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PubMed1986

Enhancement of Streptococcus faecalis infection and complement depletion in yeast-treated mice.

Enhancement of Streptococcus faecalis infection and lowering of the complement level have been demonstrated in mice injected with a heat-treated suspension of baker's yeast (Saccharomyces cerevisiae). The leucocyte response to the infection was not affected. The yeast preparation showed, in vitro, an intense anti-complementary activity on mouse serum and interfered with the microbial killing function of the mouse peritoneal macrophages. No significant stimulation of the growth of S. faecalis in vitro in the presence of the yeast was observed. The enhancement of the infection in mice treated with the yeast seems to be mediated, mainly, by complement depletion.

Animals↗
PubMed2025

Cobamide-based interactions between soil bacteria can be predicted based on monoculture growth.

Interactions between microbes shape the structure and function of microbial communities. While studying interactions is key to understanding microbial communities as a whole, gaining a detailed mechanistic view is challenging due to the scale of co-occurring interactions. The model nutrient approach enables the study of a subset of interactions involving a single nutrient class and can shed light on broader interaction mechanisms involving other nutrients. Here, we focus on cobamides, the cobalamin (vitamin B12) family of enzyme cofactors, to study nutrient competition and nutrient-sharing interactions in co-cultures and tri-cultures. We examined bacteria that were previously isolated from a grassland soil and were characterized as "dependents" (require cobamides but cannot synthesize them) or "producers" (synthesize cobamides). The outcome of competition between a pair of dependents was predictable based on monoculture growth characteristics, with the dominant microbe determined by its adaptation to a specific cobamide concentration range. Moreover, cobamide producers could support the cobamide-dependent growth of dependents in co-culture and influenced the outcome of competition between dependents in tri-culture. We analyzed the metabolic capacity encoded in the genomes of producers and dependents and found that cobamides are likely the main shared nutrient in our co- and tri-cultures. These results highlight the utility of the model nutrient approach to characterize and predict interactions in bacterial consortia of increasing complexity.

Journal Article↗
PubMed2003

The purification, crystallization and preliminary structural characterization of PhzF, a key enzyme in the phenazine-biosynthesis pathway from Pseudomonas fluorescens 2-79.

Phenazines produced by members of several bacterial genera are biologically active metabolites that function in microbial competitiveness, the suppression of soil-borne plant diseases and virulence in infectious disease. Despite recent progress towards understanding the biochemistry of phenazine synthesis, the key reactions leading to the formation of the heterocyclic scaffold common to all phenazine compounds remain obscure. Pseudomonas fluorescens 2-79 contains seven phenazine (phz) genes that encode components of the pathway for biosynthesis of phenazine-1-carboxylic acid. A central step in this pathway involves the condensation of two identical precursor molecules derived from chorismic acid and is catalysed by the product of the phzF gene. In this study, recombinant PhzF was purified and crystallized from PEG 4000/ammonium sulfate/sodium citrate pH 5.6. The crystals belong to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 56.3, c = 156.4 A. They contain one monomer in the asymmetric unit and diffract to better than 1.7 A on synchrotron beamlines. Crystals of seleno-L-methionine-labelled PhzF have been obtained and SAD data are reported.

Crystallization↗
PubMed2006

Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment.

A multilevel sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations approximately 200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. Denaturing gradient gel electrophoresis and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale-sandstone interface. delta-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family (Pelobacter, Desulphuromonas and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S degrees reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)-/S degrees -reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale.

Base Sequence↗
PubMed2006

Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens.

Whole-genome analysis of gene expression in Geobacter sulfurreducens revealed 474 genes with transcript levels that were significantly different during growth with an electrode as the sole electron acceptor versus growth on Fe(III) citrate. The greatest response was a more than 19-fold increase in transcript levels for omcS, which encodes an outer-membrane cytochrome previously shown to be required for Fe(III) oxide reduction. Quantitative reverse transcription polymerase chain reaction and Northern analyses confirmed the higher levels of omcS transcripts, which increased as power production increased. Deletion of omcS inhibited current production that was restored when omcS was expressed in trans. Transcript expression and genetic analysis suggested that OmcE, another outer-membrane cytochrome, is also involved in electron transfer to electrodes. Surprisingly, genes for other proteins known to be important in Fe(III) reduction such as the outer-membrane c-type cytochrome, OmcB, and the electrically conductive pilin "nanowires" did not have higher transcript levels on electrodes, and deletion of the relevant genes did not inhibit power production. Changes in the transcriptome suggested that cells growing on electrodes were subjected to less oxidative stress than cells growing on Fe(III) citrate and that a number of genes annotated as encoding metal efflux proteins or proteins of unknown function may be important for growth on electrodes. These results demonstrate for the first time that it is possible to evaluate gene expression, and hence the metabolic state, of microorganisms growing on electrodes on a genome-wide basis and suggest that OmcS, and to a lesser extent OmcE, are important in electron transfer to electrodes. This has important implications for the design of electrode materials and the genetic engineering of microorganisms to improve the function of microbial fuel cells.

