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Concepts and tools for predictive modeling of microbial dynamics.

Description of microbial cell (population) behavior as influenced by dynamically changing environmental conditions intrinsically needs dynamic mathematical models. In the past, major effort has been put into the modeling of microbial growth and inactivation within a constant environment (static models). In the early 1990s, differential equation models (dynamic models) were introduced in the field of predictive microbiology. Here, we present a general dynamic model-building concept describing microbial evolution under dynamic conditions. Starting from an elementary model building block, the model structure can be gradually complexified to incorporate increasing numbers of influencing factors. Based on two case studies, the fundamentals of both macroscopic (population) and microscopic (individual) modeling approaches are revisited. These illustrations deal with the modeling of (i) microbial lag under variable temperature conditions and (ii) interspecies microbial interactions mediated by lactic acid production (product inhibition). Current and future research trends should address the need for (i) more specific measurements at the cell and/or population level, (ii) measurements under dynamic conditions, and (iii) more comprehensive (mechanistically inspired) model structures. In the context of quantitative microbial risk assessment, complexity of the mathematical model must be kept under control. An important challenge for the future is determination of a satisfactory trade-off between predictive power and manageability of predictive microbiology models.

Bacteria↗

The pathogenesis of inflammatory bowel disease: translational implications for clinicians.

Research in the pathogenesis of inflammatory bowel disease (IBD) has dramatically broadened our understanding of these complex disorders. These clinical manifestations result from a dysregulated immune response in the presence of luminal bacteria. Recent identification of mutations in the NOD2 gene, a protein involved in the sensing of bacteria, offers genetic support for the model of perturbed host-microbial interactions in Crohn's disease. Several immunologic pathways have been identified that play a role in maintaining gut immune homeostasis. Abnormal expression of proinflammatory, deleterious cytokines such as tumor necrosis factor-a and interferon-g results in direct and indirect tissue damage. The search for specific causative microbial agents in IBD continues to be intense. This paper describes the advances in our understanding of IBD pathogenesis, with an emphasis on how this information is translated into patient care. The next stage of research will take advantage of such molecular biologic techniques to identify new pathogenetic mechanisms and targets for therapy tailored to individual patients.

Animals↗

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model.

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs-organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients-autotrophs-herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

Algorithms↗

Interactions of Bacillus licheniformis ATCC 10716 and normal flora of human skin.

To determine whether antibiotic production might be ecologically advantageous in the survival of Bacillus species on human skin, we applied spores of a bacitracin-producing strain of Bacillus licheniformis (ATCC 10716) to the forearms of 11 volunteers. Three additional strains of B. licheniformis which did not synthesize antibiotics, including a mutant of ATCC 10716, were used in subsequent control trials. Samples of flora were taken from inoculated and control (opposite forearm) sites during the colonization period, generally 3 weeks. Although population densities were unaltered, changes in the carriage, composition, and bacitracin sensitivity of resident flora were related with the presence of ATCC 10716 only, which suggests that microbial interactions are important in bacillus colonization and in maintenance of normal flora. Interactions were examined in vitro by comparing growth curves of representative skin bacteria, including isolates of Staphylococcus epidermidis, Staphylococcus saprophyticus, Micrococcus luteus, and a large-colony diphtheroid, grown individually, in mixed culture with each other, and together in presence of each test strain of B. licheniformis. We observed some diminution of growth of M. luteus and the diphtheroid in the first mixed culture, and the diphtheroid was completely retarded in common culture with ATCC 10716. Lesser antibiotic effects were seen on the cocci, whose rank of sensitivity was similar to that in vivo. The growth of the diphtheroid was enhanced in mixed culture with those strains of bacilli which lack antibiotic activity.

Adult↗

Anaerobic stimulated mixed culture system.

