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PubMed1995

[Interaction between anti-infective agents and phagocytes].

Metchnikoff was one of the first to suggest the need for cooperation between phagocytes and therapeutic agents for the benefit of health. After the hopes raised by the discovery and the tremendous development of antimicrobials, there is now a creeping pessimism faced with the parallel evolution of resistance strategies in the microbial world. Interest has now turned to the use of immunomodulatory drugs, alone or combined with anti-infectious agents. Another tendency is based on the possibility that antimicrobials directly interfere with the host-microbe interplay. This review is aimed at summarizing our knowledge of the interactions between antimicrobial agents and the phagocyte, still a cornerstone in the natural defence system. Despite the problems inherent in the analysis and clinical relevance of effects observed in the test tube this developing area of research could provide new therapeutic solutions beyond the year 2000.

Anti-Infective Agents↗
PubMed2025

A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.

Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.

Humans↗
PubMed2026

Cross-Kingdom Siderophores: Biosynthesis, Ecology, and Biotechnological Applications.

Microbial siderophores are high-affinity iron-binding compounds which are produced by bacteria, fungi, and actinomycetes to obtain iron and survive and interact with different species in an iron-deficient environment. While the conventional research on siderophore systems deals mainly with the study within the same taxa, modern researchers have increased their inclination toward cross-kingdom integration of siderophore behavior and their impact on host-associated environments. This can be largely attributed to differences in biosynthetic gene clusters, receptor systems, and regulatory networks, which produce distinct genotype-to-phenotype results determining microbial cooperation and competition. Current advancements in genomic research, together with omics studies like transcriptomics, proteomics, and metabolomics, have created newer insights into how siderophores function. However, the present literature evidences multiple major gaps in multi-omics data because the link between genomes and metabolomes remains weak due to inconsistent regulatory data sets and failure in identifying producer-consumer relationships in polymicrobial systems. Additionally, major constraints like molecular instability, delivery system limitations, host toxicity, limitations in upscaling, and regulatory issues delimit the use of siderophores in medical treatment, agricultural practices, and environmental biotechnology. This review aims to bridge the existing knowledge about siderophore biochemistry, biosynthesis, ecological functions, and genetic regulation across kingdoms while integrating multi-omics outlook with translational considerations. Thus, by connecting molecular mechanisms with evolutionary cross-talk, this study aims to provide a system-level framework in the world of siderophore-mediated iron uptake and therefore shapes future directions in emerging fields of microbial engineering, precision therapies, and sustainable biotechnology.

Fur regulation↗
PubMed2003

Optimizing outcomes with antimicrobial therapy through pharmacodynamic profiling.

In patients with infection, improving the probability of positive treatment outcomes depends on optimizing the interactions between the host, pathogen, and drug. In this setting, optimal regimens must be utilized which not only maximize effectiveness in a specific patient, but also minimize the development of microbial resistance. The probability of achieving a specifically targeted antimicrobial exposure can be assessed using Monte Carlo simulation, a technique which integrates an agent's in vitro potency distribution (i.e., minimum inhibitory concentrations [MICs]) with the pharmacokinetic profile. The targeted pharmacodynamic parameters assessed by this technique include the ratio of peak concentration (C(max)) to MIC (C(max) : MIC); the ratio of the area under the plasma concentration-time curve (AUC) to MIC (AUC : MIC), and the time the drug concentration exceeds the MIC (T > MIC). Some antimicrobials, e.g., the aminoglycosides, are most effective/bactericidal when they have a high C(max) : MIC ratio; others, e.g., the fluoroquinolones, are more effective when the AUC : MIC ratio is high. In both of these scenarios, organism eradication is concentration-dependent, and the therapeutic goal is to maximize drug exposure. Like the fluoroquinolones, the efficacy of telithromycin, a newly developed ketolide, is most related to the AUC : MIC ratio. Outcome for other agents, such as the beta-lactams, is best predicted by the T > MIC; in this case, organism eradication is time-dependent, and the therapeutic goal is to optimize the duration of antimicrobial exposure. This article discusses how the use of currently available antimicrobials can be optimized through an appreciation of pharmacodynamic profiling.

Anti-Bacterial Agents↗
PubMed2006

Antibacterial drug discovery--then, now and the genomics future.

