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PubMed2006

Stability in a denitrifying fluidized bed reactor.

This study evaluates changes in the microbial community structure and function of a pilot-scale denitrifying fluidized bed reactor during periods of constant operating conditions and periods of perturbation. The perturbations consisted of a shutdown period without feed, two disturbances in which biofilms were mechanically sheared from carrier particles, and a twofold step increase in feed nitrate concentration. In the absence of perturbations, nitrate removal was stable and consistently greater than 99%. The structure and dynamics of the microbial community were studied using cloning and sequencing techniques and terminal restriction fragment length polymorphism (T-RFLP) of the SSU rRNA gene. Under unperturbed operating conditions, stable function was accompanied by high constancy and low variability of community structure with the majority of terminal restriction fragments (T-RFs) appearing throughout operation at consistent relative abundances. Several of the consistently present T-RFs correlated with clone sequences closely related to Acidovorax (98% similarity), Dechloromonas (99% similarity), and Zoogloea (98% similarity), genera recently identified by molecular analyses of similar systems. Significant changes in community structure and function were not observed after the shutdown period. In contrast, following the increase in loading rate and the mechanical disturbances, new T-RFs appeared. After both mechanical disturbances, function and community structure recovered. However, function was much more resilient than community structure. The similarity of response to the mechanical disturbances despite differences in community structure and operating conditions suggests that flexible community structure and potentially the activity of minor members under nonperturbation conditions promotes system recovery.

Biodegradation, Environmental↗
PubMed1993

Neutrophil functions in patients with fractures of the upper end of the femur.

In the present study, neutrophil functions were examined in vitro in 40 patients suffering from fractures of the upper end of the femur (trochanteric and subcapital). Adherence to nylon, serum chemotaxis, and phagocytosis-bactericidal function were assayed. Three microbial strains, namely, Staphylococcus aureus, S. epidermidis, and Pseudomonas aeruginosa, were used for the experiments. Adherence of the patients' neutrophils was found normal. On the contrary, the chemotactic ability of the patients' sera was inferior to that of healthy controls; phagocytosis and bactericidal function were also significantly impaired for all three bacterial strains. The results were independent of fracture site (intracapsular or extracapsular), sex, and age. The observed host defense disorders provide additional information that helps to explain the increased susceptibility of these patients to bacterial infections.

Aged↗
PubMed2004

[Probiotics--an alternative for antibiotics?].

The condition and function of gastrointestinal (GI) tract are essential to our well being. Probiotics are defined as the microbial food supplements, which beneficially affect the host by improving its intestinal microbial balance. Probiotics are the functional food ingredients. They are used therapeutically to improve lactose tolerance and to prevent diarrhoea (especially viral diarrhoea in infants, antibiotic-associated diarrhoea, Clostridium difficile-associated diarrhoea and traveler's diarrhoea). Clinical studies suggest that probiotics might be useful in stimulation of the immune system, prevention of allergic diseases, control of GI tract inflammatory diseases and cancer prevention. Probiotic microbial species act by changing the composition of the gut microbionta. The use of non-digestible oligosaccharides (prebiotics) can fortify intestinal microflora and stimulate their growth. This review encompasses information regarding probiotic strains, prebiotics and commercially products (functional food), which can be useful in improving our health.

Anti-Bacterial Agents↗
PubMed2004

Microbial communities and their interactions in biofilm systems: an overview.

Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.

Bacteria↗
PubMed2006

Multidimensional modelling to investigate interspecies hydrogen transfer in anaerobic biofilms.

Anaerobic digestion is a multistep process, mediated by a functionally and phylogenetically diverse microbial population. One of the crucial steps is oxidation of organic acids, with electron transfer via hydrogen or formate from acetogenic bacteria to methanogens. This syntrophic microbiological process is strongly restricted by a thermodynamic limitation on the allowable hydrogen or formate concentration. In order to study this process in more detail, we developed an individual-based biofilm model which enables to describe the processes at a microbial resolution. The biochemical model is the ADM1, implemented in a multidimensional domain. With this model, we evaluated three important issues for the syntrophic relationship: (i) Is there a fundamental difference in using hydrogen or formate as electron carrier? (ii) Does a thermodynamic-based inhibition function produced substantially different results from an empirical function? and; (iii) Does the physical co-location of acetogens and methanogens follow directly from a general model. Hydrogen or formate as electron carrier had no substantial impact on model results. Standard inhibition functions or thermodynamic inhibition function gave similar results at larger substrate field grid sizes (> 10 microm), but at smaller grid sizes, the thermodynamic-based function reduced the number of cells with long interspecies distances (> 2.5 microm). Therefore, a very fine grid resolution is needed to reflect differences between the thermodynamic function, and a more generic inhibition form. The co-location of syntrophic bacteria was well predicted without a need to assume a microbiological based mechanism (e.g., through chemotaxis) of biofilm formation.