A compartmented, autoclavable culture vessel has been developed for the purpose of studying interactive associations of microorganisms which are essential to the anaerobic decomposition of sewage sludge. The unit employs sterile filter membranes to subdivide the interior culture space into individual compartments. Bacteria cultured in one compartment are denied access to adjacent compartments, even though rapid interchange of nutrients and metabolic waste products occurs throughout the unit. The obligate methane-forming anaerobe, Methanobacillus omelianskii has been successfully grown and concentrated in this system by use of a synthetic medium reduced with sodium sulfide. The feasibility of using this system to study microbial interactions was, in part, demonstrated by growing M. omelianskii in a thoroughly aerated medium which had been biologically reduced by Escherichia coli prior to inoculation with the anaerobe. Under this condition of simulated mixed culture growth, the cell yield of both microorganisms, as well as specific metabolic activities ascribed to each organism, was readily monitored.

Bacteriological Techniques↗

Carcinoembryonic antigen (CEA) and CEA-related cell adhesion molecule 1 (CEACAM1), apically expressed on human colonic M cells, are potential receptors for microbial adhesion.

In the human gut mucosa, specialized M cells deliver intact foreign macromolecules and commensal bacteria from the lumen to organized mucosal lymphoid tissues triggering immune responses. M cells are also major sites of adhesion and invasion for enteric pathogens. The molecular features of M cell apical surfaces that promote microbial normal attachment are still largely unknown. We have demonstrated previously that in the human colonic epithelium, carcinoembryonic antigen (CEA) and CEA-related cell adhesion molecule 1 (CEACAM1) are integral components of the apical glycocalyx which participate in epithelial-microbial interactions. In this study, based on the reactivity of specific monoclonal antibodies and on immunoelectron microscopy, we show that M cells of human colonic solitary lymphoid follicles express CEA and CEACAM1 on the apical surface. Recently these highly glycosylated molecules have been characterized as protein receptors for different bacteria. This leads us to propose a role for CEA and CEACAM1 in the adherence of enteric bacteria to the apical membrane of colonic M cells. We also hypothesize that, unlike colonic enterocytes, M cells lack the defense mechanism that eliminates CEA and CEACAM1 upon microbial binding and which is based on vesiculation of microvillus plasma membrane.

Antigens, CD↗

Comparative efficacy of ceftriaxone in experimental infections involving Bacteroides fragilis and Escherichia coli.

The in vivo activity of ceftriaxone was examined in an experimentally induced subcutaneous infection involving Bacteroides fragilis and Escherichia coli. Mice were challenged with 1 of 10 strains of B. fragilis or E. coli, or a dual combination of the two species. The efficacy was measured by a reduction in the count of viable organisms when antimicrobial treatment was initiated 1 h after challenge and continued for 5 days. Ceftriaxone exhibited impressive activity against E. coli but showed poor in vivo activity versus B. fragilis. The antimicrobial activity of ceftriaxone was influenced by the microbial interaction in our dual-isolate model. Pharmacokinetic studies showed that ceftriaxone penetrated into abscesses and achieved peak levels of about 40% of the peak serum levels. However, in abscesses infected with B. fragilis nearly all biological activity of ceftriaxone was lost.

Animals↗

Detection of surface-associated and intracellular glycoconjugates and glycoproteins in Neospora caninum tachyzoites.

The surface-associated molecules of the invasive stages of apicomplexan parasites such as Neospora caninum and Toxoplasma gondii are most likely crucially involved in mediating the interaction between the parasite and its host cell. In N. caninum, several antigens have recently been identified which could participate in host cell adhesion and/or invasion. These are antigens which are either constitutively expressed on the outer plasma membrane, or antigens which are only transiently localised on the surface as they are expulsed from the secretory vesicles either prior, or after host cell invasion. Some of these proteins have been characterised at the molecular level, and it has been shown that they are, with respect to protein sequences, closely related to homologous counterparts in T. gondii. Nevertheless, there is only a low degree of cross-antigenicity between the two species. In microbial interactions it has been shown that carbohydrates could also play a crucial role in host cell recognition and immunological host parasite interactions. In this study we present data which strongly suggest that the surface of N. caninum tachyzoites is glycosylated. In SDS-PAGE, glycoproteins comigrated largely with glycosylphosphatidylinositol-anchored proteins which were identified using in vivo [3H]ethanolamine labelling followed by autoradiography. The lectin Con A reacted strongly with the surface of these parasites, binding of which is indicative for the presence of N-glycans. Additional surface binding was observed, although only in a subpopulation of all tachyzoites, for wheat germ agglutinin and Jacalin. Intracellular binding sites for Con A were mainly associated with the parasite dense granules. By lectin labelling of Western blots of N. caninum protein extracts, glycoproteins were identified which reacted specifically with the lectins Con A, wheat germ agglutinin, Jacalin and soy bean agglutinin.

