infectious body fluids. RESULTS: Review of the major features of these recommendations provides an appropriate framework to consider current guideline revisions. The success of long-standing universal precautions, or UP, against bloodborne infection has been augmented with the incorporation of body substance isolation, or BSI, practices into the infection control protocol designated "standard precautions." Combination of the major tenets of UP with the BSI systems routinely employed in acute care facilities affords all health care professionals the means of preventing a spectrum of bloodborne, respiratory, contact and other potential exposures during provision of patient care. CLINICAL IMPLICATIONS: As infection control recommendations for dentistry are updated this year, they undoubtedly will include guidelines expanding previous UP to provide expanded protection for dental professionals in the multiple types of nonacute treatment settings in which routine treatment is provided.

American Dental Association↗