Bacteria, Anaerobic↗
PubMed2001

Phenotypic biomonitoring using multivariate flow cytometric analysis of multi-stained microorganisms.

A new method for monitoring phenotypic profiles of pure cultures and complex microbial communities was evaluated. The approach was to stain microorganisms with a battery of fluorescent dyes prior to flow cytometry analysis (FCM) and to analyse the data using multivariate methods, including principal component analysis and partial least squares. The FCM method was quantitatively evaluated using different mixtures of pure cultures as well as microbial communities. The results showed that the method could quantitatively and reproducibly resolve both populations and communities of microorganisms with 5% abundance in a diverse microbial background. The feasibility of monitoring complex microbial communities over time during the biodegradation of naphthalene using the FCM method was demonstrated. The biodegradation of naphthalene occurred to differing extents in microcosms representing three different types of aromatic-contaminated groundwater and a sample of bio-basin water. The FCM method distinguished each of these four microbial communities. The phenotypic profiles were compared with genotypic profiles generated by random-amplified polymorphic DNA analysis. The genotypic profiles of the microbial communities described only the microbial composition, and not their functional change, whereas the phenotypic profiles seemed to contain information on both the composition and the functional change of the microorganisms. Furthermore, event analysis of the FCM data showed that microbial communities with initially differing compositions could converge towards a similar composition if they had a capacity for high levels of degradation, whereas microbial communities with similar initial compositions could diverge if they differed in biodegrading ability.

Journal Article↗
PubMed2002

The gifts that keep on giving: physiological functions and evolutionary dynamics of male seminal proteins in Drosophila.

During mating, males transfer seminal proteins and peptides, along with sperm, to their mates. In Drosophila melanogaster, seminal proteins made in the male's accessory gland stimulate females' egg production and ovulation, reduce their receptivity to mating, mediate sperm storage, cause part of the survival cost of mating to females, and may protect reproductive tracts or gametes from microbial attack. The physiological functions of these proteins indicate that males provide their mates with molecules that initiate important reproductive responses in females. A new comprehensive EST screen, in conjunction with earlier screens, has identified approximately 90% of the predicted secreted accessory gland proteins (Acps). Most Acps are novel proteins and many appear to be secreted peptides or prohormones. Acps also include modification enzymes such as proteases and their inhibitors, and lipases. An apparent prohormonal Acp, ovulin (Acp26Aa) stimulates ovulation in mated Drosophila females. Another male-derived protein, the large glycoprotein Acp36DE, is needed for sperm storage in the mated female and through this action can also affect sperm precedence, indirectly. A third seminal protein, the protease inhibitor Acp62F, is a candidate for contributing to the survival cost of mating, given its toxicity in ectopic expression assays. That male-derived molecules manipulate females in these ways can result in a molecular conflict between the sexes that can drive the rapid evolution of Acps. Supporting this hypothesis, an unusually high fraction of Acps show signs consistent with their being targets of positive Darwinian selection.

Animals↗
PubMed2002

The multifaceted Paneth cell.

Paneth cells (PCs) were described over a century ago as granulated cells located at the base of small intestinal crypts, the 'crypts of Lieberkühn.' Various histochemical staining procedures were developed that identified PCs based on their distinctive granule-staining pattern. Early on, PCs were proposed to perform a specialized function other than absorption of digested nutrients, the predominant task of the small intestinal epithelium. Since then, many constituents of the PC granules have been biochemically characterized. The presence of various granule-associated antimicrobial substances and their release upon microbial challenge suggest that PCs function as specialized defense cells in the small intestine. Altered resistance to microbial infection in animal models with disrupted or augmented PC function provides further support for the host defense role of PCs. Other PC components suggest that PCs may also participate in the regulation of lumenal ionic composition, crypt development, digestion, and intestinal inflammation.