Bacterial Outer Membrane Proteins↗
PubMed1993

Tetanus toxin selectively impairs anti-tumoral but not anti-microbial macrophage-mediated effector functions.

The present study was designed to establish the susceptibility of macrophage-mediated effector functions to tetanus toxin (TT). Using the murine macrophage cell line, GG2EE, generated in vitro by v-raf/v-myc oncogenes, we have previously provided evidence that TT selectively inhibits interferon gamma (IFN-gamma), but not basal, lysozyme activity. Here we show that while neither phagocytic nor candidacidal activities are affected by TT treatment, antitumoral activity is significantly impaired after exposure to TT. This phenomenon, which is dose-dependent, is fully ascribed to the holotoxin, as heat inactivated TT, C or A-B fragments result ineffective. Furthermore, C but not A-B fragment competes with TT in abrogating its inhibitory effects. Overall, these data indicate that TT is not a broad-spectrum, down-regulating signal on macrophage-mediated functions, thus implying that its toxic action is exerted on specific molecular targets.

Animals↗
PubMed2000

Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies.

The aim of this review is to interpret recent studies in which molecular methods were used to identify and characterize prokaryotes in lake sediments and related habitats. In the first part studies based on the phylogenetic diversity of prokaryotes found in lacustrine habitats are summarized. The application of various cultivation-independent methods for the characterization of distinct groups of sediment bacteria is exemplified with morphologically conspicuous, colorless sulfur bacteria in the second part of this review. Finally, traditional and recently developed methods are described which could be used for linking the function of microbial populations with their identification. The potential of these approaches for the study of lake sediments is discussed in order to give a perspective for future studies in this habitat.

Bacteria↗
PubMed1995

Characterization and Ecology of Carboxymethylcellulase-Producing Anaerobic Bacterial Communities Associated with the Intestinal Tract of the Pinfish, Lagodon rhomboides.

Carboxymethylcellulase (CMCase)-producing obligate anaerobes were isolated from the intestinal tract contents but not the feeding habitat of seagrass-consuming pinfish. Taxonomic characterization of these CMCase-producing strains revealed four taxonomic clusters; three were clostridial and one was of unknown taxonomic affinity. Our results demonstrated that the CMCase-producing obligate anaerobe community from pinfish differed from functionally similar microbial communities in terrestrial herbivores.

Journal Article↗
PubMed2001

Resolution of viable and membrane-compromised bacteria in freshwater and marine waters based on analytical flow cytometry and nucleic acid double staining.

The membrane integrity of a cell is a well-accepted criterion for characterizing viable (active or inactive) cells and distinguishing them from damaged and membrane-compromised cells. This information is of major importance in studies of the function of microbial assemblages in natural environments, in order to assign bulk activities measured by various methods to the very active cells that are effectively responsible for the observations. To achieve this task for bacteria in freshwater and marine waters, we propose a nucleic acid double-staining assay based on analytical flow cytometry, which allows us to distinguish viable from damaged and membrane-compromised bacteria and to sort out noise and detritus. This method is derived from the work of S. Barbesti et al. (Cytometry 40:214-218, 2000) which was conducted on cultured bacteria. The principle of this approach is to use simultaneously a permeant (SYBR Green; Molecular Probes) and an impermeant (propidium iodide) probe and to take advantage of the energy transfer which occurs between them when both probes are staining nucleic acids. A full quenching of the permeant probe fluorescence by the impermeant probe will point to cells with a compromised membrane, a partial quenching will indicate cells with a slightly damaged membrane, and a lack of quenching will characterize intact membrane cells identified as viable. In the present study, this approach has been adapted to bacteria in freshwater and marine waters of the Mediterranean region. It is fast and easy to use and shows that a large fraction of bacteria with low DNA content can be composed of viable cells. Admittedly, limitations stem from the unknown behavior of unidentified species present in natural environments which may depart from the established permeability properties with respect to the fluorescing dyes.

