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PubMed2006

Emerging and re-emerging infectious diseases: influenza as a prototype of the host-pathogen balancing act.

To respond to emerging and re-emerging infections, it is necessary to understand the interactions between microbial pathogens and their hosts and the impact of environmental and social factors on these interactions. The importance of understanding host-pathogen interactions is underscored by the emergence of virulent H5N1 avian influenza viruses and their transmission to humans, and the potential pandemic threat they pose.

Animals↗
PubMed2006

Microbial ecology of drinking water distribution systems.

The supply of clean drinking water is a major, and relatively recent, public health milestone. Control of microbial growth in drinking water distribution systems, often achieved through the addition of disinfectants, is essential to limiting waterborne illness, particularly in immunocompromised subpopulations. Recent inquiries into the microbial ecology of distribution systems have found that pathogen resistance to chlorination is affected by microbial community diversity and interspecies relationships. Research indicates that multispecies biofilms are generally more resistant to disinfection than single-species biofilms. Other recent findings are the increased survival of the bacterial pathogen Legionella pneumophila when present inside its protozoan host Hartmannella vermiformis and the depletion of chloramine disinfectant residuals by nitrifying bacteria, leading to increased overall microbial growth. Interactions such as these are unaccounted for in current disinfection models. An understanding of the microbial ecology of distribution systems is necessary to design innovative and effective control strategies that will ensure safe and high-quality drinking water.

Animals↗
PubMed2001

Microbial toxins in plant-pathogen interactions: Biosynthesis, resistance mechanisms, and significance.

In the history of phytopathology, microbial toxins have been the objects of extensive studies as possible pathogenicity or virulence factors for the producer pathogens. The recent development of molecular genetic techniques provided an experimental basis to thoroughly test the role of these secondary metabolites in pathogenesis. Some of them did prove to be highly associated with disease initiation or enhanced virulence in certain plant-pathogen interactions. In this review, we describe recent progresses in the field of plant-pathogen interactions focusing on two toxins; i.e., tabtoxin from Pseudomonas syringae and trichothecenes from Fusarium and other fungi. These microbial toxins have convincingly been shown to play causal roles in plant disease development. Studies on the biosynthesis and resistance mechanisms of these producers are outlined, and the significance of this knowledge is discussed in relation to practical applications in agriculture.

Journal Article↗
PubMed2003

Interpreting deposition patterns of microbial particles in laboratory-scale column experiments.

The transport and fate of microbial particles in subsurface environments is controlled by their capture (natural filtration) by sediment grains. Typically, filtration models used to describe microbe removal in porous media predict exponential decrease in microbial particle concentration with travel distance. However, a growing body of laboratory-scale column experiments suggests that the retained microbial particle profiles decay nonexponentially. The observed behavior may be attributed to the heterogeneity in the interactions between microbial particles and sediment grains, most likely due to the inherent variability in the microbial particles. This factor can be incorporated into classical colloid filtration (deposition) theory by inclusion of a distribution in the deposition rate coefficient. We show that certain distributions of the deposition rate coefficient (i.e., log-normal, bimodal, and power-law distributions) give rise to nonexponential deposition patterns. Comparisons of model predictions to experimental data indicate that the observed nonexponential deposition behavior of bacteria and virus particles may be attributed to a broad range (i.e., a power-law distribution) of microbial deposition rates. Other mechanisms such as particle release and blocking by previously deposited microbial particles are also shown to be potential sources of deviation from the classical filtration theory. Our results further suggest that monitoring fluid-phase particle concentration is insufficient for accurate characterization of the deposition and transport behavior of microbial particles in saturated porous media. Rather, the shape of the microbial particle retention profile is shown to be a key indicator of the mechanisms controlling microbial deposition and transport.

Environmental Monitoring↗
PubMed2026

Host life-history strategy is a critical determinant of virulent phage infection propensity.

