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PubMed2005

Ligand specificity of human surfactant protein D: expression of a mutant trimeric collectin that shows enhanced interactions with influenza A virus.

Surfactant protein D is a pattern recognition molecule that plays diverse roles in immune regulation and anti-microbial host defense. Its interactions with known ligands are calcium-dependent and involve binding to the trimeric, C-type carbohydrate recognition domain. Surfactant protein D preferentially binds to glucose and related sugars. However, CL-43, a bovine serum lectin, which evolved through duplication of the surfactant protein D gene in ruminants, prefers mannose and mannose-rich polysaccharides. Surfactant protein D is characterized by two relatively conserved motifs at the binding face, along the edges of the shallow carbohydrate-binding groove. For CL-43, sequence alignments demonstrate a basic insertion, Arg-Ala-Lys (RAK), immediately N-terminal to the first motif. We hypothesized that this insertion contributes to the differences in saccharide selectivity and host defense function and compared the activities of recombinant trimeric neck + carbohydrate recognition domains of human surfactant protein D (NCRD) with CL-43 (RCL-43-NCRD) and selected NCRD mutants. Insertion of the CL-43 RAK sequence or a control Ala-Ala-Ala sequence (AAA) into the corresponding position in NCRD increased the efficiency of binding to mannan and changed the inhibitory potencies of competing saccharides to more closely resemble those of CL-43. In addition, RAK resembled CL-43 in its greater capacity to inhibit the infectivity of influenza A virus and to increase uptake of influenza by neutrophils.

Amino Acid Sequence↗

PubMed2000

Intravascular catheter-related infections: a preventable challenge in the critically ill.

In modem medicine, central venous catheters (CVCs) have a pivotal role in the management of critically ill patients. The most serious complication of effective CVC placement is catheter-related bloodstream infection (CRBSI). Microbial colonization and CRBSI are the byproducts of the interaction of 4 factors: (1) microbial factors (hydrophobicity and exopolysaccharide production), (2) host factors (such protein adhesins as fibrin and fibronectin that attach to the catheter surface), (3) catheter material (hydrophobicity, surface charges, thrombogenicity), and (4) iatrogenic factors (total parenteral nutrition, interleukin-2). The organisms most frequently associated with CRBSI are Staphylococcus epidermidis, Staphylococcus aureus, and Candida spp. CRBSIs were traditionally diagnosed through semiquantitative or quantitative cultures of the catheter tip. However, the diagnosis can be achieved without catheter removal through cultures of blood specimens collected simultaneously though the CVC and a peripheral vein. Currently, the most effective method of preventing a CRBSI is the use of a CVC coated with antimicrobial agents. Intravenous administration of vancomycin for 7 days is adequate for an uncomplicated CRBSI caused by coagulase-negative staphylococci, and at least 10 days of therapy with beta-lactams is required for an uncomplicated infection caused by methicillin-sensitive S. aureus. CRBSI caused by Candida albicans or Candida parapsilosis can be treated with at least 14 days of therapy with fluconazole or amphotericin B. In the case of Candida krusei, only amphotericin B is effective.

Bacteremia↗

PubMed2026

Complete genomes from a xenic Dolichospermum flosaquae FBCC-A233 culture reveal genome-inferred metabolic asymmetry with associated bacteria.