Bacteria↗
PubMed2006

Molecular studies reveal frequent misidentification of Aspergillus fumigatus by morphotyping.

Aspergillus fumigatus has been understood to be the most common cause of invasive aspergillosis (IA) in all epidemiological surveys. However, recent studies have uncovered a large degree of genetic heterogeneity between isolates morphologically identified as A. fumigatus, leading to the description of a new species, Aspergillus lentulus. Here, we examined the genetic diversity of clinical isolates identified as A. fumigatus using restriction enzyme polymorphism analysis and sequence-based identification. Analysis of 50 clinical isolates from geographically diverse locations recorded the presence of at least three distinct species: A. lentulus, Aspergillus udagawae, and A. fumigatus. In vitro, A. lentulus isolates demonstrated decreased susceptibility to antifungal drugs currently used for IA, including amphotericin B, voriconazole, and caspofungin; A. udagawae isolates demonstrated decreased in vitro susceptibility to amphotericin B. Results of the present study demonstrate that current phenotypic methods to identify fungi do not differentiate between genetically distinct species in the A. fumigatus group. Differential antifungal susceptibilities of these species may account for some of the reported poor outcomes of therapy in clinical studies.

Aspergillus fumigatus↗
PubMed1992

Consequences of microbial attachment: directing host cell functions with adhesins.

We take the view that adherence is not just a static process of holding hands but rather elicits a response in the targeted cell. From this point of view, adherence is an active process with an outcome. This outcome or fate is predictable only when several parameters of the host cell-adhesin interaction are known: is the adhesin acting alone or in series with other products, is the receptor up- or down-regulated at the time of ligation, which domain of the receptor is bound, and finally, which intracellular response circuits are connected to the receptor in the cell type targeted? Variations in these parameters are the basis for the ability of the adhesins of pathogens to orchestrate outcomes as disparate as simple address recognition versus actin nucleation, cytokine induction, activation of plasmin, derangement of leukocyte migration, or deposition of antibody on host cell membranes. The recognition of the relatedness of some eukaryotic and prokaryotic adhesive domains and the shared use of existing eukaryotic cell-cell interaction systems between host and pathogen suggest that the cellular interactions of interest in eukaryotic cell biology can be revealed by taking clues from the pathogens, which have studied and adapted to them the longest.

Animals↗
PubMedDate not supplied

Effect of different combinations of dietary additives on bacterial translocation and survival in gut-derived sepsis.

BACKGROUND: Dietary arginine, glutamine, and fish oil each have been shown to improve resistance to infection. The purpose of this study was to assess the potential benefit of different combinations and amounts of these components on bacterial translocation and related mortality during gut-derived sepsis. METHODS: Balb/c mice were fed for 10 days with an AIN-76A diet supplemented with different combinations and percentages of arginine, glutamine, glycine, fish oil, and medium-chain triglycerides. Controls were fed a complete AIN-76A diet or chow. After 10 days of feeding, all animals were transfused. On day 15, the animals were gavaged with 10(10) 111In-radiolabeled or unlabeled Escherichia coli and given a 30% burn injury. Animals gavaged with unlabeled bacteria were observed for survival (n = 317). Groups that showed the best survival as well as control groups were gavaged with labeled bacteria and killed 4 hours postburn (n = 60) for harvest of mesenteric lymph nodes, liver and spleen. RESULTS: Mice fed diets enriched with 5% fish oil + 2% arginine, 2% arginine + 2% glutamine, or 5% fish oil + 2% glutamine had higher survival than control groups. The animals fed fish oil+glutamine had significantly reduced translocation to the liver and spleen. Animals fed arginine+glutamine had an enhanced ability to kill translocated organisms in the liver compared with other groups. Fish oil+arginine improved both barrier function and microbial killing. CONCLUSIONS: Feeding with arginine+glutamine, fish oil+arginine, or fish oil+glutamine supplemented diets positively affects the outcome in a gut-derived sepsis model.

Animals↗
PubMed2001

Ontogeny of Toll-like receptors Tlr2 and Tlr4 in mice.