Animals↗

Predictive modeling of mixed microbial populations in food products: evaluation of two-species models.

Predictive microbiology is an emerging research domain in which biological and mathematical knowledge is combined to develop models for the prediction of microbial proliferation in foods. To provide accurate predictions, models must incorporate essential factors controlling microbial growth. Current models often take into account environmental conditions such as temperature, pH and water activity. One factor which has not been included in many models is the influence of a background microflora, which brings along microbial interactions. The present research explores the potential of autonomous continuous-time/two-species models to describe mixed population growth in foods. A set of four basic requirements, which a model should satisfy to be of use for this particular application, is specified. Further, a number of models originating from research fields outside predictive microbiology, but all dealing with interacting species, are evaluated with respect to the formulated model requirements by means of both graphical and analytical techniques. The analysis reveals that of the investigated models, the classical Lotka-Volterra model for two species in competition and several extensions of this model fulfill three of the four requirements. However, none of the models is in agreement with all requirements. Moreover, from the analytical approach, it is clear that the development of a model satisfying all requirements, within a framework of two autonomous differential equations, is not straightforward. Therefore, a novel prototype model structure, extending the Lotka-Volterra model with two differential equations describing two additional state variables, is proposed to describe mixed microbial populations in foods.

Evaluation Studies as Topic↗

Biogeochemistry of dihydrogen (H2).

Hydrogen has had an important and evolving role in Earth's geo- and biogeochemistry, from prebiotic to modern times. On the earliest Earth, abiotic sources of H2 were likely stronger than in the present. Volcanic out-gassing and hydrothermal circulation probably occurred at several times the modern rate, due to presumably higher heat flux. The H2 component of volcanic emissions was likely buffered close to the modern value by an approximately constant mantle oxidation state since 3.9 billion years ago, and may have been higher before that, if the early mantle was more reducing. The predominantly ultramafic character of the early, undifferentiated crust could have led to increased serpentinization and release of H2 by hydrothermal circulation, as in modern ultramafic-hosted vents. At the same time, the reactive atmospheric sink for H2 was likely weaker. Collectively, these factors suggest that steady state levels of H2 in the prebiotic atmosphere were 3-4 orders of magnitude higher than at present, and possibly higher still during transient periods following the delivery of Fe and Ni by large impact events. These elevated levels had direct or indirect impacts on the redox state of the atmosphere, the radiation budget, the production of aerosol hazes, and the genesis of biochemical precursor compounds. The early abiotic cycling of H2 helped to establish the environmental and chemical context for the origins of life on Earth. The potential for H2 to serve as a source of energy and reducing power, and to afford a means of energy storage by the establishment of proton gradients, could have afforded it a highly utilitarian role in the earliest metabolic chemistry. Some origin of life theories suggest the involvement of H2 in the first energy-generating metabolism, and the widespread and deeply-branching nature of H2-utilization in the modern tree of life suggests that it was at least a very early biochemical innovation. The abiotic production of H2 via several mechanisms of water-rock interaction could have supported an early chemosynthetic biosphere. Such processes offer the continued potential for a deep, rock-hosted biosphere on Earth or other bodies in the solar system. The continued evolution of metabolic and community-level versatility among microbes led to an expanded ability to completely exploit the energy available in complex organic matter. Under the anoxic conditions that prevailed on the early Earth, this was accomplished through the linked and sequential action of several metabolic classes of organisms. By transporting electrons between cells, H2 provides a means of linking the activities of these organisms into a highly functional and interactive network. At the same time, H2 concentrations exert a powerful thermodynamic control on many aspects of metabolism and biogeochemical function in these systems. Anaerobic communities based on the consumption of organic matter continue to play an important role in global biogeochemistry even into the present day. As the principal arbiters of chemistry in most aquatic sediments and animal digestive systems, these microbes affect the redox and trace-gas chemistry of our oceans and atmosphere, and constitute the ultimate biological filter on material passing into the rock record. It is in such communities that the significance of H2 in mediating biogeochemical function is most strongly expressed. The advent of phototrophic metabolism added another layer of complexity to microbial communities, and to the role of H2 therein. Anoxygenic and oxygenic phototrophs retained and expanded on the utilization of H2 in metabolic processes. Both groups produce and consume H2 through a variety of mechanisms. In the natural world, phototrophic organisms are often closely juxtaposed with a variety of other metabolic types, through the formation of biofilms and microbial mats. In the few examples studied, phototrophs contribute an often swamping term to the H2 economy of these communities, with important implications for their overall function-including regulation of the redox state of gaseous products, and direct release of large quantities of H2 to the environment. As one of the dominant sources of biological productivity for as much as 2 billion years of Earth's history, these communities have been among the most important agents of long-term global biogeochemical change. On the modern Earth, H2 is present at only trace levels in the atmosphere and oceans. Nonetheless, its function as an arbiter of microbial interactions and chemistry ensures an important role in biogeochemical cycling. The significance of H2 in a global sense may soon increase, as the search for alternative fuels casts attention on the clean-energy potential of hydrogen fuel cells. Already, H2 utilization plays an important role in all three phylogenetic domains of life. Humans may soon add an important new term to this economy. Considerable research is focused on the H2-producing capacities of phototrophic and other microorganisms as potential contributors in this regard. Regardless of source, the large scale utilization of H2 as an energy source could carry important consequences for biogeochemistry.

