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PubMed2003

Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes.

Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.

Bacterial Proteins↗
PubMed1994

Effects of sieving, storage, and incubation temperature on the phospholipid Fatty Acid profile of a soil microbial community.

Disturbances typically associated with the study of soil microbial communities, i.e., sieving, storage, and subsequent incubation at elevated temperatures, were investigated with phospholipid fatty acid (PLFA) analyses. Treatment effects were quantified by statistical analyses of the mole percentage distribution of the individual fatty acids. Changes in the concentrations of individual fatty acids over a 7-week storage period at 4.5 degrees C were generally not statistically significant. Sieving effects (mesh size, 4 or 2 mm) on CO(2) evolution and the PLFA profile were monitored over 3 weeks; the physical disturbance had only minor effects, although some damage to fungal hyphae by the first sieving (<4 mm) was suggested by a decrease in the signature fatty acid 18:2 omega6c. Temperature effects were investigated by incubating soil for up to 3 weeks at 4.5, 10, or 25 degrees C. Principal component analyses demonstrated a significant shift in the PLFA composition at 25 degrees C over the first 2 weeks, while changes at the other two temperatures were minor. Several of the changes observed at 25 degrees C could be explained with reference to mechanisms of temperature adaptation or as a response to conditions of stress, including a decrease in the degree of unsaturation, an increased production of cyclopropyl fatty acids, and increased ratios of the branched-chain fatty acids iso-15:0 and iso-17:0 over anteiso-15:0 and anteiso-17:0, respectively. A decrease in the total amount of PLFA was also indicated.

Journal Article↗
PubMed2004

Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?

The gut contains our largest collection of resident microorganisms. One obvious question is how microbial communities establish and maintain themselves within a perfused intestine. The answers, which may come in part from observations made by environmental engineers and glycobiologists, have important implications for immunologists who wish to understand how indigenous microbial communities are accommodated. Here we propose that the mucus gel layer overlying the intestinal epithelium is a key contributor to the structural and functional stability of this microbiota and its tolerance by the host.

Animals↗
PubMed1998

The epidemiology of Salmonella typhimurium in cattle: plasmid profile analysis of definitive phage type (DT) 204c.

During the period 1979-1991, Salmonella Typhimurium DT 204c was the cause of a major epidemic of salmonellosis in calves in the UK. Plasmid profile analysis of DT 204c isolates from England and Wales commenced in 1986 and isolates from all subsequent incidents were examined by this technique. Forty-three different plasmid profile types (PPTs) were detected, of which the commonest, designated type E, constituted 44.6-80.2% of the annual incidents during the study period. Some PPTs, e.g., F and P, were detected throughout most years of the study, whereas PPTs O and 6 persisted for short periods. Until 1984, most isolates were resistant to neomycin, but the subsequent predominant PP type E was sensitive to this antibacterial agent. It was concluded that during the epidemic there was an evolution of new genotypes, of which only some persisted; again, antibacterial resistance genes may be acquired or lost. The study demonstrated the value of PP typing for epidemiological studies.

Animals↗
PubMed1999

Nonribosomal peptide synthesis and toxigenicity of cyanobacteria.

Nonribosomal peptide synthesis is achieved in prokaryotes and lower eukaryotes by the thiotemplate function of large, modular enzyme complexes known collectively as peptide synthetases. These and other multifunctional enzyme complexes, such as polyketide synthases, are of interest due to their use in unnatural-product or combinatorial biosynthesis (R. McDaniel, S. Ebert-Khosla, D. A. Hopwood, and C. Khosla, Science 262:1546-1557, 1993; T. Stachelhaus, A. Schneider, and M. A. Marahiel, Science 269:69-72, 1995). Most nonribosomal peptides from microorganisms are classified as secondary metabolites; that is, they rarely have a role in primary metabolism, growth, or reproduction but have evolved to somehow benefit the producing organisms. Cyanobacteria produce a myriad array of secondary metabolites, including alkaloids, polyketides, and nonribosomal peptides, some of which are potent toxins. This paper addresses the molecular genetic basis of nonribosomal peptide synthesis in diverse species of cyanobacteria. Amplification of peptide synthetase genes was achieved by use of degenerate primers directed to conserved functional motifs of these modular enzyme complexes. Specific detection of the gene cluster encoding the biosynthetic pathway of the cyanobacterial toxin microcystin was shown for both cultured and uncultured samples. Blot hybridizations, DNA amplifications, sequencing, and evolutionary analysis revealed a broad distribution of peptide synthetase gene orthologues in cyanobacteria. The results demonstrate a molecular approach to assessing preexpression microbial functional diversity in uncultured cyanobacteria. The nonribosomal peptide biosynthetic pathways detected may lead to the discovery and engineering of novel antibiotics, immunosuppressants, or antiviral agents.