Cyanobacteria form phycosphere communities with associated bacteria, but genome-resolved resources are needed to formulate testable hypotheses about their metabolic interactions. Here, we reconstructed three complete circular genomes from a unialgal xenic culture, including Dolichospermum flosaquae FBCC-A233 and two associated alphaproteobacterial genomes assigned to Sphingorhabdus sp. and Brevundimonas sp. Genome-wide read mapping and genome-quality assessment supported the three recovered genomes as high-quality circular reconstructions. Comparative genome analysis placed the cyanobacterial genome within the Dolichospermum flosaquae species cluster under the GTDB framework, while the associated bacterial genomes represented Sphingorhabdus sp. and a putative undescribed Brevundimonas species-level lineage. Genome architecture analysis indicated reduced genome size and gene content in Brevundimonas relative to genus-level references although additional metrics did not support a strong conclusion of classical genome streamlining. Selected KEGG module and KO-level reconstructions indicated genome-inferred metabolic asymmetries across the consortium. FBCC-A233 encoded photosynthesis- and nitrogen-related modules and a BioU-mediated de novo biotin biosynthesis route, whereas the associated bacteria lacked complete de novo biotin biosynthesis but retained biotin-dependent carboxylase genes. FBCC-A233 also encoded extensive anaerobic corrinoid biosynthesis potential; however, canonical DMB-containing cobalamin completion, cobamide identity, and complete transporter systems were not resolved. Together, these complete genomes provide a genome-resolved resource for investigating genome-inferred metabolic differentiation and ecological interactions in cyanobacteria-associated bacterial consortia.IMPORTANCEPhycosphere interactions between cyanobacteria and associated bacteria can shape aquatic microbial communities, but many proposed interactions remain difficult to evaluate without genome-resolved resources. This study provides three complete circular genomes from a unialgal xenic Dolichospermum flosaquae culture, capturing the cyanobacterium and two co-maintained bacterial associates. Our analysis identifies genome-inferred metabolic asymmetries, particularly in biotin- and cobamide-related pathways. D. flosaquae FBCC-A233 encoded candidate de novo biotin and corrinoid biosynthesis capacity, whereas the associated bacteria lacked complete de novo pathways but retained cofactor-dependent enzymes. These findings nominate cofactor-related dependencies as experimentally testable hypotheses while emphasizing unresolved uptake, export, cobamide identity, and growth-dependence mechanisms. The complete genomes and KO-level reconstructions generated here provide a resource for future studies of cyanobacteria-associated consortia.

Genome, Bacterial↗

PubMed2004

GenomeViz: visualizing microbial genomes.

BACKGROUND: An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on a finer scale. We have developed GenomeViz to enable rapid visualization and subsequent comparisons of several microbial genomes in an interactive environment. RESULTS: Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created. CONCLUSIONS: GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously.

Bacterial Proteins↗

PubMed2005

Microbial responses to zinc in soil microcosms with and without a natural assemblage of enchytraeids.

The presence of higher trophic levels in studies on the toxicity on soil contaminants to microbial processes increases ecological realism. This study assessed the toxicity of zinc to soil microbial processes in the presence and absence of enchytraeids (Oligochaeta, Annelida). We incubated microcosms under standard conditions without or inoculated with a natural assemblage of enchytraeid species. Total zinc concentrations of 365 to 1,360 mg/kg caused no mortality of enchytraeids during six weeks' incubation. Soil nitrate concentrations showed a negative trend under zinc addition and soil ammonium concentrations were the highest at zinc concentrations of 1,360 mg/kg, indicating impairment of ammonium oxidation. Zinc decreased bacterial carbon biomass and caused a dose-response decrease of the respiration, but this was not observed in the presence of enchytraeids. Respiration, ammonium concentrations, and soil moisture contents were increased by enchytraeids. We observed no interaction between the addition of zinc and the presence of enchytraeids. The effect of enchytraeids on soil-moisture contents and microbial processes, and the importance of enchytraeid-microbial interactions are discussed.

Animals↗

PubMed1981

Fermentation in the rumen and human large intestine.

Fermentation of food by the microbial community of the rumen is essential for the maintenance and growth of ruminants. The microbial ecosystem and its interaction with the host are described, along with recent attempts to manipulate the composition and activity of the microbial community by adding antibiotics and other chemicals to ruminant diets. A similar microbial community and fermentation occur in the large intestine or cecum of most nonruminant animals including the large intestine of humans. The microbial ecosystems of the rumen and human large intestine are compared.

Animals↗

PubMed1996

Influence of temperature on the co-adhesion of oral microbial pairs in saliva.

