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Functional ingredient production: application of global metabolic models.

The biotechnology industry continuously explores new ways to improve the performance of microbial strains in fermentation processes. Recent focus has been on new genome-wide modelling approaches in functional genomics, which aim to take full advantage of genome sequence data, transcription profiling, proteomics and metabolite profiling for strain improvement. The integration of global metabolic models with genetic and regulatory models will be essential for the practice of metabolic engineering for strain improvement to move forward, simply because we cannot rely on our intuition to grasp the complexity of the biological systems involved.

Bacterial Physiological Phenomena↗

Short sequence repeats in microbial pathogenesis and evolution.

Repetitive DNA is ubiquitous in microbial genomes. Different classes of short sequence repeats (SSRs) have been identified and demonstrated to be generally heterogeneous in a locus-dependent manner, reflected in variation in the number of repeat units present at a given genomic site or by sequence heterogeneity among individual units. Both types of variability can be used to assess intra-species genetic diversity. Repeat variability often affects the coding potential of the region in which the repetitive element is located. This implies that determination of the primary structure of variable numbers of tandem repeats can be used for epidemiological identification purposes, and also for the analysis of gene function. Precise assessment of SSR structure can also generate insight into the regulation of gene expression. Together, DNA repeat analysis in microbial species provides information on both functional and evolutionary aspects of genetic diversity among microbial isolates.

Candida albicans↗

A review of antimicrobial peptides: defensins and related cationic peptides.

Cationic antimicrobial peptides are present throughout the plant and animal kingdoms and bear striking structural and functional similarities across species lines. They provide primitive, nonspecific means of combating a variety of bacteria, fungi, enveloped viruses, and protozoa. Some are also cytotoxic against host cells, including neoplastic cells. Cationic antimicrobial peptides may play various roles in inflammation and tissue repair. Antimicrobial peptides are found in epithelial tissues regularly exposed to microbial attack as well as in cells whose primary function is defense against potential pathogens. They constitute an important part of the nonoxidative antimicrobial arsenal of leukocytes. They are preformed and/or readily synthesized when the cells are stimulated by exposure to pathogens. They exert their effects directly by inserting into membranes of target cells and forming ion channels which increase membrane permeability; however, antimicrobial peptides can also act as opsonins to facilitate phagocytosis. Resistance to defensins is a virulence factor for organisms such as Salmonella sp. The study of cationic antimicrobial peptides is increasing our understanding of innate immunity, inflammation, and the pathogenesis of genetic diseases such as specific granule disease in humans. Therapeutic applications of antimicrobial peptides are currently under investigation.

Journal Article↗

Cloning of environmental genomic fragments as physical markers for monitoring microbial populations in coking wastewater treatment system.

The association between community functional shift and dynamics of genomic DNA composition can be used to identify functionally relevant populations as indicator organisms for systems monitoring. In this work, fingerprinting-based community DNA hybridization was used to monitor community structural dynamics and identify genomic fragments whose abundance shifts were concomitant to changes in COD removal capacity in a reactor. A laboratory-scale anaerobic-anoxic-oxic fixed biofilm system treating coking wastewater was operated with (LR mode) or without effluent recirculation (LNR mode). The contribution to total chemical oxygen demand (COD) removal by the anoxic reactor increased from 4% in LNR mode to 26% in LR mode. Long primer RAPD (randomly amplified polymorphic DNA) community fingerprints of the anoxic reactor also changed most significantly from the one similar to the anaerobic reactor to one similar to the oxic reactor. DNA hybridization revealed one signature band of 2.1 kb shared by the anoxic and oxic reactors in LR, but not LNR mode. Clone library profiling of this band resulted in one predominant 2.1-kb genomic fragment (B3) with no homologous sequences in GenBank. Real-time polymerase chain reaction indicated that copy numbers of B3 in the anoxic reactor under LR mode were 69 times higher than that under LNR mode, concomitant to a significant increase in COD removal capacity in this reactor. The different patterns of distribution of B3 in the laboratory system and a comparable malfunctioning industrial system demonstrated the potential of this genomic fragment as physical markers in systems monitoring. In addition, this genomic fragment may allow sequence-guided isolation of the host microbe.

Bacteria↗

The application of the WLF equation to predict lag time as a function of temperature for three psychrotrophic bacteria.