Bacterial Toxins↗
PubMed2001

Effect of sediment toxicity on anaerobic microbial metabolism.

Mineralization of a readily biodegradable aromatic compound (benzoate) by intrinsic microorganisms in the anoxic sediment was used to quantify the inhibitory effect of heavily contaminated sediment from the Arthur Kill estuary (NY/NJ Harbor system, USA) on the anaerobic metabolism by naturally present bacterial populations. In anoxic microcosms, the effect of varying ratios of contaminated sediment:site water and contaminated sediment:noncontaminated sediment (Flax Pond, Stony Brook, NY, USA) were investigated. In all cases, increasing the ratio of Arthur Kill sediment in the microcosms showed an inhibitory effect on the rate of 14C-benzoate mineralization as measured by the evolution of 14CO2. This inhibitory effect could be alleviated through dilution of the sediment with noncontaminated sediment, resulting in some cases in mineralization rates that were greater by an order of magnitude. The toxicity of the sediment was confirmed by whole-sediment Microtox bioassay. Analysis of the sediment revealed high (>200 mg/kg) levels of Pb, Cu, Zn, and Cr, suggesting that heavy metals may contribute to overall sediment toxicity.

Bacteria, Anaerobic↗
PubMed2001

Roots: evolutionary origins and biogeochemical significance.

Roots, as organs distinguishable developmentally and anatomically from shoots (other than by occurrence of stomata and sporangia on above-ground organs), evolved in the sporophytes of at least two distinct lineages of early vascular plants during their initial major radiation on land in Early Devonian times (c. 410-395 million years ago). This was some 15 million years after the appearance of tracheophytes and c. 50 million years after the earliest embryophytes of presumed bryophyte affinity. Both groups are known initially only from spores, but from comparative anatomy of extant bryophytes and later Lower Devonian fossils it is assumed that, during these times, below-ground structures (if any) other than true roots fulfilled the functions of anchorage and of water and nutrient acquisition, despite lacking an endodermis (as do the roots of extant Lycopodium spp.). By 375 million years ago root-like structures penetrated almost a metre into the substratum, greatly increasing the volume of mineral matter subject to weathering by the higher than atmospheric CO(2) levels generated by plant and microbial respiration in material with restricted diffusive contact with the atmosphere. Chemical weathering consumes CO(2) in converting silicates into bicarbonate and Si(OH)(4). The CO(2) consumed in weathering ultimately came from atmospheric CO(2) via photosynthesis and respiration; this use of CO(2) probably accounts for most of the postulated 10-fold decrease in atmospheric CO(2) from 400-350 million years ago, with significant effects on shoot evolution. Subsequent evolution of roots has yielded much-branched axes down to 40 microm diameter, a lower limit set by long-distance transport constraints. Finer structures involved in the uptake of nutrients of low diffusivity in soil evolved at least 400 million years ago as arbuscular mycorrhizas or as evaginations of "roots" ("root hairs").

Biological Evolution↗
PubMed2005

Critical pathways in microbial virulence.

The virulence of a microbe represents a combination of complex factors including the agent's transmissibility and the severity of the disease associated with infection and is also significantly influenced by the susceptibility of the colonized host. Virulence factors may be defined as those products of the organism which are required to complete the various stages of the life cycle leading to pathology in the host. In this review, we examine some of the approaches which have been adopted in other fields of infectious disease in order to categorically identify virulence factors using a classical genetics approach with relevant models or human subjects. The absence of an accurate experimental model for periodontal disease means that our understanding of the microbial virulence determinants and pathways in this disease remains hypothetical and based largely on observations in vitro. However, factors which enable the organism to persist in spite of the elevated immune and inflammatory pressure at sites of disease are liable to be critical. Periodontal bacterial genomics is liable to make a significant impact on the field through an increased appreciation of the role of gene acquisition and gene loss in the evolution of periodontal bacteria and of the consequences of strain variation in gene content on virulence potential.