Coaggregation (interactions between two planktonic microorganisms) and co-adhesion (interactions between sessile and planktonic microorganisms) are believed to be important factors in the formation of dental plaque by many investigators, although others doubt whether coaggregation and co-adhesion occur in vivo. It is known that coaggregation and co-adhesion generally occur equally well in buffer as in saliva, but the influence of temperature on the co-adhesion of coaggregating oral microbial pairs in saliva is unknown. Therefore, co-adhesion of streptococci suspended in saliva to glass with adhering actinomyces present (1.0 x 10(6) cells cm-2) was studied in a parallel plate flow chamber in the temperature range from 22 degrees C to 40 degrees C. In the range from 22 degrees C up to 35 degrees C both pairs studied, Streptococcus oralis 34 with Actinomyces naeslundii 5951 and Streptococcus oralis J22 with A. naeslundii 5951, displayed similar co-adhesion kinetics and co-adhesion in a stationary end-point, but around and above 37 degrees C co-adhesion almost disappeared. Hence, we conclude that co-adhesion of coaggregating oral microbial pairs in saliva may be critically influenced by temperature, especially around the temperatures prevailing in the oral cavity.

Actinomyces↗

PubMed2005

Microbial community and biochemistry process in autosulfurotrophic denitrifying biofilm.

The 16S rDNA-based molecular technique was applied to analyze the microbial community of autotrophic denitrification bacteria in a biofilm developed on the surface of sulfur particles and then the biochemistry process involved in this biofilm was discussed based on the microbial community analysis. Six key operational taxonomy units were identified, which were all unknown species belonging to a wide range of bacteria from four major subdivisions (alpha, beta, gamma and delta) of the kingdom Proteobacteria and from the kingdom Chlorobia (green sulfur bacteria). One species was chemoautotrophic and related to Thiobacillus denitrificans, two species were photoautotrophic, and three were chemoheterotrophic. Contrary to expectation, T. denitrificans-like bacteria constituted only 32% of the microbial community. As a result of the study, the entire microbiology of the autosulfurotrophic denitrification process as well as the interactions between the different microbial groups in the biofilm may need to be reconsidered.

Biofilms↗

PubMed1995

[Current problems of microbial safety of the interior environment of orbital stations after extended period of operation].

The authors give considerations to one of the core hygienic problems arising in the process of long-term operation of orbital stations, i.e. ensuring microbial health of the milieu interior. Data pertaining the origin, interactions, and transformation of the microbial risk factors are analyzed as applied to this class of spacecraft. A concept of microbial health of the milieu interior including both medical and technological aspects relating to the reliability of space hardware is proposed. Based on the result of investigations in space flight, the developed criteria and indices of microbial health can be turned to practical use. The currently central tasks to be solved within the context of the problem and in view of the construction of international space station ALPHA are listed.

Aerospace Medicine↗

PubMed2003

Microbially influenced corrosion as a model system for the study of metal microbe interactions: a unifying electron transfer hypothesis.

The general term biomineralisation refers to biologically induced mineralisation in which an organism modifies its local microenvironment creating conditions such that there is chemical precipitation of mineral phases extracellularly. Most usually this results from an oxidation or reduction carried out by some microbial species, with the formation of a recognised biomineralised product. These reactions play a major role in microbial physiology and ecology, and are of central importance to such engineering consequences as microbial mining and microbially influenced corrosion. This paper will examine metal microbe interactions, both in naturally occurring microbial ecosystems and in two particular cases of biocorrosion, with the objective of putting forward a unifying hypothesis relevant to the understanding of each of these apparently disparate processes.

Anaerobiosis↗

PubMed1991

Substrate interactions of benzene, toluene, and para-xylene during microbial degradation by pure cultures and mixed culture aquifer slurries.

Benzene, toluene, and p-xylene (BTX) were degraded by indigenous mixed cultures in sandy aquifer material and by two pure cultures isolated from the same site. Although BTX compounds have a similar chemical structure, the fate of individual BTX compounds differed when the compounds were fed to each pure culture and mixed culture aquifer slurries. The identification of substrate interactions aided the understanding of this behavior. Beneficial substrate interactions included enhanced degradation of benzene and p-xylene by the presence of toluene in Pseudomonas sp. strain CFS-215 incubations, as well as benzene-dependent degradation of toluene and p-xylene by Arthrobacter sp. strain HCB. Detrimental substrate interactions included retardation in benzene and toluene degradation by the presence of p-xylene in both aquifer slurries and Pseudomonas incubations. The catabolic diversity of microbes in the environment precludes generalizations about the capacity of individual BTX compounds to enhance or inhibit the degradation of other BTX compounds.