Many mathematical models for microbial growth rates or lag times have been proposed. Most of these models either predict well, but are empirical and offer no insight into mechanism or they reflect mechanism but are too complex or do not fit the data adequately. The Williams-Landel-Ferry (WLF) equation (used by polymer chemists) is empirical, but shows some relation to first principles, and hence may offer some insight into mechanism. This model also has only three parameters and therefore a fairly simple form. The WLF equation was fit to lag times derived from three datasets previously developed in our laboratory. The fits obtained with the WLF equation were as good as the best fits obtained with other models (e.g Arrhenius, Davey, response surface and square root). The WLF model was able to account for 98 to 99% of the variance in the three datasets, indicating a very good fit overall. The parameter estimates of the WLF model were not as highly correlated as those of some of the other models. Many of the models, including the WLF equation did not predict well at very long lag times. Weighted least squares non-linear regression improved the fit for these long lag times.

Listeria monocytogenes↗

Comparative Responses of Invasive and Native Plant Species to Combined Cd and Microplastic Pollution.

The co-occurrence of heavy metal contamination and biodegradable microplastic (polylactic acid, PLA) pollution poses increasing risks to terrestrial plant communities and soil functioning, yet species-specific responses to combined stress remain poorly understood. Cd and microplastics frequently co-occur in agricultural soils, where microplastics can alter cadmium mobility, bioavailability, and transport pathways, potentially modifying metal toxicity and plant stress responses compared with single-pollutant exposure. We investigated the responses of the invasive Bidens pilosa and the native Solanum nigrum grown in monoculture and mixed culture under combined cadmium (Cd) and biodegradable microplastic (PLA) stress by integrating plant growth, photosynthetic performance, oxidative physiology, and rhizosphere biochemical processes. Combined Cd-MP exposure markedly reduced plant growth, chlorophyll content (SPAD), photosystem II efficiency (Fv/Fm), nitrogen accumulation, biomass production, and rhizosphere enzyme activities associated with carbon, nitrogen, and phosphorus cycling. However, B. pilosa maintained greater physiological stability under stress, characterized by higher antioxidant enzyme activities (SOD, CAT, POD), lower reactive oxygen species (H2O2, O2˙-) accumulation, and reduced lipid peroxidation (MDA), whereas S. nigrum exhibited stronger oxidative damage and functional impairment. Multivariate analyses further revealed that root antioxidant capacity was closely associated with rhizosphere microbial enzyme activity, suggesting a root-centered regulatory mechanism linking plant stress tolerance to soil functioning. Overall, the invasive species showed greater tolerance to combined contamination and maintained relatively higher rhizosphere functional activity than the native species, indicating that multi-pollutant stress may alter competitive interactions between invasive and native plants in contaminated environments.

Cadmium↗

Induction of a homeostatic circuit in lung tissue by microbial compounds.

TGFbeta presented and activated by integrin alphavbeta6 expressed on alveolar epithelial cells (AEC) continuously inhibits the functionality of alveolar macrophages (AM). Despite this inhibition, AM retain their ability to respond to inhaled microorganisms. Herein we describe a homeostatic circuit through which the effects of microbial products on macrophages transiently circumvent this inhibition by repressing alphavbeta6 expression on AEC. Subsequent production of matrix metalloproteinases by activated AM activates latent TGFbeta, reinduces alphavbeta6 expression, and thereby reinstates tonic inhibition of AM function. Our results reveal how AM can be activated while minimizing their potential to inflict collateral damage to the adjacent lung tissue and indicate that tissue-specific microenvironmental factors shape organ-specific defense strategies against microbial invasion.

Animals↗

Protozoan bacterivory and Escherichia coli survival in drinking water distribution systems.