Anaerobiosis↗

[Pathogenesis of Helicobacter pylori infection].

Helicobacter pylori (H. pylori), a long term colonizer of human stomach is known to infect a half of mankind. Gastric and duodenal ulcer, gastric adenocarcinoma and MALT lymphoma develop in a subset of infected individuals. Pathogenesis of H. pylori infection is based on the long-term host to bacterial interaction and affected by the virulence factors of the bacterium, environmental and host factors (age, sex, blood type). Mucosal inflammation is the basic principle mechanism underlying the disease development in which tissue destruction may be initiated and maintained by both the bacterial toxins (CagA, VacA, LPS) and immune responses by the host. Immune evasion with bacterial modulation of host response affects the long-term host colonization. Colonization is also affected by urease and/or motility of the bacterium, presence of lipopolysaccharide (LPS) and various bacterial enzymes. Gastric mucosal atrophy and intestinal metaplasia can develop during the course of H. pylori infection predisposing to carcinogenesis. Host cytokine gene polymorphism would be the one explanation for host susceptibility to peptic ulcer or gastric cancer. Investigation into the pathogenesis of H. pylori related diseases could provide an answer to the impact of chronic host to microbial interaction resulting human diseases.

Gastrointestinal Diseases↗

Helicobacter pylori.

PURPOSE OF REVIEW: Helicobacter pylori is an important human pathogen, responsible for most peptic ulcer disease, gastritis and gastric malignancies. H. pylori has several unique features: it is highly adapted for gastric colonization, yet it produces clinical consequences in a small minority, its genome is known, and it is the only bacterium strongly associated with cancer. H. pylori is therefore of great interest to clinicians and researchers of many, often disparate, disciplines. We highlight recent advances in this fast changing field from many different areas. RECENT FINDINGS: The major contentious clinical issues relate to the synergistic gastrotoxic interactions of H. pylori with non-steroidal anti-inflammatory drugs, and a possible association of H. pylori with atherosclerotic events. Accumulating evidence implicates genetic variation in the inflammatory response to H. pylori in the etiology of the increased risk of gastric cancer after H. pylori infection. Studies of pathogenesis have been aided by increasingly sophisticated murine models. The effects in gastric epithelial cells of two of the major virulence factors (genes within the cag pathogenicity island and the vacuolating cytotoxin, VacA) of H. pylori illustrate the complex network of cellular reactions activated by H. pylori. The metabolism of H. pylori is dependent on the availability of hydrogen. SUMMARY: Basic science research into H. pylori continues to elucidate the mechanisms by which H. pylori infection causes disease. These findings have implications for the design of novel therapies and for improving clinical strategies to identify at-risk individuals. Many are also worthy of consideration for other epithelial-microbial interactions.