Toll-like receptors (TLR:) have recently been linked to the immunostimulatory function of microbial toxins in human and mice. TLR: signals activation of nuclear factor kappaB that leads to the production of a number of proinflammatory mediators. TLR:4 mediates the endotoxin-induced inflammatory response, whereas TLR:2 may be involved in the response to yeast and Gram-positive bacterial products. To better understand age-related changes in acute inflammatory response, we studied the ontogeny of TLR:2 and TLR:4 mRNA in murine fetal lung, liver, and placenta by quantitative reverse transcriptase-PCR. Different expression patterns were seen between the tissues and between the TLR: This is in accordance with the evidence that there are differences in the receptors for different microbial toxins and that the response is organ specific. We additionally show that the expression of TLR: was dependent on the stage of differentiation. In the liver, the levels of Tlr2 and Tlr4 were high regardless of the age. In the lung, Tlr2 and Tlr4 expression levels were barely detectable in immature fetus (d 14-15). Tlr2 and Tlr4 were increased several-fold during prenatal development and further increased after birth. The present results support the finding of a deficient inflammatory response of the immature lung to microbial toxins.

Animals↗
PubMed1994

The roles of magnesium in biotechnology.

This review highlights the important roles played by magnesium in the growth and metabolic functions of microbial and animal cells, and therefore assigns a key role for magnesium ions in biotechnology. The fundamental biochemical and physiological actions of magnesium as a regulatory cation are outlined. Such actions are deemed to be relevant in an applied sense, because Mg2+ availability in cell culture and fermentation media can dramatically influence growth and metabolism of cells. Manipulation of extracellular and intracellular magnesium ions can thus be envisaged as a relatively simplistic, but nevertheless versatile, means of physiological cell engineering. In addition, biological antagonism between calcium and magnesium at the molecular level may have profound consequences for the optimization of biotechnological processes that exploit cells. In fermentation, for example, it is argued that the efficiency of microbial conversion of substrate to product may be improved by altering Mg:Ca concentration ratios in industrial feedstocks in a way that makes more magnesium available to the cells. With particular respect to yeast-based biotechnologies, magnesium availability is seen as being crucially important in governing central pathways of carbohydrate catabolism, especially ethanolic fermentation. It is proposed that such influences of magnesium ions are expressed at the combined levels of key enzyme activation and cell membrane stabilization. The former ensures optimum flow of substrate to ethanol and the latter acts to protect yeasts from physical and chemical stress.

Animals↗
PubMed2004

Reducing concentrate supplementation in dairy cow diets while maintaining milk production with pea-wheat intercrops.

In the first of 2 experiments, 40 dairy cows were used to evaluate the milk production potential and concentrate-sparing effect of feeding dairy cows a basal diet of pea-wheat intercrop silages instead of perennial rye-grass silage (GS). Dairy cows were offered GS or 2 intercrop silages prepared from wheat and either Magnus peas (MW, a tall-straw variety) or Setchey peas (SW, a short-straw variety) ad libitum. The respective intercrops were supplemented with 4 kg/d of a dairy concentrate (CP = 240 g/kg dry matter; MW4 and SW4), and the GS were supplemented with 4 (GS4) or 8 (GS8) kg/d of the same concentrate. The second experiment measured the forage DM intake, digestibility, rumen function, and microbial protein synthesis from the forages by offering them alone to 3, nonlactating cows (3 x 3 Latin square design with 21-d periods). Forage dry matter intake was greater in cows fed the intercrop silages than those fed GS. Milk production was greater in cows fed SW4 than those fed GS4 or MW4, but similar to cows fed GS8. Dietary treatment did not affect milk fat, protein, or lactose concentrations. The intercrops had greater N retention, and were more digestible than the GS, and these factors probably contributed to the greater forage DM intakes and greater milk production from the intercrop silages compared with the GS. Rumen volatile fatty acid concentrations were similar across forages, but urinary purine derivative excretion was greater in the cows fed the intercrop silages than the GS, suggesting that rumen microbial protein synthesis was enhanced by feeding the intercrops. In conclusion, similar milk yield and milk composition can be obtained by feeding SW and 4 kg of concentrates as that obtained with GS and 8 kg of concentrates. Feeding intercrop silages instead of GS with the same amount of concentrates increased forage intakes, N retention, and microbial protein synthesis.