Drug discovery research in the area of infectious diseases, in particular that dealing with antibacterial/antibiotic susceptibility and resistance, is in a process of continuing evolution. Steeped in the history of the highly successful intervention with chemotherapeutic agents to treat human infections, the emergence of drug-resistant pathogens worldwide presents a serious unmet medical need, if not a pending catastrophe. Research in both academia and industry over the past 30 years using molecular biology, genetics and more recently--bacterial genomics--has assembled key enabling technologies to increase productivity and success rates in the discovery and development of novel antibacterial agents. However genomics is not limited only to antibacterial target selection but provides the opportunity to further understand key interactions in the use of antibacterial compounds as therapeutic agents (such as resistance emergence, susceptibility, efflux, interactions between compound and pathogen, etc.). Genomics also offers the potential for insights into: bacterial niche adaptation, host susceptibility, treatment regimens, antibiotic resistance, pharmacokinetics (e.g., host metabolism differences), safety and the microbial genesis of chronic diseases (e.g., gastric ulceration).

Anti-Bacterial Agents↗
PubMed2005

Lipids, lipases, and lipid-modifying enzymes in plant disease resistance.

Lipids and lipid metabolites influence pathogenesis and resistance mechanisms associated with plant-microbe interactions. Some microorganisms sense their presence on a host by perceiving plant surface waxes, whereas others produce toxins that target plant lipid metabolism. In contrast, plants have evolved to recognize microbial lipopolysaccharides (LPSs), sphingolipids, and lipid-binding proteins as elicitors of defense response. Recent studies have demonstrated that the plasma membrane provides a surface on which some plant resistance (R) proteins perceive pathogen-derived effectors and thus confer race-specific resistance. Plant cell membranes also serve as reservoirs from which biologically active lipids and precursors of oxidized lipids are released. Some of these oxylipins, for example jasmonic acid (JA), are important signal molecules in plant defense. Arabidopsis thaliana is an excellent model plant to elucidate the biosynthesis and metabolism of lipids and lipid metabolites, and the characterization of signaling mechanisms involved in the modulation of plant defense responses by phytolipids. This review focuses on recent studies that highlight the involvement of lipids and lipid metabolites, and enzymes involved in lipid metabolism and modification in plant disease resistance.

Lipase↗
PubMed2000

Public health genetics: an emerging interdisciplinary field for the post-genomic era.

Public health genetics is an exciting interdisciplinary area that brings all the public health sciences to bear on the emerging challenge of interpreting the medical and public health significance of genetic variation within populations. Sequencing of the human genome will generate an avalanche of genetic information to be linked with information about microbial, chemical, and physical exposures; nutrition, metabolism, lifestyle behaviors, and medications. The public health genetics mini-symposium in this volume includes articles dealing with educational innovations, host-pathogen interactions in infectious diseases, nutrition/genetic interactions in cancers, and population screening for hemochromatosis. Additional topics addressed here are ecogenetics and risk assessment, the genetics of unhealthful behaviors, and ethical and policy issues. Finally, a set of principles for community-based health research in populations is presented as a public health-oriented counterpart to the principle of autonomy and the practice of informed consent that have become key elements of ethics in medical care and medical research with individuals.

Ethics, Medical↗
PubMed2001

C-reactive protein, inflammation, and innate immunity.

The circulating acute phase reactant C-reactive protein (CRP) has traditionally been characterized as an effector of nonclonal host resistance since it activates the classical complement cascade and mediates phagocytosis, but it is also capable of regulating inflammation. The three-dimensional structure of human CRP has revealed the molecular basis for complement activation and binding of phosphate monoesters. CRP gene expression by liver hepatocytes in response to cytokines (IL-1beta and IL-6) released in tissues requires several transcription factors which interact. Elevated levels of CRP are a prognostic marker for coronary artery disease; however, the role of CRP in atheriosclerosis remains unknown. CRP also mediates direct host protection to some microbial pathogens via its opsonic activity through certain Fcgamma-receptors. The CRP response may be one of the links between nonspecific innate immunity and specific clonal immunity.

C-Reactive Protein↗
PubMed2001

Salmonella interactions with host cells: type III secretion at work.

The bacterial pathogen Salmonella enterica has evolved a very sophisticated functional interface with its vertebrate hosts. At the center of this interface is a specialized organelle, the type III secretion system, that directs the translocation of bacterial proteins into the host cell. Salmonella spp. encode two such systems that deliver a remarkable array of bacterial proteins capable of modulating a variety of cellular functions, including actin cytoskeleton dynamics, nuclear responses, and endocytic trafficking. Many of these bacterial proteins operate by faithful mimicry of host proteins, in some cases representing the result of extensive molecular tinkering and convergent evolution. The coordinated action of these type III secreted proteins secures the replication and survival of the bacteria avoiding overt damage to the host. The study of this remarkable pathogen is not only illuminating general paradigms in microbial pathogenesis but is also providing valuable insight into host cell functions.