Animals↗
PubMed2006

Histidine biosynthesis in plants.

The study of histidine metabolism has never been at the forefront of interest in plant systems despite the significant role that the analysis of this pathway has played in development of the field of molecular genetics in microbes. With the advent of methods to analyze plant gene function by complementation of microbial auxotrophic mutants and the complete analysis of plant genome sequences, strides have been made in deciphering the histidine pathway in plants. The studies point to a complex evolutionary origin of genes for histidine biosynthesis. Gene regulation studies have indicated novel regulatory networks involving histidine. In addition, physiological studies have indicated novel functions for histidine in plants as chelators and transporters of metal ions. Recent investigations have revealed intriguing connections of histidine in plant reproduction. The exciting new information suggests that the study of plant histidine biosynthesis has finally begun to flower.

Arabidopsis↗
PubMed2003

Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore.

Retinal proteins are photoreceptors found in many living organisms. They possess a common chromophore, retinal, that upon absorption of light isomerizes and thereby triggers biological functions ranging from light energy conversion to phototaxis and vision. The photoisomerization of retinal is extremely fast, highly selective inside the protein matrix, and characterized through optimal sensitivity to incoming light. This article describes the first report of an ab initio quantum mechanical description of the in situ isomerization dynamics of retinal in bacteriorhodopsin, a microbial retinal protein that functions as a light-driven proton pump. The description combines ab initio multi-electronic state molecular dynamics of a truncated retinal chromophore model (N-methyl-gamma-methylpenta-2,4-dieniminium cation fragment) with molecular mechanics of the protein motion and unveils in complete detail the photoisomerization process. The results illustrate the essential role of the protein for the characteristic kinetics and high selectivity of the photoisomerization: the protein arrests inhomogeneous photoisomerization paths and funnels them into a single path that initiates the functional process. Supported by comparison with dynamic spectral modulations observed in femtosecond spectroscopy, the results identify the principal molecular motion during photoisomerization.

Bacteriorhodopsins↗
PubMed2003

Scaling up: the next challenge in environmental microbiology.

Great strides have recently been made in identifying and characterizing the staggering diversity of microorganisms conducting primary and secondary production, nutrient transformation and mineralization processes that underlie ecosystem and regional biogeochemical, trophodynamic and ecological change. We are now faced with the challenge of assigning and coupling function to structure in highly complex and interactive microbial communities mediating such change. Previous and ongoing ecophysiological work has shown that microbial processes controlled by environmental variables and limiting resources are highly specific in terms of what, when, where and why they are active, not to mention how they impact ecosystem dynamics. As such, it is imperative that we assess the activities and roles of key microbial 'players' along the appropriate environmental scales and gradients catalysing ecological change. Here, we discuss conceptual and technical challenges for some key microbially mediated environmental processes, problems and extremes that require synthesizing our growing knowledge of microbial community structure with emerging knowledge of function in aquatic ecosystems. We emphasize the importance of assessing ecological change over a range of relevant time scales that vary from minutes to millennia and spatial scales that range from microscale aggregates to ocean basins.

Biodiversity↗
PubMed2005

Bacterial virulence strategies that utilize Rho GTPases.

The ability to modify central host cellular functions is a major advantage to many bacterial pathogens that use such strategies as part of their virulence mechanisms. Small GTPases, including Rho GTPases, make particularly attractive targets for pathogens because of their central roles in modulating cellular functions such as cytoskeletal control. Such modifications of these GTPases can include direct chemical modification of the GTPase or interfacing with some of the regulatory elements associated with GTPase control. Pathogens use these alterations in GTPase functions for a variety of functions, including killing the host cell, mediating bacterial uptake into the host cell (invasion), reprogramming actin to form a lesion in host cells underlying adherent bacteria, to mediate intracellular survival by affecting intracellular trafficking, or to provide polymerized actin mechanisms to propel microbes around inside host cells and into adjacent cells. Collectively, these examples represent many key microbial virulence mechanisms that have led to a much deeper understanding of both microbial pathogens and GTPase functions.

Animals↗
PubMed2001

The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation.

The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.

Journal Article↗
PubMed1999

Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles.

The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.

Bacteria↗
PubMed2001

Microbiological quality and shelf life modeling of ready-to-eat cicorino.