Animals↗
PubMed1994

Mosquito control then, now, and in the future.

This is a memorial lecture honoring the late Professor Stanley B. Freeborn of the University of California. In the spirit of his life-long academic and research interests in mosquitoes and mosquito-borne diseases, I am presenting here the evolution of vector control technology, especially that pertaining to mosquitoes and mosquito-borne diseases during the 20th century. Vector control technology in the first half of this century was relatively simple, utilizing source reduction, larvivorous fish, petroleum hydrocarbon oils, and some simple synthetic and botanical materials. During the 2nd half of this century, however, various classes of synthetic organic chemicals, improved petroleum oil formulations, insect growth regulators, synthetic pyrethroids, and microbial control agents were developed and employed in mosquito control and control of other disease-vectoring insects. Among these groups of control agents, petroleum oil formulations have endured to be used through the whole century. It is likely that petroleum oil formulations, insect growth regulators, and microbial control agents will provide the main thrust against vectors at least during the first quarter of the 21st century. It is also possible that effective tools through the development of vaccines and molecular entomology techniques might become available for the control of vectors and vector-borne diseases during this period of the 21st century.

Animals↗
PubMed2016

The impact of metagenomic interplay on the mosquito redox homeostasis.

Mosquitoes are exposed to oxidative challenges throughout their life cycle. The primary challenge comes from a blood meal. The blood digestion turns the midgut into an oxidative environment, which imposes pressure not only on mosquito fecundity and other physiological traits but also on the microbiota in the midgut. During evolution, mosquitoes have developed numerous oxidative defense mechanisms to maintain redox homeostasis in the midgut. In addition to antioxidants, SOD, catalase, and glutathione system, sufficient supply of the reducing agent, NADPH, is vital for a successful defense against oxidative stress. Increasing evidence indicates that in response to oxidative stress, cells reconfigure metabolic pathways to increase the generation of NADPH through NADP-reducing networks including the pentose phosphate pathway and others. The microbial homeostasis is critical for the functional contributions to various host phenotypes. The symbiotic microbiota is regulated largely by the Duox-ROS pathway in Drosophila. In mosquitoes, Duox-ROS pathway, heme-mediated signaling, antimicrobial peptide production and C-type lectins work in concert to maintain the dynamic microbial community in the midgut. Microbial mechanisms against oxidative stress in this context are not well understood. Emerging evidence that microbial metabolites trigger host oxidative response warrants further study on the metagenomic interplay in an oxidative environment like mosquito gut ecosystem. Besides the classical Drosophila model, hematophagous insects like mosquitoes provide an alternative model system to study redox homeostasis in a symbiotic metagenomic context.

Animals↗
PubMed2004

IFN-inducible GTPases and immunity to intracellular pathogens.

By eliciting host antimicrobial programs in nearly all nucleated cells interferons (IFNs) help orchestrate the innate immune response of mammals to a diverse array of microbial pathogens. Recent work has highlighted the complexity of this transcriptional repertoire and the emergence of several families of IFN-inducible guanosine 5' triphosphatases (GTPases)--p47, guanylate-binding protein (GBP), Mx and very large inducible GTPases (VLIG)--that subsume pathogen-specific roles. Such specificity arises from a combination of both the type and timing of inductive stimuli, target-cell population, subcellular binding partners and the infectious agent encountered. Evolution of different GTPase families to combat compartmentalized versus cytosolic pathogens reveals a hitherto unexpected level of intracellular discrimination during vertebrate host defense.

Animals↗
PubMed1998

Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates.

Microbial dehalogenases are involved in the biodegradation of many important chlorinated pollutants. Some recent studies of haloalkane dehalogenase, dichloromethane dehalogenase, tetrachlorohydroquinone dehalogenase and perchloroethylene and trichloroethylene reductive dehalogenases have addressed the issue of recruitment and adaptation of proteins to dehalogenate novel substrates.

Biodegradation, Environmental↗
PubMed2000

Teicoplanin Chemistry and Microbiology.