Arthrobacter↗

PubMed2002

Neutrophil-mediated host response to Porphyromonas gingivalis.

Periodontal diseases are infections initiated by specific species of microorganisms and are among the most common human infections. The pathogenesis of periodontitis is mediated by interactions between host and microbial factors, complicated by genetic and environmental risk factors. Periodontal disease also represents a unique model in which to study the roles of bacterial and host-related factors, a model in which patients do not suffer from life-threatening disease. The aim of this paper is to focus on recent findings relating to neutrophil-mediated host response mechanisms in Porphyromonas gingivalis-induced periodontal disease. Virulence factors of Porphyromonas gingivalis such as the gingipains, fimbrillin peptides, capsule polysaccharides, lipopolysaccharides, haemagglutinating and haemolysing activities, toxic products of metabolism, outer membrane vesicles, and other enzymes have important roles in eliciting host responses in various ways. These factors significantly affect epithelial/endothelial cells, but their major effect is observed on the modulation of neutrophil response. Periodontitis represents an important model for neutrophil-mediated host tissue injury. In this model, neutrophils, primed or stimulated by the presence or persistence of infection, express an elevated and excessive response. This, in turn, leads to tissue destruction mediated by neutrophil activity. It is essential to understand the mechanisms underlying the interactions between the neutrophils and the microbial virulence factors to be able to develop rational, novel treatment strategies.

Adhesins, Bacterial↗

PubMed2001

Interactions of quinupristin-dalfopristin with eight other antibiotics as measured by time-kill studies with 10 strains of Staphylococcus aureus for which quinupristin-dalfopristin alone was not bactericidal.

Quinupristin-dalfopristin (Q-D) and eight other antimicrobial agents were tested alone and in combination with Q-D in time-kill studies against 10 strains of macrolide-lincosamide-streptogramin B-resistant Staphylococcus aureus. Although Q-D is normally a bactericidal drug, it was only bacteriostatic for these isolates. Gentamicin alone was bactericidal against 7 of the 10 strains, and Q-D did not alter that killing effect. However, when vancomycin, cefepime, ceftazidime, imipenem, piperacillin-tazobactam, and ciprofloxacin were bactericidal when tested alone, the killing rates were reduced when combined with Q-D. The clinical significance of this in vitro antagonism is unknown at this time, and more studies are needed.

Anti-Bacterial Agents↗

PubMedDate not supplied

Receptins: a novel term for an expanding spectrum of natural and engineered microbial proteins with binding properties for mammalian proteins.

A new term 'receptin', derived from recipere (lat.), is proposed to denote microbial binding proteins that interact with mammalian target proteins. An example of such a 'receptin' is staphyloccocal protein A which binds to the Fc part of many mammalian immunoglobulins. Several other types of 'receptins' are listed. This term may easily be distinguished from the similar term 'receptor', describing a binding site on a cell surface, mostly eukaryotic, where a secondary effect is induced inside the cell upon binding to a ligand. A receptin, however, does not necessarily have to induce a secondary event. Receptins include so called MSCRAMMs, adhesins, and also engineered receptins, affibodies, and engineered ligands. It denotes any protein of microbial origin, cell-bound or soluble, which can bind to a mammalian protein. It fulfills the need for an umbrella terminology for a large group of binding structures. In contrast, the term 'lectin' represents a group of proteins with affinity for carbohydrate structures. The new term 'receptin' includes a number of key microbial proteins involved in host-parasite interactions and in virulence. Some receptins are promising vaccine candidates.

Animals↗

PubMed2003

In vitro evaluation of combination of terbinafine with itraconazole or amphotericin B against Zygomycota.