Animals↗

Altered host:pathogen interactions conferred by the Blau syndrome mutation of NOD2.

Blau syndrome (BS) is a rare familial granulomatous disease manifested by uveitis, arthritis and skin rash. BS has recently been found to be associated with a distinctive mutation in NOD2, which encodes an intracellular toll-like receptor. We have compared host cell interaction with bacterial challenge in U937 cells expressing wild type human NOD2 (NOD2(wt)), mutant NOD2 (NOD2(Blau)), or a vector control (VC). The cells were incubated with Salmonella typhimurium. Intracellular uptake was assessed by harvesting the cells at different time points following invasion and quantitating the CFU, recovered after gentamicin treatment to kill extracellular organisms. Expression of TNF-alpha, TLR2 and TLR4 was determined by semi-quantitative RT-PCR under resting conditions and after stimulation by bacteria. Invasion of target cells with S. typhimurium was diminished in the presence of NOD2(Blau). Expression of TNF-alpha mRNA was enhanced following bacterial invasion in all cell lines but NOD2(Blau) was associated with a more rapid decline in TNF-alpha expression. Kinetics of intracellular clearance of bacteria indicated a relative defect in NOD2(Blau) compared to controls. This clearance defect may be related to the lack of sustained TNF-alpha seen in the early stages. These events were not related to differential TLR2 or TLR4 expression since there were no significant differences seen between the cell lines after bacterial stimulation. Our findings indicate that the NOD2 mutation associated with this syndrome alters host:microbial interaction, and this may have relevance to triggering factors in the ocular and joint inflammation seen in BS.

Arthritis↗

Interactions between Streptomyces californicus and Stachybotrys chartarum can induce apoptosis and cell cycle arrest in mouse RAW264.7 macrophages.

Exposure to complex mixtures of bacteria and fungi in moisture-damaged buildings is a potential cause of inflammatory related symptoms among occupants. The present study assessed interactions between two characteristic moldy house microbes Streptomyces californicus and Stachybotrys chartarum. Differences in cytotoxic and inflammatory responses in mouse (RAW264.7) macrophages were studied after exposure to the spores of co-cultivated microbes, the mixture of separately cultivated spores, and the spores of either of these microbes cultivated alone. The RAW264.7 cells were exposed to six doses (1 x 10(4) to 3 x 10(6) spores/ml) for 24 h, and the time course of the induced responses was evaluated after 4, 8, 16, and 24 h of exposure (1 x 10(6) spores/ml). The cytotoxic potential of the spores was characterized by the MTT test, DNA content analysis, and enzyme assay for caspase-3 activity. The production of cytokines (IL-1beta, IL-6, IL-10, TNFalpha, and MIP2) was measured immunochemically and nitric oxide by the Griess method. Co-cultivation increased the ability of the spores to cause apoptosis by more than 4-fold and the proportion of RAW264.7 cells at the G2/M stage increased nearly 2-fold when compared to the response induced by the mixture of spores. In contrast, co-cultivation decreased significantly the ability of the spores to trigger the production of NO and IL-6 in RAW264.7 cells. In conclusion, these data suggest that co-culture of S. californicus and S. chartarum can result in microbial interactions that significantly potentiate the ability of the spores to cause apoptosis and cell cycle arrest in mammalian cells.

Animals↗

Concomitant induction of systemic resistance to Pseudomonas syringae pv. lachrymans in cucumber by Trichoderma asperellum (T-203) and accumulation of phytoalexins.