The development of bacterial communities in drinking water distribution systems leads to a food chain which supports the growth of macroorganisms incompatible with water quality requirements and esthetics. Nevertheless, very few studies have examined the microbial communities in drinking water distribution systems and their trophic relationships. This study was done to quantify the microbial communities (especially bacteria and protozoa) and obtain direct and indirect proof of protozoan feeding on bacteria in two distribution networks, one of GAC water (i.e., water filtered on granular activated carbon) and the other of nanofiltered water. The nanofiltered water-supplied network contained no organisms larger than bacteria, either in the water phase (on average, 5 x 10(7) bacterial cells liter-1) or in the biofilm (on average, 7 x 10(6) bacterial cells cm-2). No protozoa were detected in the whole nanofiltered water-supplied network (water plus biofilm). In contrast, the GAC water-supplied network contained bacteria (on average, 3 x 10(8) cells liter-1 in water and 4 x 10(7) cells cm-2 in biofilm) and protozoa (on average, 10(5) cells liter-1 in water and 10(3) cells cm-2 in biofilm). The water contained mostly flagellates (93%), ciliates (1.8%), thecamoebae (1.6%), and naked amoebae (1.1%). The biofilm had only ciliates (52%) and thecamoebae (48%). Only the ciliates at the solid-liquid interface of the GAC water-supplied network had a measurable grazing activity in laboratory test (estimated at 2 bacteria per ciliate per h). Protozoan ingestion of bacteria was indirectly shown by adding Escherichia coli to the experimental distribution systems. Unexpectedly, E. coli was lost from the GAC water-supplied network more rapidly than from the nanofiltered water-supplied network, perhaps because of the grazing activity of protozoa in GAC water but not in nanofiltered water. Thus, the GAC water-supplied network contained a functional ecosystem with well-established and structured microbial communities, while the nanofiltered water-supplied system did not. The presence of protozoa in drinking water distribution systems must not be neglected because these populations may regulate the autochthonous and allochthonous bacterial populations.

Animals↗

Role of hydraulic retention time and granular medium in microbial removal in tertiary treatment reed beds.

The main objective of this paper is to evaluate the role of hydraulic retention time (HRT) and granular medium in faecal coliform (FC) and somatic coliphage (SC) removal in tertiary reed beds. Experiments were carried out in a pilot plant with four parallel reed beds (horizontal subsurface flow constructed wetlands), each one containing a different type of granular medium. This pilot plant is located in a wastewater treatment plant in Montcada i Reixac, near Barcelona, in northeastern Spain. The microbial inactivation ratios obtained in the different beds are compared as a function of three selected HRTs. Secondary effluent from the wastewater treatment plant was used as the influent of the pilot system. The microbial inactivation ratio ranged between 0.1 and 2.7 log-units for FC and from 0.5 to 1.7 log-units for SC in beds with coarser granular material (5-25mm), while it ranged between 0.7 and 3.4 log-units for FC and from 0.9 to 2.6 log-units for SC in the bed with finer material (2-13mm). HRT and granular medium are both key factors in microbial removal in the tertiary reed beds. The microbial inactivation ratio rises as the HRT increases until it reaches a saturation value (in general at an HRT of 3 days). The value of the microbial inactivation ratio at the saturation level depends on the granular medium contained in the bed. The specific surface area necessary to reach 2-3 log-units of FC and SC is approximately 3m(2)/person-equivalent.

Biodegradation, Environmental↗

Natural killer cells: emerging concepts in immunity to infection and implications for assessment of immunodeficiency.

PURPOSE OF REVIEW: As the molecular networks that connect innate and adaptive immunity are untangled, the prominence of natural killer (NK) cells in host defense continues to emerge. Herein we highlight recent findings pertaining to NK cell development, trafficking, and interactions with other innate and adaptive immune cells in the context of predicting how NK cells may be involved in a wider range of clinical immunodeficiency. RECENT FINDINGS: NK cells contribute vital roles in innate and adaptive immunity, especially in collaboration with dendritic cells (DC). Fascinating new details have been reported about cell surface integrins and receptors that regulate NK functions, as well as the cytokine/chemokine networks that provide for NK-DC interactions. Moreover, NK cells appear to play an important role in the attenuation or resolution of an immune response through either action against CD8 T cells or indirect control of certain DC. These findings shed important insights as to how NK cells and DC cooperate to control primary infections and shape the subsequent adaptive immune responses. SUMMARY: Natural killer cells are heterogeneous lymphocytes that provide an essential function in host defense. NK cells respond early to microbial assault and interact with other cells of the innate immune system, but they recognize and intercept pathogenic infections through highly specific mechanisms that are similar to T cells. Thus, NK cells are positioned as a cellular bridge between innate and adaptive immunity. It is imperative, then, to include a careful assessment of NK cell populations and functions in most cases of suspected immunodeficiency.

Animals↗

Synthesis and anti-microbial activities of some pyridinium salts with alkoxymethyl hydrophobic group.