The chemistry, microbiology and mode of action of teicoplanin, as well as the mechanism, control and epidemiology of glycopeptide resistance, are discussed in detail. The antibacterial activity of teicoplanin against Gram-positive bacteria, including those expressing resistance to unrelated compounds, is similar to that of vancomycin but with increased potency, particularly against Streptococcus spp and Enterococcus spp. Some strains of coagulase-negative Staphylococcus spp, particularly S. haemolytieus, are less susceptible to teicoplanin than to vancomycin. Teicoplanin is active against vancomycin resistance caused by VanB and VanC, but is not active against VanA resistant strains. The epidemiology of GISA and VISA strains of S. aureus is, as yet, poorly understood with more work necessary to elucidate the sequence of events leading to their evolution. Despite the increasing importance of glycopeptide resistance, teicoplanin has proved its clinical worth and continues to have important potential in the treatment of life-threatening Gram-positive sepsis.

Anti-Bacterial Agents↗
PubMed2006

Mutations conferring aminoglycoside and spectinomycin resistance in Borrelia burgdorferi.

We have isolated and characterized in vitro mutants of the Lyme disease agent Borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16S rRNA mutations A1185G and C1186U, homologous to Escherichia coli nucleotides A1191 and C1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. A 16S rRNA A1402G mutation, homologous to E. coli A1408, conferred >90-fold resistance to kanamycin and >240-fold resistance to gentamicin. Two mutations were identified in the gene for ribosomal protein S12, at a site homologous to E. coli residue Lys-87, in mutants selected in streptomycin. Substitutions at codon 88, K88R and K88E, conferred 7-fold resistance and 10-fold resistance, respectively, to streptomycin on B. burgdorferi. The 16S rRNA A1185G and C1186U mutations, associated with spectinomycin resistance, appeared in a population of B. burgdorferi parental strain B31 at a high frequency of 6 x 10(-6). These spectinomycin-resistant mutants successfully competed with the wild-type strain during 100 generations of coculture in vitro. The aminoglycoside-resistant mutants appeared at a frequency of 3 x 10(-9) to 1 x10(-7) in a population and were unable to compete with wild-type strain B31 after 100 generations. This is the first description of mutations in the B. burgdorferi ribosome that confer resistance to antibiotics. These results have implications for the evolution of antibiotic resistance, because the 16S rRNA mutations conferring spectinomycin resistance have no significant fitness cost in vitro, and for the development of new selectable markers.

Aminoglycosides↗
PubMedDate not supplied

[Strains of ganciclovir-resistant cytomegalovirus].

BACKGROUND: In countries where the resistance of cytomegalovirus to ganciclovir has been studied, strains resistant to therapeutic doses of this drug have been isolated. When a change in treatment has been impossible the patient has shown bad clinical evolution. The aim of this study was to investigate the presence of these strains in our medium, observe whether the resistances appear in patients previously treated with ganciclovir and determine its implication in the evolution of cytomegalovirus infection. PATIENTS AND METHODS: One hundred twenty-three stains of cytomegalovirus, isolated during the period 1990-1998, corresponding to the following 94 patients were studied: 17 breast feeding children of healthy parents who were negative controls (sensitive strains), 43 organ transplant recipients, 29 AIDS patients, 2 with other immunodeficiencies and 3 children with intrauterine infection. Seventeen patients were studied due to the insidious course of the infection despite treatment. The remaining were random. The technique used was that of growth inhibition of the strains seeded on different gradients of ganciclovir: 0, 1, 5, 10 and 20 microM. The inoculate consisted in a cellular suspension evaluated according to the degree of viral growth. The strains presenting an inhibitory doses 50% (ID 50%) greater than 10 microM were considered as resistant. RESULTS: Eighty-two strains presented an ID 50% lower than 5 microM, 24 from 5 to 10 microM and in the 17 remaining strains, corresponding to 12 patients, the ID 50% was greater than 10 microM. The evolution of these latter 12 patients with strains considered to be resistant to ganciclovir was of death in 8. All were immunodepressed and with a history of having previously received ganciclovir. Another currently has a chronic evolution and the three remaining patients, who presented better immunity, became cured. All patients has a chronic evolution and the three remaining patients, who presented better immunity, became cured. All patients had undergone previous treatment with ganciclovir except two: one patient with Wegener disease treated with acyclovir 15 days before, and the other was an infant of an HIV positive mother who had received the drug. CONCLUSIONS: The presence of cytomegalovirus strains resistant to ganciclovir was confirmed in our patients. The previous use of ganciclovir and, in one case of acyclovir, appears to be implicated in the appearance of resistance. The evolution of the immunodepressed patients with infection by resistant strains was mortal except when their immunity was improved.

