No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Which bug bugs you more? Microbiome competition and toxin interference
Abstract
The last decade has seen a surge of interest in understanding the functional relationships between the elements that make up the diverse ecology of the gut microbiome. This ecological web includes bacteria, viruses, and microbes that enter, populate and leave living hosts. They affect metabolism and stimulate the immune system, directly or indirectly modulating most physiological functions.
Specific animal models are being explored in the context of their particular roles in this ecological web. For example, consider the importance of the insect gut microbiota as an invisible third faction in the chemical arms race that has given rise to a large portion of Earth's terrestrial diversity. Mathematical modeling has recently begun to play a role in our understanding of the functioning of the microbiome and how the microbiome is affected by the outside world.
In this paper, we present a mathematical model that describes the spatial dynamics of several competing bacterial populations along with a toxin that inhibits the growth of one of bacterial populations and is degraded by the other bacteria. The model consists of a system of four non-linear partial differential equations describing the interactions of the bacteria as they flow through the digestive tract. The model simulations and analysis give insight into possible mechanisms to explore in future laboratory experiments.
ResearchGate has not been able to resolve any citations for this publication.
Many microbial communities live in highly competitive surroundings, in which the fight for resources determines their survival and genetic persistence. Humans live in a close relationship with microbial communities, which includes the health- and disease-determining interactions with our microbiome. Accordingly, the understanding of microbial competitive activities are essential at physiological and pathophysiological levels. Here we provide a brief overview on microbial competition and discuss some of its roles and consequences that directly affect humans.
The foreign body reactions are commonly referred to the network of immune and inflammatory reactions of human or animals to foreign objects placed in tissues. They are basic biological processes, and are also highly relevant to bioengineering applications in implants, as fibrotic tissue formations surrounding medical implants have been found to substantially reduce the effectiveness of devices. Despite of intensive research on determining the mechanisms governing such complex responses, few mechanistic mathematical models have been developed to study such foreign body reactions. This study focuses on a kinetics-based predictive tool in order to analyze outcomes of multiple interactive complex reactions of various cells/proteins and biochemical processes and to understand transient behavior during the entire period (up to several months). A computational model in two spatial dimensions is constructed to investigate the time dynamics as well as spatial variation of foreign body reaction kinetics. The simulation results have been consistent with experimental data and the model can facilitate quantitative insights for study of foreign body reaction process in general.
The inhibition is an important phenomenon, which promotes the stable coexistence of species, in the chemostat. Here, we study a model of two microbial species in a chemostat competing for a single resource in the presence of an external lethal inhibitor. The model is a four-dimensional system of ordinary differential equations. We give a complete analysis for the existence and local stability of all steady states. We describe the bifurcation diagram which gives the behavior of the system with respect to the operating parameters represented by the dilution rate and the input concentrations of the substrate and the inhibitor. This diagram, is very useful to understand the model from both the mathematical and biological points of view.
Covering: up to 2018
Insects live in a world full of toxic compounds such as plant toxins and manmade pesticides. To overcome the effects of these toxins, herbivorous insects have evolved diverse, elaborate mechanisms of resistance, such as toxin avoidance, target-site alteration, and detoxification. These resistance mechanisms are thought to be encoded by the insects' own genomes, and in many cases, this holds true. However, recent omics analyses, in conjunction with classic culture-dependent analyses, have revealed that a number of insects possess specific gut microorganisms, some of which significantly contribute to resistance against phytotoxins and pesticides by degrading such chemical compounds. Here, we review recent advances in our understanding on the symbiont-mediated degradation of natural and artificial toxins, with a special emphasis on their underlying genetic basis, focus on the importance of environmental microbiota as a resource of toxin-degrading microorganisms, and discuss the ecological and evolutionary significance of these symbiotic associations.
Herbivory, defined as feeding on live plant tissues, is characteristic of highly successful and diverse groups of insects and represents an evolutionarily derived mode of feeding. Plants present various nutritional and defensive barriers against herbivory; nevertheless, insects have evolved a diverse array of mechanisms that enable them to feed and develop on live plant tissues. For decades, it has been suggested that insect-associated microbes may facilitate host plant use, and new molecular methodologies offer the possibility to elucidate such roles. Based on genomic data, specialized feeding on phloem and xylem sap is highly dependent on nutrient provisioning by intracellular symbionts, as exemplified by Buchnera in aphids, although it is unclear whether such symbionts play a substantive role in host plant specificity of their hosts. Microorganisms present in the gut or outside the insect body could provide more functions including digestion of plant polymers and detoxification of plant-produced toxins. However, the extent of such contributions to insect herbivory remains unclear. We propose that the potential functions of microbial symbionts in facilitating or restricting the use of host plants are constrained by their location (intracellular, gut or environmental), and by the fidelity of their associations with insect host lineages. Studies in the next decade, using molecular methods from environmental microbiology and genomics, will provide a more comprehensive picture of the role of microbial symbionts in insect herbivory.
A model of the chemostat with an external nutrient and an external inhibitor is considered. A preliminary analysis reduces the problem to a three-dimensional competitive system. The theory of monotone flows is applied to obtain several global results. Global results fail when questions of multiple limit cycles cannot be answered. An example of an attracting limit cycle is given. The chemostat with inhibitor can model competition between two populations of microorganisms, where one strain is resistant to an antibiotic or competition in detoxification, a system where one strain can take up the pollutant while the other is inhibited by it.