A novel class of functionalized cationic surfactant has been obtained. The work-up procedure of synthesis is very simple, the yield is high and the pyridinium salts with alkoxymethyl hydrophobic group are easily purified. All the salts examined showed anti-microbial activities. Some of them exhibited strong activity and wide anti-bacterial spectra similar to the activity of benzalkonium chloride. The relationship between chemical structure and anti-microbial activity was analysed by the QSAR method.

Anti-Bacterial Agents↗

Probiotic-derived extracellular vesicles as food-based nanocarriers: Mechanisms, functional applications, and future perspectives in food systems.

Probiotic-derived extracellular vesicles (PDEVs) are a promising type of postbiotic nanoparticle derived by fermentation of probiotics, and have gained growing interest as a potential application in food science and nutrition. These are lipid bilayer vesicles of nanoscale, which are naturally released by probiotic cells and contain a wide variety of bioactive molecules, such as proteins, nucleic acids, and metabolites. Moreover, PDEVs are highly stable, biocompatible, and can be easily engineered to have surfaces with high functionality, which makes them good candidates in functional engineering. In contrast to traditional live probiotics, PDEVs overcome the difficulties of preserving microbial viability during processing and storage, thus providing superior safety, stability, and predictable biological performance. This is a systematic review of the various functions of PDEVs in food systems. We conclude on the processes through which PDEVs control intestinal barrier integrity, alter gut microbiota composition, and alter host immune responses, and their potential to enhance gut health when added to functional foods. In addition to their health-promoting effects, PDEVs have shown significant potential as natural antimicrobial agents to preserve food and as effective nanocarriers of hydrophobic bioactive compounds, including fucoxanthin, to improve their stability, bioavailability, and targeted delivery. Moreover, PDEVs can be used as new regulators of microbial fermentation. However, it should be noted that a lot of the evidence that is available is still preliminary and the effectiveness of these applications in real food-processing and storage conditions has not been fully proven. Although they have potential, there are a number of challenges that still hinder the widespread use of PDEVs in the food industry. These involve the creation of scalable and cost-effective production processes, batch-to-batch consistency, vesicle stability in a variety of food matrices, and regulatory and safety considerations. Other emerging engineering approaches, such as surface functionalization and cargo loading, are also discussed in this review and could further increase the specificity, functionality, and application versatility of PDEVs in food systems. Moving forward, the incorporation of PDEVs into the next generation functional foods, novel food preservation methods, and customized nutrition plans should be prioritized in future studies. Further developments in these fields can make PDEVs useful platforms at the interface of food microbiology, nanotechnology, and human health.

Probiotics↗

On the character and functions of sphingolipids.

Sphingolipids form a large group of membrane lipids showing a diversity of molecular species. Specific functions associated with the saccharide part of glycosphingolipids including co-receptor functions, cell homing phenomena, and attachment by microbes and microbial toxins may not be unique for sphingolipids. However, there are saccharides which appear only in ceramide-bound form and not in other glycoconjugates, and such glycolipids have often been selected as attachment sites by microbes. During the last few years convincing evidence has been presented in favor of ceramide and sphingosine being signaling molecules for various cell functions. The influence of sphingolipids (ceramide) on the properties of the membrane bilayer is still largely unknown. However, based on the structure of ceramide and some experimental evidence one may formulate its role in membrane stability and barrier properties determined by hydrogen bonding in the amide region of ceramide. Furthermore, a natural variation in the number of hydroxyl groups (of fatty acid and long-chain base) may be important for regulation of the potential hydrogen bonds.

Animals↗

Enhancement of drug susceptibility in Plasmodium falciparum in vitro and Plasmodium berghei in vivo by mixed-function oxidase inhibitors.