Bacteriophages shape microbial communities through two major lifestyles: virulent (obligately lytic) and temperate (capable of lysogeny). Prevailing phage ecology frameworks focus on how environmental conditions, host density, and physiological state modulate infection modality. This perspective overlooks how host traits exert selective pressure on the distribution of virulent and temperate lifestyles across bacterial species, which limits understanding of phage ecology. To address this critical knowledge gap, we adopt a host-centric, trait-based perspective and use 5821 complete bacterial genomes to build a host life-history space predominantly defined by genome size, metabolic capacity, and growth rate potential. After mapping phage lifestyle association signals, prophage burden formed a continuous gradient across this space. Also, virulent phage association was positively correlated with prophage burden, revealing a nested structure of lifestyle signals. Functional trait analysis identified enrichment of resource-acquisition modules underlying both temperate and virulent associations. Overall, these findings indicate that phage lifestyle is significantly influenced by host life-history strategies, highlighting fast-growing, metabolically versatile hosts as favorable targets for virulent phage isolation and biocontrol applications.

Bacteriophages↗
PubMed1991

[Microbial pathogenicity factors and host defense mechanisms--parameters of post-traumatic infections].

The clinical features of posttraumatic infections are due to the interactions between microbial pathogenicity factors and the host defense. The virulence mechanisms of microorganisms include the adherence, chemotaxis, invasion, resistance, and production of toxins. In addition, the humoral and cellular components of the immune system are impaired in trauma patients. The influence of pathogenic microorganisms on immune effector cells results in the release of various inflammatory mediators which participate in the protective host response to infection but induce local and systemic damage provided they are excessively produced and/or ineffectively metabolized.

Bacteria↗
PubMed2025

Concurrent stimulation of diflufenican biodegradation and changes in the active microbiome in gravel revealed by Total RNA.

The use of slowly degraded pesticides poses a particular problem when these are applied to urban areas such as gravel paths. The urban gravel provides an environment very different from agricultural soils; i.e., it is both lower in carbon and microbial activity. We, therefore, endeavored to stimulate the degradation of the pesticide diflufenican added to urban gravel microcosms amended with dry alfalfa to increase microbial activity. In the present study, alfalfa addition significantly increased the formation of diflufenican's primary metabolite, 2-[3-(trifluoromethyl)phenoxy]nicotinic acid (AE-B), indicating stimulated biotransformation. The concurrent changes of the active microbial communities within the gravel were explored using shotgun metatranscriptomic sequencing of ribosomal RNA and messenger RNA. Although bacterial taxa remained dominant (87.0%-98.5% relative abundance), the alfalfa treatment led to a 4-5-fold increase in eukaryotic groups, including fungi and microbial grazers. Several microbial taxa potentially involved in the degradation of complex carbon compounds and aromatic pollutants-including Bacteroidetes, Verrucomicrobia, Sordariomycetes, Mortierellales, Tremellales, Sphingopyxis, and Phenylobacterium-increased in relative abundance following alfalfa amendment. Functional gene profiling revealed elevated expression of genes related to microbial activity and biomass production. Genes with potential roles in the breakdown of complex carbon structures (e.g., xylanases/chitin deacetylases) and in the transformation of aromatic compounds (e.g., ring-cleaving dioxygenases) were revealed. We conclude that complex carbon amendments can enhance the microbial activity, promoting the biotransformation of diflufenican in urban gravel environments. These findings provide new insights into the interactions between microbial community dynamics, gene expression profiles, and pesticide biotransformation in non-agricultural matrices.IMPORTANCEPesticides used on urban areas, e.g., gravel paths, are likely to have different effects and fates than when these are used on agricultural soils. Hence, studies into the degradation of pesticides applied to urban matrices are needed. We have previously shown that metabolites of the persistent pesticide diflufenican are even more persistent in urban soils, and it has also previously been shown that these metabolites leach from gravel surfaces. The reasons behind this are that the urban gravel provides an environment very different from agricultural soils; i.e., it is both lower in carbon and microbial activity. In the present study, we, therefore, endeavored to stimulate the degradation of the pesticide diflufenican added to urban gravel microcosms amended with dry alfalfa to increase microbial activity, concurrently studying the changes in the active microbiome by Total RNA-metatranscriptomics.

Biodegradation, Environmental↗
PubMed2005

Rifaximin, a poorly absorbed antibiotic: pharmacology and clinical potential.