Animal Feed↗
PubMedDate not supplied

[Microbiological processes of the carbon and sulfur cycle in cold methane seeps in the North Atlantic].

Functioning of microbial communities in surface sediments of the Haakon Mosby underwater mud volcano (lat. 72 degrees N) and in gas seepage fields of the Vestnesa Ridge was investigated using Mir-1 and Mir-2 deep-sea submersibles during the 40th expedition of the research vessel Academician Mstislav Keldysh. Large areas of sedimentary deposits of the Haakon Mosby mud volcano (HMMV) and pockmarks of the Vestnesa Ridge (VR) are covered with bacterial mats 0.1 to 0.5 cm thick. The microbial community making up bacterial mats of the HMMV was predominated by large filamentous bacteria with filaments measuring up to 100 microns in length and 2 to 8 microns in width. The occurrence of rosettes allowed the observed filamentous bacteria to be referred to the morphologically similar genera Leucothrix or Thiothrix. Three morphological types of filamentous bacteria were identified in bacterial mats covering VR pockmarks. Filaments of type one are morphologically similar with representatives of the genera Thioploca or Desmanthos. Type two filaments had numerous inclusions of sulfur and resembled representatives of the genus Thiothrix. The third morphological type was constituted by single filaments made up of tightly connected disk-like cells and can, apparently, be assigned to the genus Beggiatoa. The rates of methane oxidation (up to 1570 microliters C/(dm3 day)) and sulfate reduction (up to 17 mg S/(dm3 day)) measured in surface sediments of HMMV and VR were close to the maximum rates of these processes observed in badly polluted regions of the northwestern shelf of the Black Sea. High rates of microbiological processes correlated with the high number of bacteria. The rate of methane production in sediments studied was notably lower and ranged from 0.1 to 3.5 microliters CH4/(dm3 day). Large areas of the HMMV caldera were populated by pogonophoras, represented by the two species, Sclerolinum sp. and Oligobrachia sp. The mass development of Sclerolinum sp. in the HMMV caldera was by the activity of aerobic methane-oxidizing bacteria localized inside the cells of these animals. Bacterial cells were also found in the trophosome tissue of Oligobrachia sp., but in cells of these bacteria, we did not observe the membrane structures typical of methanotrophs. The localization pattern of pogonophoras on the surface of reduced sediments suggests that the predominant bacteria in Oligobrachia tissues are sulfur-oxidizing endosymbionts.

Bacteria↗
PubMed2001

Testing microbiologic response to antiinfective medications with incomplete data.

Clinical trials of antiinfective medications often require estimates of the proportions of patients, n, who are free of disease-causing pathogens at the end of treatment, as well as the proportions of all pathogens that have been eradicated. Each patient is infected with several species of pathogens, but the response to study medication for some of these pathogens may be unknown because some specimens were lost or because the patient received nonstudy medication that was known to be effective against these species. This paper develops a statistical model that estimates pi for each treatment and that accounts for the unknown pathogen responses as well as overdispersion of the remaining responses due to within-patient effects. The data are modeled with the Poisson distribution for the numbers of pathogen species per patient and the beta-binomial model for pathogen eradication. The Poisson and beta-binomial parameters are estimated through maximum likelihood estimation, and the treatment difference in the pi valves and its standard error are estimated by transforming the underlying parameters. Confidence intervals based on these estimates are constructed to test the hypothesis of noninferiority of the test treatment.

Algorithms↗
PubMedDate not supplied

[Aspects of Vibrio cholerae lipopolysaccharide].

In this review information on the chemical structure, biosynthesis, antigenic and biological properties of V. cholerae lipopolysaccharide (LPS) is presented. The specific structural feature of this LPS is a small size of the polysaccharide chain of O-antigen. In vibrios of serogroup O 139 it is oligosaccharide. The modification of the O-chain (methylation of individual sugars, shortened chain, etc.) plays an essential role in the antigenic specificity of V. cholerae LPS. All these factors affect of endotoxin function, the microbial resistance to external influences. V. cholerae LPS takes part in the formation of microcapsules and biofilms. The evolutional development of V. cholerae in this direction determines, to some extent, their increased resistance in the environment. In human body the heterogeneity of the LPS composition permits the preservation of vibrios and ensures, together with cholerogen, their pathogenetic action.

Animals↗