A number of compounds, as exemplified by verapamil and desipramine, have been shown to enhance the susceptibility of resistant malaria parasites to chloroquine. The mechanism by which these agents reverse resistance is still controversial but is though to involve alterations in drug transport causing an increase in steady-state drug concentrations. We have proposed that an alternative resistance mechanism may involve the metabolic deactivation of the drug in some resistant parasites via cytochrome P-450 mixed-function oxidases. If the hypothesis is true, it should be possible to alter drug susceptibility in malaria parasites by the use of agents known to inhibit or induce cytochrome P-450 activities. We have assessed the ability of known inhibitors of cytochrome P-450 enzymes (cimetidine, metyrapone, and alpha-naphthoflavone) to enhance chloroquine susceptibility in Plasmodium falciparum culture-adapted and wild-type isolates in vitro and P. berghei in vivo. In all three systems, the inhibitor cimetidine enhanced parasite susceptibility to chloroquine, and this increase in susceptibility was unrelated to changes in chloroquine steady-state concentrations in vitro or to alterations in host pharmacokinetics in vivo. Additionally, the cytochrome P-450 inducer phenobarbital produced slight decreases in P. falciparum drug susceptibility in vitro. We have compared the ability of the cytochrome P-450 inhibitors cimetidine and metyrapone to enhance drug susceptibility with that of verapamil by using wild-type malaria isolates obtained from Cameroon. Verapamil completely reversed resistance, i.e., to below the cutoff point of 70 nM, in all the resistant isolates. Cimetidine enhanced chloroquine susceptibility in 60% of the isolates and reduced 50% inhibitory concentrations by at least 43% in all the resistant isolates. The compounds tested had little or no effect on the 50% inhibitory concentrations for the susceptible isolates. The data support a possible role for detoxification in chloroquine resistance, and even in the absence of such a process we have observed apparent chemosensitization by agents whose common biological feature is the inhibition of cytochrome P-450 enzymes. Additionally, sensitization has been observed in wild-type isolates of P. falciparum obtained form immune residents of an area of endemicity as well as culture-adapted parasites.

Adolescent↗

Successful treatment of a patient with recurrent furunculosis by vitamin C: improvement of clinical course and of impaired neutrophil functions.

BACKGROUND: Neutrophils play a critical role in host defense against a variety of microbial pathogens. There is much information to suggest a role for vitamin C in the physiology of neutrophils. Thus, the effects of vitamin C treatment were studied in a patient with a history of recurrent furunculosis who showed altered neutrophil functions. METHODS: Superoxide generation was measured by cytochrome C reduction. Phagocytosis of opsonized zymosan by neutrophils and chemotaxis on agarose plates were determined. RESULTS: Chemotaxis, phagocytosis, and superoxide generation of the patient's neutrophils were significantly lower than those of the matched control. Treatment with vitamin C (500 mg/day) for 30 days caused a dramatic clinical response and a significant improvement of all three neutrophil functions to values similar to those of the controls. CONCLUSIONS: We suggest that the patient described here had a temporary defect in neutrophil functions. The treatment with vitamin C probably prevented neutrophil oxidation, thus contributing to recovery of neutrophil function and arrest of furunculosis.

Adult↗

Saliva and salivary gland alterations in HIV infection: a review.

HIV-1 can be recovered sporadically from whole saliva and individual salivary gland secretions, but the concentration of virus, when present, is low. Saliva possesses antiviral activity, and although virus may be found in the mouth, the mouth is not a transmission route of HIV-1. After HIV-1 infection, salivary gland function is altered. Flow rates may decrease, and certain electrolytes and anti-microbial proteins are elevated. A proportion of patients develop severe salivary gland disease. Most patients, however, maintain adequate salivary gland function and retain ability to produce antimicrobial proteins in saliva.

Antiviral Agents↗

Ecosystems: development, functions and consequences of disturbances, with special reference to the oral cavity.

Some general rules for the development and maintenance of microbial ecosystems are outlined. Studies on germ-free animals have given valuable baselines concerning structures and functions in the host per se. The oral cavity represents several consortia of micro-organisms, governed by factors deriving from the host, the diet and/or the micro-organisms. Alterations in these factors, as well as intake of antibiotics, etc., may give disturbances, which can be analyzed according to general guidelines.

Animals↗

Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization.

The BLOLOG redox technology based on tetrazolium dye reduction as an indicator of sole-carbon-source utilization was evaluated as a rapid, community-level method to characterize and classify heterotrophic microbial communities. Direct incubation of whole environmental samples (aquatic, soil, and rhizosphere) in BIOLOG plates containing 95 separate carbon sources produced community-dependent patterns of sole-carbon-source utilization. Principal-component analysis of color responses quantified from digitized images of plates revealed distinctive patterns among microbial habitats and spatial gradients within soil and estuarine sites. Correlation of the original carbon source variables to the principal components gives a functional basis to distinctions among communities. Intensive spatial and temporal analysis of microbial communities with this technique can produce ecologically relevant classifications of heterotrophic microbial communities.

Journal Article↗