Rifaximin (4-deoxy-4'-methylpyrido[1',2'-1,2]imidazo- [5,4-c]-rifamycin SV) is a synthetic antibiotic designed to modify the parent compound, rifamycin, in order to achieve low gastrointestinal (GI) absorption while retaining good antibacterial activity. Both experimental and clinical pharmacology clearly show that this compound is a nonsystemic antibiotic with a broad spectrum of antibacterial action covering Gram-positive and Gram-negative organisms, both aerobes and anaerobes. Being virtually nonabsorbed, its bioavailability within the GI tract is rather high with intraluminal and fecal drug concentrations that largely exceed the minimal inhibitory concentration values observed in vitro against a wide range of pathogenic organisms. The GI tract represents, therefore, the primary therapeutic target and GI infections the main indication. The appreciation of the pathogenic role of gut bacteria in several organic and functional GI diseases has increasingly broadened its clinical use, which is now extended to hepatic encephalopathy, small intestine bacterial overgrowth, inflammatory bowel disease and colonic diverticular disease. Potential indications include the irritable bowel syndrome and chronic constipation, Clostridium difficile infection and bowel preparation before colorectal surgery. Because of its antibacterial activity against the microorganism and the lack of strains with primary resistance, some preliminary studies have explored the rifaximin potential for Helicobacter pylori eradication. Oral administration of this drug, by getting rid of enteric bacteria, could also be employed to achieve selective bowel decontamination in acute pancreatitis, liver cirrhosis (thus preventing spontaneous bacterial peritonitis) and nonsteroidal anti-inflammatory drug (NSAID) use (lessening in that way NSAID enteropathy). This antibiotic has, therefore, little value outside the enteric area and this will minimize both antimicrobial resistance and systemic adverse events. Indeed, the drug proved to be safe in all patient populations, including young children. Although rifaximin has stood the test of time, it still attracts the attention of both basic scientists and clinicians. As a matter of fact, with the advancement of the knowledge on microbial-gut interactions in health and disease novel indications and new drug regimens are being explored. Besides widening the clinical use, the research on rifaximin is also focused on the synthesis of new derivatives and on the development of original formulations designed to expand the spectrum of its clinical use.

Animals↗
PubMed1997

Economic costs and trade impacts of microbial foodborne illness.

This article presents the economic costs of foodborne diseases for selected countries, the approaches used to calculate these costs, and a discussion on the interaction between microbial food safety issues and international trade in food. The human illness costs due to foodborne pathogens are estimated most completely in the United States of America, where, each year, 7 foodborne pathogens (Campylobacter jejuni, Clostridium perfringens, Escherichia coli O157:H7. Listeria monocytogenes, Salmonella, Staphylococcus aureus, and Toxoplasma gondii) cause an estimated 3.3-12.3 million cases of foodborne illness and up to 3900 deaths. These 7 pathogens are found in animal products and cost the United States an estimated $6.5-$34.9 billion (1995 US$) annually. The presence of foodborne pathogens in a country's food supply not only affects the health of the local population, but also represents a potential for spread to pathogens to visitors to the country and to consumers in countries which import food products. With more complete data on foodborne illnesses, deaths, costs and international trade rejections in each country, indicators could be developed by which changes in food safety can be monitored.

Cost of Illness↗
PubMed2026

Impacts of host genetics on gut microbiome composition in Alzheimer's disease.

BACKGROUND: Host-microbiome interactions play essential roles in the development of Alzheimer's disease (AD), yet the host genetic impacts on gut microbial alterations in AD remain poorly understood. RESULTS: Here, we simultaneously profiled host genotype and gut microbiome in 252 Chinese individuals with varying degrees of cognitive disability. Using the latent Dirichlet allocation topic model, we identified the Anaerostipes-enriched enterosignature (ES-Ana) at the microbial subgroup level as significantly negatively associated with cognitive disability, which could be recapitulated in external cohorts. With the whole-genome sequencing data, we performed microbiome genome-wide association studies for the ES-Ana relative abundance. We prioritized 41 lead genetic variants and confirmed that the high ES-Ana relative abundance showed a negative correlation with the polygenic risk score of AD, indicating its protective effect against AD. Furthermore, we identified 174 ES-Ana-associated genes, which are enriched in AD-related biological functions and phenotypes, and exhibite pervasive underexpression in glial cells during brain aging. CONCLUSIONS: In summary, our study reveals the complex genetic effects on the gut microbiota in AD, and provides novel evidence for the roles of the gut-brain axis in AD. Video Abstract.