The authors investigate the effects of random motility on the ability of a microbial population to survive in pure culture and to be a good competitor for scarce nutrient in mixed culture in a flow reactor model consisting of a nonlinear parabolic system of partial differential equations. For pure culture (*a single population), a sharp condition is derived which distinguishes between the two outcomes: (1) washout of the population from the reactor or (2) persistence of the population and the existence of a unique single-population steady state. The simulations suggest that this steady state is globally attracting. For the case of two populations competing for scarce nutrient, they obtain sufficient conditions for the uniform persistence of the two populations, for the existence of a coexistence steady state, and for the ability of one population to competitively exclude a rival. Extensive simulations are reported which suggest that (1) all solutions approach some steady state solution, (2) all possible outcomes exhibited by the classical competitive Lotka-Volterra ODE model can occur in the model, and (3) the outcome of competition between two bacterial strains can depend rather subtly on their respective random motility coefficients.
We show that weakLpdissipativity implies strongL∞dissipativity and therefore implies the existence of global attractors for a general class of reaction–diffusion systems. This generalizes the results of Alikakos and Rothe. The results on positive steady states (especially for systems of three equations) in our earlier work (J. Differential Equations130(1996), 59–91) are improved.
Presented is a chemostat model in which one microbial population excretes a poison that increases the mortality of another, with toxin production increasing as the growth rate of the toxic species decreases. The model is intended to explore the role of allelopathy in blooms of harmful algae, such as red tide (Karenia brevis) and golden algae (Prymnesium parvum). This study introduces the model and its biological basis, and proceeds to the analysis of its asymptotic states. All theoretical results are supported by a set of numerical simulations. A discussion of biological conclusions and similarities to other mathematical models is also presented.
There are bacteria that can form strong biofilms in porous media. These biofilms can be used as biobarriers to restrict the flow of pollutants. For certain contaminants, a second species of bacteria that can actually react with the contaminants can be added to the biobarrier to actually degrade the pollutants. We propose some mathematical models for the formation of these reacting biobarriers under different hypotheses, and numerically solve the resulting equations for the flow, transport and reactions. Qualitative comparisons with some experimental results are also given.
The dynamics of pure and simple competition between two microbial species are examined for the case of interaction arising in a distributed and nonstagnant environment. The environment is modeled as a tubular reactor. It is shown that for relatively small values of the dispersion coefficient (i.e., for small, but nonzero, backmixing of the medium), the two competing populations can coexist in a stable steady state. It has been assumed that the species grow uninhibited and that if there are maintenance requirements they are satisfied from endogenous sources. From numerical studies it has been found that a necessary condition for coexistence is that the net specific growth rate curves of the two competitors cross each other at a positive value of the concentration of the rate-limiting substrate. The model equations have been numerically solved by using the methods of orthogonal and spline collocation.
We present a continuous time model of the dynamics of two species competing for a single limiting resource in the presence of a substance that inhibits the growth of one of the species. Resource and inhibitor are both derived from external sources. These inputs, and all other model parameters, are assumed to be constant in space and time. There exist conditions that permit the stable coexistence of the competitors, provided that the sensitive species is more efficient in exploiting the limiting resource, and the resistant species removes the inhibitor from the environment. There exists a subset of these conditions wherein the sensitive species can become established if and only if the resistant species is already established. If the resistant species does not remove the inhibitor from the environment, then coexistence of sensitive and resistant species is structurally unstable. If the resistant species produces the inhibitor, then coexistence is dynamically unstable. We review several studies of bacterial competition in the presence of antibiotics that support these conclusions.
The study considers two organisms competing for a nutrient in an open system in the presence of an inhibitor (or toxicant). The inhibitor is input at a constant rate and is lethal to one competitor while being taken up by the other without harm. This is in contrast to previous studies, where the inhibitor decreases the reproductive rate of one of the organisms. The mathematical result of the lethal effect, modeled by a mass action term, is that the system cannot be reduced to a monotone dynamical system of one order lower as is common with chemostat-like problems. The model is described by four non-linear, ordinary differential equations and we seek to describe the asymptotic behavior as a function of the parameters of the system. Several global exclusion results are presented with mathematical proofs. However, in the case of coexistence, oscillatory behavior is possible and the study proceeds with numerical examples. The model is relevant to bioremediation problems in nature and to laboratory bio-reactors.
Mathematical models of the effect of inhibitors on microbial competition are surveyed. The term inhibitor is used in a broad sense and includes toxins, contaminants, allelopathic agents, etc. This includes both detoxification where the inhibitor is viewed as a pollutant and control where the inhibitor is viewed as an aid to controlling a bioreactor. The inhibitor may be supplied externally or may be created as an anti-competitor toxin. This includes plasmid-bearing, plasmid-free competition. The literature is spread across journals in different disciplines and with different notation. The survey attempts to present the mathematical models and the results of the corresponding analysis within a common framework and notation. Detailed mathematical proofs are not given but the methods of proof are indicated, references cited, and the results presented in tables. Open problems are indicated where there is a gap in the theory.
Gaussian elimination with pivoting for multidiagonal systems
- C Christov