Actins↗
PubMed2002

Disease consequences of pathogen adaptation.

Experimental evolution studies demonstrate that pathogens evolve rapidly, have a large capacity for increased virulence and cause disease in many different ways. A large proportion of genetic diversity for host susceptibility to infectious, autoimmune and 'genetic' diseases, and to cancer, is probably caused by pathogens and/or host counteradaptations. Recent advances in diverse fields support this claim and suggest many underused approaches for identifying and experimentally dissecting the complicated host-pathogen interactions that often lead to disease.

Adaptation, Physiological↗
PubMed1998

Temporal changes in the frequency of colicinogeny in Escherichia coli from house mice.

Escherichia coli was isolated from feral house mice (Mus domesticus) during the course of a mouse plague in the state of Victoria, Australia. The isolates were characterized for the production of colicins and their resistance to the co-occurring colicins. Of the 447 isolates examined, 59% were found to be colicinogenic. Phenotypic and PCR-based genotypic methods were used to determine the types of colicins being produced. Colicin E2 was the most common, representing 27% of the colicin-producing isolates. Colicin Ia was produced by 3% of the colicinogenic isolates. The remaining colicins could not be identified, but phenotypic and PCR data argue that at least nine different colicin types are present in this collection of E. coli. The frequency of colicinogenic isolates declined from 71% to 43% over the 7 months of the study. All colicin types appeared to decline in frequency. Concurrently, the resistance of isolates to colicin E2 increased from about 50% to 70%. Two hypotheses are proposed to explain the decline in the frequency of colicinogeny in this population of E. coli. The first relates to the within-host interactions occurring among colicinogenic, colicin-susceptible and colicin-resistant populations within a host. The second relates to the among-host interactions between susceptible and colicinogenic populations and the effect of host population densities on these interactions.

Animals↗
PubMed2006

Nutritional requirements and antibiotic resistance patterns of Helicobacter species in chemically defined media.

The growth of the gastric pathogen Helicobacter pylori in the absence of serum remains challenging, and nutritional requirements have only partially been defined, while almost nothing is known about nutritional requirements of other Helicobacter spp. Although previous data showed that H. pylori grows in the chemically defined medium F-12, but not in other tissue culture media examined, the specific components responsible for growth were not entirely understood. Here we describe the optimization of amino acids, metals, and sodium chloride for H. pylori. Iron, zinc, and magnesium were critical for growth; copper was not required. Optimization of sodium chloride was further beneficial. Nutritional requirements and antibiotic resistance patterns of several other Helicobacter spp. revealed that all except H. felis grew in serum-free, unsupplemented F-12. All Helicobacter spp. were resistant to at least six antimicrobial agents when cultured in the presence of serum. However, in the absence of serum, H. pylori, H. mustelae, and H. muridarum became sensitive to polymyxin B and/or trimethoprim. Much of the data were obtained using a convenient ATP assay to quantify growth. H. pylori has surprisingly few absolute requirements for growth: 9 amino acids, sodium and potassium chloride, thiamine, iron, zinc, magnesium, hypoxanthine, and pyruvate. These data suggest that H. pylori and other Helicobacter spp. are not as fastidious as previously thought. The data also suggest that chemically defined media described herein could yield the growth of a wide range of Helicobacter spp., allowing a more detailed characterization of Helicobacter physiology and interactions with host cells.

Adenosine Triphosphate↗
PubMed1992

Clonal unresponsiveness results from an interaction between staphylococcal enterotoxin B and T cells expressing unexpected V beta elements.

The ability of staphylococcal toxins to stimulate large numbers of T cells has led to their designation as a superantigen. Previous studies have indicated that activation of T cells bearing particular V beta elements may be responsible for the toxic effects of these bacterial products. However, the widespread expression of functionally similar proteins by unrelated bacterial species suggests the possibility that these products may represent a successful microbial strategy for subversion of the host antibacterial response. We have examined the effects of the staphylococcal enterotoxin B (SEB) on T cell clones that express different V beta elements. We note that SEB stimulates clones bearing previously defined V beta elements to proliferate and to produce cytokines. In addition, we demonstrate that an interaction between SEB and the TCR of clones that express additional V beta elements, including V beta 2 and V beta 6, results in a sterile form of immunological activation. This activation phenotype is characterized by proliferation without detectable cytokine production and is followed by profound immunological unresponsiveness in vitro and in vivo. We propose that reduced levels of antibacterial responses resulting from this form of T cell unresponsiveness may account for the highly conserved expression of superantigens by diverse bacterial species.