Alzheimer Disease↗
PubMed2003

Toll-like receptors and the genetics of innate immunity.

PURPOSE OF REVIEW: The discovery that mammalian Toll-like receptors recognize microbial products and initiate innate immune responses to them has spawned a new field of biology, namely the study of molecular interactions linking microbial recognition to innate and adaptive immune responses. This field has grown very rapidly in recent years, due largely to recent advances in genetic technology. This review summarizes recent work in which genetic approaches have been used to identify novel and important facets of Toll-like receptor function. RECENT FINDINGS: Recent genetic studies have uncovered a wealth of information relating to ligand-receptor interactions, Toll-like receptor gene regulation, signal transduction, dendritic cell activation and allele-phenotype associations. SUMMARY: Information emerging from genetic studies of Toll-like receptors has improved our understanding of innate and acquired immunity. This improved understanding promises to facilitate the future development of novel therapies for many different inflammatory diseases including asthma, sepsis and atherosclerosis.

Animals↗
PubMed2005

A whole cell BIAcore assay to evaluate P1-mediated adherence of Streptococcus mutans to human salivary agglutinin and inhibition by specific antibodies.

Researchers now recognize the utility of surface plasmon resonance technology to evaluate interactions of microbial pathogens with host components. The surface adhesin and candidate vaccine antigen P1 of Streptococcus mutans, the main causative agent of dental caries, interacts with a high molecular weight glycoprotein called salivary agglutinin, or gp340, in the salivary pellicle. We optimized a BIAcore assay to measure P1-mediated Ca(2+) dependent binding of S. mutans whole cells to this physiological ligand immobilized on a Pioneer F1 sensor chip. Regeneration conditions allowed cells to be eluted from the sensor chip permitting multiple reuse of the agglutinin-coated surface. An isogenic P1-deficient S. mutans mutant did not bind to immobilized agglutinin demonstrating specificity of the detected interaction. Glutaraldehyde-fixation of bacterial cells showed the assay measured a whole cell-ligand interaction and was not an artifact of solubilized or leached proteins. Adherence inhibition assays demonstrated varying degrees of disruption of the S. mutans-agglutinin interaction by anti-P1 monoclonal antibodies recognizing different epitopes, whereas a polyclonal reagent demonstrated more complete inhibition. This report describes an improved method to assess salivary agglutinin-mediated adherence of S. mutans in vitro under physiological-like conditions and to evaluate the effectiveness of antibodies of differing specificities to inhibit binding.

Agglutinins↗
PubMed2001

Inhibitory effects of resin composite containing bactericide-immobilized filler on plaque accumulation.

OBJECTIVE: Previously, we have reported that incorporation of the antibacterial monomer 12-methacryloyloxydodecylpyridinium bromide (MDPB) was effective in immobilizing bactericide in the resin matrix, and an antibacterial composite without release of the agent could be achieved. In this study, an attempt was made to increase the density of bactericide immobilized in composite, and the inhibitory effects of this modified antibacterial composite on plaque accumulation were determined, focusing on the reliability of the effects and the mechanisms to affect the plaque formation. METHODS: An experimental composite containing immobilized bactericide at 2.83% was prepared by the incorporation of MDPB into a prepolymerized resin filler of control composite, and elution of antibacterial components and inhibition of in vitro plaque accumulation by Streptococcus mutans were determined. The inhibitory effects of the experimental composite on the attachment, glucan synthesis and growth of S. mutans on the surface were also examined in addition to the comparison of surface roughness and hydrophobicity with controls. The results were analyzed using the Student's t-test. RESULTS: The experimental composite had reproducible inhibitory effects against plaque accumulation compared with control (p<0.05), although it showed no elution of unpolymerized MDPB. The plaque-inhibitory effect of the experimental composite was found to depend upon the ability to inhibit the attachment, glucan synthesis, and growth of bacteria on its surface as no significant differences in the surface characteristics were obtained between control and experimental composites (p>0.05). SIGNIFICANCE: It was indicated that the experimental composite containing bactericide-immobilized filler has the possibility to be used clinically with an effective anti-plaque property.