Growth of the microbial population resident in ready-to-use fresh cut cicorino, a variety of Chichorium intybus, was determined in the various preparation steps with the aim of defining the hazard critical control points. The investigation concerned cut cicorino from two producers. During the process a 1- to 1.5-fold increase of microbial counts was observed, and the retail product showed values of 10(5) to 10(6) CFU/g. The shelf life of the product was kinetically modeled in order to check the effects of storage temperature and assess the microbial indexes most relevant for hygiene and quality of the distributed product. A modified Gompertz function described the kinetics of microbial growth and allowed definition of a stability time and its dependence on temperature. Stability times were of 0.3, 3.7, and 4.7 days at storage temperatures of 20, 10, and 5 degrees C, respectively. Q10 (the fold decrease of stability time for an increase of 10 degrees C) was 3.85. The results from this study may be used to predict the effects of temperatures experienced in the distribution chain on bacterial levels in cicorino.

Bacteria↗
PubMed2026

In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.

BACKGROUND: Understanding how metabolic capabilities diverge across microbial species is essential for deciphering community function, ecological interactions, and the design of synthetic microbiomes. Despite shared core pathways, microbial phenotypes can differ markedly due to evolutionary adaptations and metabolic specialization. Genome-scale metabolic models (GEMs) provide a systems-level framework to explore these differences; however, their complexity hinders direct comparison. RESULTS: We introduce NIS (Neidhardt-Ingraham-Schaechter), a computational workflow that integrates the redGEM, lumpGEM, and redGEMX algorithms to systematically reduce genome-scale models into biologically interpretable modules. This approach enables direct, quantitative comparison of fueling pathways, biomass biosynthetic routes, and environmental exchange processes while retaining essential metabolic information. We first demonstrate the utility of NIS by analyzing Escherichia coli and Saccharomyces cerevisiae, which revealed both conserved and divergent strategies in central metabolism, biosynthetic cost, and substrate utilization. We then applied NIS to the core honeybee gut microbiome, uncovering distinct metabolic traits, functional redundancy, and complementarity that help explain auxotrophy, cross-feeding interactions, and microbial coexistence. CONCLUSIONS: NIS provides an automated, scalable, and reproducible framework for dissecting microbial metabolic networks beyond gene content or taxonomy. By linking metabolism to ecological function, NIS offers new opportunities to interpret microbial community dynamics and to support the rational design of microbiomes in health, agriculture, and environmental applications. Video Abstract.

Metabolic Networks and Pathways↗
PubMed1984

[Pathology and physiology of microbes. IV. Economic and metabolic coefficients in assessing the functional states of Salmonella typhi].

The study of economic and metabolic coefficients under different conditions of batch and continuous cultivation with the use of S. typhi, a facultative anaerobe, as a model has demonstrated that the functional state of the microbial population is determined by the phase of the development of the culture, the composition of the culture medium, the conditions of aeration and stirring, the concentration of the energy-providing substrate and the dilution rate in continuous cultivation. The economic coefficient with respect to the energy-providing substrate has been found to be the main characteristic of the functional state of the population: the high values of this characteristic correspond to the physiological state of the population. The decrease of the economic coefficient below a certain critical value is indicative of the pathological state of the population.

Aerobiosis↗
PubMed2002

Peptide ligands in antibacterial drug discovery: use as inhibitors in target validation and target-based screening.

There is an urgent need to develop novel classes of antibiotics to counter the inexorable rise of resistant bacterial pathogens. Modern antibacterial drug discovery is focused on the identification and validation of novel protein targets that may have a suitable therapeutic index. In combination with assays for function, the advent of microbial genomics has been invaluable in identifying novel antibacterial drug targets. The major challenge in this field is the implementation of methods that validate protein targets leading to the discovery of new chemical entities. Ligand-directed drug discovery has the distinct advantage of having a concurrent analysis of both the importance of a target in the disease process and its amenability to functional modulation by small molecules. VITA is a process that enables a target-based paradigm by using peptide ligands for direct in vitro and in vivo validation of antibacterial targets and the implementation of high-throughput assays to identify novel inhibitory molecules. This process can establish sufficient levels of confidence indicating that the target is relevant to the disease process and inhibition of the target will lead to effective disease treatment.

Animals↗