AIDS-Related Opportunistic Infections↗
PubMed2005

Reactive oxygen species and development in microbial eukaryotes.

Reactive oxygen species (ROS) have been regarded as inevitable harmful by-products of aerobic metabolism. Growing evidence, however, suggests that ROS play important physiological roles. This raises questions about the pathways that different groups of organisms use to produce and sense ROS. In microbial eukaryotes, recent data show (i) increased ROS levels during cell differentiation, (ii) the existence of ROS-producing enzymes, such as NADPH oxidases (NOX), (iii) the involvement of NOX in developmental processes, and (iv) a conservation in the signal-transduction mechanisms used to detect ROS. This shows that manipulation of reactive species, as strategy to regulate cell differentiation, is ubiquitous in eukaryotes and suggests that such strategy was selected early in evolution.

Antioxidants↗
PubMed2006

Antibiotic resistance in Escherichia coli outpatient urinary isolates: final results from the North American Urinary Tract Infection Collaborative Alliance (NAUTICA).

The North American Urinary Tract Infection Collaborative Alliance (NAUTICA) study determined the antibiotic susceptibility to commonly used agents for urinary tract infections of outpatient Escherichia coli urinary isolates obtained from various geographic regions in the USA and Canada. NAUTICA involved 40 medical centres (30 from the USA and 10 from Canada). From April 2003 to June 2004 inclusive, each centre submitted up to 50 consecutive outpatient midstream urine isolates. All isolates were identified to species level by each laboratory's existing protocol. Susceptibility testing was determined using the Clinical and Laboratory Standards Institute (CLSI) microdilution method. Ampicillin (resistant>or=32 microg/mL), sulphamethoxazole/trimethoprim (SMX/TMP) (resistant>or=4 microg/mL), nitrofurantoin (resistant>or=128 microg/mL), ciprofloxacin (resistant>or=4 microg/mL) and levofloxacin (resistant>or=8 microg/mL) resistance breakpoints used were those published by the CLSI. Of the 1142 E. coli collected, 75.5% (862) were collected from the USA and 280 (24.5%) were from Canada. Patient demographics revealed a mean age of 48.1 years (range, 2 months to 99 years), with female patients representing 79.4% of patients and males representing 20.6%. Overall, resistance to ampicillin was 37.7%, followed by SMX/TMP (21.3%), nitrofurantoin (1.1%), ciprofloxacin (5.5%) and levofloxacin (5.1%). Resistance rates for all antimicrobials were higher in US medical centres compared with Canadian centres (P<0.05). Fluoroquinolone resistance was highest in patients>or=65 years of age (P<0.05). Resistance rates demonstrated considerable geographic variability both in the USA and Canada. This study reports higher rates of antibiotic resistance in US versus Canadian outpatient urinary isolates of E. coli and demonstrates the continuing evolution of resistance to antimicrobial agents.

Adolescent↗
PubMed2002

Evolution of size distribution and transfer of mineral particles between flocs in activated sludges: an insight into floc exchange dynamics.

The aggregation behavior of activated sludge flocs was investigated by monitoring the size distribution of flocs and transfer of mineral particles between flocs, under various conditions of agitation and dilution. The results showed that (i) the shape of the floc size distribution can be fitted with a gamma function, (ii) a steady-state mean floc size is reached for a given stirring rate, (iii) this stable floc size is shifted towards floc growth as sludge concentration is increased, (iv) under cycled-shear conditions, microbial aggregates break up and re-form in an almost reversible manner, (v) blending of raw sludge and sludge spiked with Aquatal mineral particles results in particle exchange between flocs and (vi) the detailed study of exchange kinetics indicates that some flocs do not participate to the aggregation dynamics. These experimental results suggest that the activated sludge floc size is governed by a flocculation/deflocculation balance, implying an exchange of floc constituents between microbial aggregates.

Biofilms↗