Anti-Infective Agents, Local↗
PubMed2005

Host epithelial interactions with Helicobacter pylori: a role for disrupted gastric barrier function in the clinical outcome of infection?

Infection of the human stomach with Helicobacter pylori may develop into gastritis, ulceration, adenocarcinoma and mucosal lymphomas. The pathogenic mechanisms that determine the clinical outcome from this microbial-epithelial interaction remain poorly understood. An increasing number of reports suggests that disruptions of epithelial barrier function may contribute to pathology and postinfectious complications in a variety of gastrointestinal infections. The aim of this review is to critically discuss the implications of H pylori persistence on gastric disease, with emphasis on the role of myosin light chain kinase, claudins and matrix metalloproteinases in gastric permeability defects, and their contribution to the development of cancer. These mechanisms and the associated signalling events may represent novel therapeutic targets to control disease processes induced by H pylori, a microbial pathogen that colonizes the stomach of over 50% of the human population.

Cell Membrane Permeability↗
PubMed2000

Effect of Supplemental Electron Donors on the Microbial Reduction of Fe(III), Sulfate, and CO(2) in Coal Mining-Impacted Freshwater Lake Sediments.

In acidic mining-impacted lake sediments, the microbial reduction of Fe(III) is the dominant electron-accepting process, whereas the reduction of sulfate seems to be restricted to a narrow sediment zone of elevated pH and lower amounts of total and reactive iron. To evaluate the microbial heterogeneity and the commensal interactions of the microbial community, the flow of supplemental carbon and reductant was evaluated in four different zones of the sediment in anoxic microcosms at the in situ temperature of 12 degrees C. Substrate consumption, product formation, and the potential to reduce Fe(III) and sulfate were similar with both upper and lower sediment zones. In the upper acidic iron-rich sediment zone, the rate of Fe(II) formation 204 nmol ml(-1) d(-1) was enhanced to 833 nmol ml(-1) d(-1) and 462 nmol ml(-1) d(-1) by supplemental glucose and H(2), respectively. Supplemental lactate and acetate were not consumed under acidic conditions and decreased the rate of Fe(II) formation to 130 nmol ml(-1) d(-1) and 52 nmol ml(-1) d(-1), respectively. When the pH of the upper sediment increased above pH 5, acetate-dependent reduction of sulfate was initiated even though the pool of Fe(III) was not depleted. In deeper sediment zones with elevated pH, the rapid consumption of acetate was always coincident to a decrease in the concentration of sulfate and soluble Fe(II), indicating the formation of Fe(II) sulfides. Although the reduction of Fe(III) was still an ongoing process in deeper sediment zones, the formation of Fe(II) was only slightly enhanced by the consumption of glucose or cellobiose, but not by H(2) or acetate. H(2)-utilizing acetogens seemed to be involved in the consumption of H(2). These collective results indicated (i) that the reduction of Fe(III) predominated over the reduction of sulfate as long as the sediment remained acidic and carbon-limited, and (ii) that the sulfate-reducing microbiota in this heterogeneous sediment were better adapted to the geochemical gradients present than were other neutrophilic dissimilatory Fe(III) reducers.

Journal Article↗
PubMed2000

Symbiosis and pathogenesis: evolution of the microbe-host interaction.