Most studies on the reduction of disease incidence in soil treated with Trichoderma asperellum have focused on microbial interactions rather than on plant responses. This study presents conclusive evidence for the induction of a systemic response against angular leaf spot of cucumber (Pseudomonas syringae pv. lachrymans) following application of T. asperellum to the root system. To ascertain that T. asperellum was the only microorganism present in the root milieu, plants were grown in an aseptic hydroponic growth system. Disease symptoms were reduced by as much as 80%, corresponding to a reduction of 2 orders of magnitude in bacterial cell densities in leaves of plants pretreated with T. asperellum. As revealed by electron microscopy, bacterial cell proliferation in these plants was halted. The protection afforded by the biocontrol agent was associated with the accumulation of mRNA of two defense genes: the phenylpropanoid pathway gene encoding phenylalanine ammonia lyase (PAL) and the lipoxygenase pathway gene encoding hydroxyperoxide lyase (HPL). This was further supported by the accumulation of secondary metabolites of a phenolic nature that showed an increase of up to sixfold in inhibition capacity of bacterial growth in vitro. The bulk of the antimicrobial activity was found in the acid-hydrolyzed extract containing the phenolics in their aglycone form. High-performance liquid chromatography analysis of phenolic compounds showed a marked change in their profile in the challenged, preelicited plants relative to that in challenged controls. The results suggest that similar to beneficial rhizobacteria, T. asperellum may activate separate metabolic pathways in cucumber that are involved in plant signaling and biosynthesis, eventually leading to the systemic accumulation of phytoalexins.

Cucumis sativus↗

The human intestinal microflora.

The major host defense mechanisms against bacterial overgrowth in the small bowel are the normal propulsive activity of the bowel itself and gastric acid secretion. Microbial interactions are a major factor in regulating the indigenous bacterial flora. Studies of the bacterial enzymes of the gut suggest that changes in diet may lead to marked changes in the colonic flora. Antibiotics affect the composition of the colonic microflora. The microflora also influence the degradation of mucin, the conversion of urobilin to urobilinogen, of cholesterol to coprostanol, and the production of short chain fatty acids. Current interests are focused on the bacterial flora of tropical sprue, the role of bacteria in colorectal cancer, and the involvement of intestinal microflora in the enterohepatic circulation of sex steroid hormones.

Animals↗

Respirometric activities of heterotrophic and nitrifying populations in aerobic granules developed at different substrate N/COD ratios.

Aerobic granules were successfully developed at substrate N/COD ratios ranging from 5/100 to 30/100 by weight. By measuring respective respirometric activities of heterotrophic, ammonia-oxidizing, and nitrite-oxidizing bacteria, it was found that the relative abundance of nitrifying bacteria over heterotrophs in aerobic granules was closely related to the substrate N/COD ratios. Results further showed that the populations of both ammonia and nitrite oxidizers were significantly enriched with the increase of the substrate N/COD ratio, while a decreasing trend of heterotrophic population was observed in the aerobic granules. These seem to indicate that high substrate N/COD ratio favors the selection of nitrifying bacteria in the aerobic granules, while the relative activity of nitrifying population against heterotrophic population evolved until a balance between two populations was reached in the aerobic granular sludge community. Moreover, cell elemental composition was correlated with the shift in microbial populations, e.g., the enriched nitrifying population in the aerobic granules resulted in a high cell nitrogen content normalized to cell carbon content. This study provides a good insight into microbial interaction in aerobic granules.

Aerobiosis↗

Liberation of amino acids by heterotrophic nitrogen fixing bacteria.

Large amounts of amino acids are produced by nitrogen-fixing bacteria such as Azotobacter, Azospirillum, Rhizobium, Mesorhizobium and Sinorhizobium when growing in culture media amended with different carbon and nitrogen sources. This kind of bacteria live in close association with plant roots enhanced plant growth mainly as a result of their ability to fix nitrogen, improving shoot and root development suppression of pathogenic bacteria and fungi, and increase of available P concentration. Also, it has been strongly evidenced that production of biologically substances such as amino acids by these rhizobacteria are involved in many of the processes that explain plant-grown promotion. This paper reviews literature concerning amino acids production by nitrogen-fixing bacteria. The role of amino acids in microbial interactions in the rhizosphere and establishment of plant bacterial association is also discussed.

Amino Acids↗