Animals↗
PubMed1995

Biofilms in device-related infections.

The use of various medical devices including indwelling vascular catheters, cardiac pacemakers, prosthetic heart valves, chronic ambulatory peritoneal dialysis catheters and prosthetic joints has greatly facilitated the management of serious medical and surgical illness. However, the successful development of synthetic materials and introduction of these artificial devices into various body systems has been accompanied by the ability of microorganism to adhere to these devices in the environment of biofilms that protect them from the activity of antimicrobial agents and from host defense mechanisms. A number of host, biomaterial and microbial factors are unique to the initiation, persistence and treatment failures of device-related infections. Intravascular catheters are the most common devices used in clinical practice and interactions associated with these devices are the leading cause of nosocomial bacteremias. The infections associated with these devices include insertion site infection, septic thrombophlebitis, septicemia, endocarditis and metastatic abscesses. Other important device-related infections include infections of vascular prostheses, intracardiac prostheses, total artificial hearts, indwelling urinary catheters, orthopedic prostheses, endotracheal tubes and extended wear lenses. The diagnosis and management of biofilm-associated infections remain difficult but critical issues. Appropriate antimicrobial therapy is often not effective in eradicating these infections and the removal of the device becomes necessary. Several improved diagnostic and therapeutic modalities have been reported in recent experimental studies. The clinical usefulness of these strategies remains to be determined.

Animals↗
PubMed2005

DNA extraction from low-biomass carbonate rock: an improved method with reduced contamination and the low-biomass contaminant database.

Caves represent a unique environment in which to study subsurface geomicrobial interactions and processes. One of the primary techniques used to study such geologic samples is molecular phylogenetic analysis, but this technique is hampered by low microbial biomass and calcium in the host rock, often leading to poor and irreproducible DNA extraction. We describe an improved protocol to recover extremely low amounts of DNA from calcium-rich geologic samples. This protocol relies on the use of the synthetic DNA molecule poly-dIdC, to act both as blocking agent and carrier molecule to increase the yield of DNA, and dialysis to remove calcium inhibitors of PCR amplification. Further, we demonstrate that many traditionally used laboratory substrates contain microbial DNA that can be amplified through the polymerase chain reaction (PCR) and contaminate molecular phylogenetic profiles. While the number of potential contaminants can be minimized, it cannot be eliminated from extraction techniques. We have therefore established the low-biomass contaminant (LBC) database, which contains the 16S rRNA gene sequences of species that have been identified as common laboratory contaminants. These identified contaminants provide a reference database to allow investigators to critically evaluate certain species identified within their phylogenetic profile when examining such low-biomass environments.

Base Sequence↗
PubMed2000

Use of an affinity proteomics approach for the identification of low-abundant bacterial adhesins as applied on the Lewis(b)-binding adhesin of Helicobacter pylori.

Microbial attachment to host cell surfaces is considered to be the first essential step for colonization and infection. In most known cases, attachment is mediated by a specific protein-carbohydrate interaction. We have used a carbohydrate-containing crosslinking probe to select bacterial surface adhesins for trypsin digestion, MALDI-TOF mass spectrometry and identification against genome sequence. The present paper describes this functional proteomics approach for identification of the recently cloned low-abundant Lewis(b)-binding adhesin of Helicobacter pylori. Protein identification was obtained through the enrichment of approximately 300 fmol of adhesin from solubilized cells.

Adhesins, Bacterial↗
PubMed2006

Designer probiotics for prevention of enteric infections.

Many microbial pathogens, including those responsible for major enteric infections, exploit oligosaccharides that are displayed on the surface of host cells as receptors for toxins and adhesins. Blocking crucial ligand-receptor interactions is therefore a promising therapeutic strategy. One approach is to express molecular mimics of host receptors on the surface of harmless recombinant bacteria that can survive in the gut. These 'designer probiotics' bind bacterial toxins in the gut lumen with very high avidity, thereby preventing disease. This article discusses recent progress with this strategy.

Adhesins, Bacterial↗