Symbiotic and pathogenic bacteria have in common that they live in or on host organisms or host cells. To make a successful living in eukaryotic hosts, bacteria must possess the traits to recognize a given host and establish adherence. When the bacterial location is internal or intracellular, they must further have the ability to invade, to establish a niche, and finally to multiply within a host. The underlying mechanisms which allow this form of existence show similarities between symbiotic and pathogenic bacteria. The final outcome, however, may result in a wide spectrum of consequences for the host ranging from the acquisition of novel metabolic pathways to damage or death. Despite the vastly different forms of interactions, symbiotic and pathogenic bacteria have in common that they are adapted to a particular environmental niche represented by the host organism or compartment thereof. This contribution reviews the evolutionary forces which have shaped the microbial-host interactions. Particular emphasis is placed on the genetic and molecular mechanisms that drive bacterial evolution in response to the selective pressures of the host environment.

Animals↗
PubMed2006

Physiological aspects. Part 1 in a series of papers devoted to surfactants in microbiology and biotechnology.

Surfactants, both chemical and biological, are amphiphilic compounds which can reduce surface and interfacial tensions by accumulating at the interface of immiscible fluids and increase the solubility, mobility, bioavailability and subsequent biodegradation of hydrophobic or insoluble organic compounds. Investigations on their impacts on microbial activity have generally been limited in scope to the most common and best characterized surfactants. Recently a number of new biosurfactants have been described and accelerated advances in molecular and cellular biology are expected to expand our insights into the diversity of structures and applications of biosurfactants. Biosurfactants play an essential natural role in the swarming motility of microorganisms and participate in cellular physiological processes of signaling and differentiation as well as in biofilm formation. Biosurfactants also exhibit natural physiological roles in increasing bioavailability of hydrophobic molecules and can complex with heavy metals, and some also possess antimicrobial activity. Chemical- and indeed bio-surfactants may also be added exogenously to microbial systems to influence behaviour and/or activity, mimicking the latter effects of biosurfactants. They have been exploited in this way, for example as antimicrobial agents in disease control and to improve degradation of chemical contaminants. Chemical surfactants can interact with microbial proteins and can be manipulated to modify enzyme conformation in a manner that alters enzyme activity, stability and/or specificity. Both chemical- and bio-surfactants are potentially toxic to specific microbes and may be exploited as antimicrobial agents against plant, animal and human microbial pathogens. Because of the widespread use of chemical surfactants, their potential impacts on microbial communities in the environment are receiving considerable attention.

Bacteria↗
PubMed2025

Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.

Microbiomes influence diverse ecosystems, and viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, host identification for these viruses remains challenging due to the limitations in scaling cultivation-based approaches and the uncertain reliability and relative low resolution of in silico predictions - particularly for understudied viral taxa. Towards this, Hi-C proximity ligation uses sequenced, cross-linked virus and host genomic fragments to infer virus-host linkages and has now been applied in at least 10 studies. However, its accuracy remains unknown. Here we assess Hi-C performance in recovering virus-host interactions using synthetic communities (SynComs) composed of four marine bacterial strains and nine phages with known interactions and then apply optimized bioinformatic protocols to natural soil samples. In SynComs, standard Hi-C sample preparations and analyses showed poor normalized contact score performance (26% specificity, 100% sensitivity, incorrect matches up to class level) that could be dramatically improved by Z-score filtering (Z&#x2009;&#x2265;&#x2009;0.5, 99% specificity), though at reduced sensitivity (62% down from 100%). Detection limits were established as reproducibility was poor below minimal phage abundances of 105 PFU/mL. Applying optimized bioinformatic protocols to natural soil samples, we compared virus-host linkages inferred from proximity-ligated Hi-C sequencing with predictions generated by in silico homology-based and machine learning-based bioinformatic approaches. Prior to Z-score thresholding, agreement was relatively high at the phylum to family levels (72%), but not at the genus (43%) or species (15%) levels. Z-score thresholding reduced sensitivity (only 34% of predictions were retained), with only modest improvements in congruence with bioinformatic methods (48% or 18% at genus or species levels, respectively). Regardless, this led to 79 genus-level-congruent virus-host linkages and 293 new ones revealed by Hi-C alone, i.e., providing many new virus-host interactions to explore in already well-studied climate-critical soils. Overall, these findings provide empirical benchmarks and methodological guidelines to improve the accuracy and reliability of Hi-C for virus-host linkage studies in complex microbial communities.

Benchmarking↗