The combined activity in vitro of amphotericin B/terbinafine and itraconazole/terbinafine was assessed against 17 clinical isolates of Zygomycota using a checkerboard technique. Itraconazole/terbinafine combination exhibited a potent synergistic effect against the most of strains. Amphotericin B/terbinafine combination showed an indifferent interaction for Rhizopus oryzae, and an additive effect for the other species.

Amphotericin B↗

PubMedDate not supplied

[Structure of a primed microbial community as an integral method of evaluating the microbiologic state of soil].

The paper describes a laboratory method of initiated microbial cenosis which makes it possible to evaluate the microbiological state of soil and to predict its change under the action of various anthropogenic factors. To this end, the structure and characteristics of a microbial cenosis initiated by a substrate are studied using a scanning electron microscope in combination with classical techniques of microbiology: the actual predominance and proportions of individual microbial groups (bacteria, actinomycetes, fungi, algae, protozoa and microscopic invertebrates); the interaction and interrelation between individual microbial populations in the cenosis; the biological properties of predominating microorganisms; the ratio between active and resting forms; the rate and character of growth of individual microbial populations in the cenosis and their succession. All these indices taken together may serve as a criterion for integral evaluation of the effect produced by various physico-chemical factors on the microbiological state of soil.

Actinomycetales↗

PubMed1998

In vitro antimicrobial effects of various combinations of penicillin and clindamycin against four strains of Streptococcus pyogenes.

Previous studies using mouse models of Streptococcus pyogenes necrotizing fasciitis demonstrated that clindamycin had greater efficacy than penicillin. Frequently both agents are used concurrently in the treatment of severe S. pyogenes infections. This study investigated interactions between penicillin and clindamycin. E-test and broth microdilution assays suggested additivity or indifference, while timed-killing assays demonstrated concentration-dependent variable effects. Timed-kill studies utilizing clinical concentrations suggest that there is no antagonism with the combination of drugs but that the combination does not have a bactericidal advantage over either penicillin or clindamycin alone.

Clindamycin↗

PubMed2003

Molecular interaction of Porphyromonas gingivalis with host cells: implication for the microbial pathogenesis of periodontal disease.

Porphyromonas gingivalis is a predominant periodontal pathogen, which expresses a number of potential virulence factors involved in the pathogenesis of periodontitis. Among them, fimbriae are a critical factor to mediate the bacterial interaction with host tissues, which promotes the bacterial adhesion to and invasion of the targeted sites. Fimbriae are capable of binding to human salivary components, commensal bacteria, and a variety of host cells including macrophages, epithelial cells, and fibroblasts. Human extracellular matrix (ECM) proteins such as vitronectin and fibronectin play important roles in cellular signal transduction via binding to receptor integrins. Fimbriae showed significant binding affinity to ECM proteins and clearly inhibited the molecular interactions between vitronectin/fibronectin and their receptor alphavbeta3 and alpha5beta1 integrins overexpressed on Chinese hamster ovary (CHO) cell strain. P. gingivalis fimbriae are likely to interrupt the cellular signaling via ECM proteins/integrins in periodontal regions. Fimbriae are also thought to be critically important in invasive events of the organism to host cells. The fimA genes, encoding FimA (a subunit of fimbriae), of P. gingivalis strains are classified into 5 types, I to V. Recent clinical investigations demonstrated the close relationship between the organisms with type II fimA and periodontitis development. Recombinant FimA (rFimA) proteins of types I to V were generated to compare their adhesion/invasion abilities to human gingival fibroblasts (HGF) and a human epithelial cell line (HEp-2 cells), respectively. There were no significant differences in the adhesion ability of microspheres (MS) coated with these rFimAs to HGF; however, the adhesion of type II rFimA-MS to HEp-2 cells was significantly greater than that of other rFimA types. It was also observed that the type II rFimA-MS markedly invaded the epithelial cells and accumulated around the nuclei. Collectively, these findings suggest that fimbriae of P. gingivalis, especially type II, are involved in the initiation and progression of human periodontitis.

Animals↗