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Register a new userMetabolite mediated modeling of microbial community dynamics captures emergent behavior more effectively than species-species modeling
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Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We seek a modeling strategy that can capture emergent behavior when built from sets of universal individual interactions. Our investigation reveals that species-metabolite interaction modeling is better able to capture emergent behavior in community composition dynamics than direct species-species modeling. Using publicly available data, we examine the ability of species-species models and species-metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species-species interaction models and quadratic species-metabolite interaction models, and conclude that only species-metabolite models have the necessary complexity to to explain a wide variety of interdependent growth outcomes. We also show that general species-species interaction models cannot match patterns observed in community growth dynamics, whereas species-metabolite models can. We conclude that species-metabolite modeling will be important in the development of accurate, clinically useful models of microbial communities.
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In this paper we present a discrete dynamical population modeling of invasive species, with reference to the swamp crayfish Procambarus clarkii. Since this species can cause environmental damage of various kinds, it is necessary to evaluate its expected in not yet infested areas. A structured discrete model is built, taking into account all biological information we were able to find, including the environmental variability implemented by means of stochastic parameters (coefficients of fertility, death, etc.). This model is based on a structure with 7 age classes, i.e. a Leslie mathematical population modeling type and it is calibrated with laboratory data provided by the Department of Evolutionary Biology (DEB) of Florence (Italy). The model presents many interesting aspects: the population has a high initial growth, then it stabilizes similarly to the logistic growth, but then it exhibits oscillations (a kind of limit-cycle attractor in the phase plane). The sensitivity analysis shows a good resilience of the model and, for low values of reproductive female fraction, the fluctuations may eventually lead to the extinction of the species: this fact might be exploited as a controlling factor. Moreover, the probability of extinction is valuated with an inverse Gaussian that indicates a high resilience of the species, confirmed by experimental data and field observation: this species has diffused in Italy since 1989 and it has shown a natural tendency to grow. Finally, the spatial mobility is introduced in the model, simulating the movement of the crayfishes in a virtual lake of elliptical form by means of simple cinematic rules encouraging the movement towards the banks of the catchment (as it happens in reality) while a random walk is imposed when the banks are reached.
Niche and neutral theory are two prevailing, yet much debated, ideas in ecology proposed to explain the patterns of biodiversity. Whereas niche theory emphasizes selective differences between species and interspecific interactions in shaping the community, neutral theory supposes functional equivalence between species and points to stochasticity as the primary driver of ecological dynamics. In this work, we draw a bridge between these two opposing theories. Starting from a Lotka-Volterra (LV) model with demographic noise and random symmetric interactions, we analytically derive the stationary population statistics and species abundance distribution (SAD). Using these results, we demonstrate that the model can exhibit three classes of SADs commonly found in niche and neutral theories and found conditions that allow an ecosystem to transition between these various regimes. Thus, we reconcile how neutral-like statistics may arise from a diverse community with niche differentiation.
Population dynamics of a competitive two-species system under the influence of random events are analyzed and expressions for the steady-state population mean, fluctuations, and cross-correlation of the two species are presented. It is shown that random events cause the population mean of each specie to make smooth transition from far above to far below of its growth rate threshold. At the same time, the population mean of the weaker specie never reaches the extinction point. It is also shown that, as a result of competition, the relative population fluctuations do not die out as the growth rates of both species are raised far above their respective thresholds. This behavior is most remarkable at the maximum competition point where the weaker species population statistics becomes completely chaotic regardless of how far its growth rate in raised.
Cyclic dominance is frequently believed to be a mechanism that maintains diversity of competing species. But this delicate balance could also be fragile if some of the members is weakened because an extinction of a species will involve the annihilation of its predator hence leaving only a single species alive. To check this expectation we here introduce a fourth species which chases exclusively a single member of the basic model composed by three cyclically dominant species. Interestingly, the coexistence is not necessarily broken and we have detected three consecutive phase transitions as we vary only the invasion strength of the fourth pestilent species. The resulting phases are analyzed by different techniques including the study of the Hamming distance density profiles. Some of our observations strengthen previous findings about cyclically dominant system, but they also offer new revelations and counter-intuitive phenomenon, like supporting pestilent species may result in its extinction, hence enriching our understanding about these very simple but still surprisingly complex systems.
The competitive exclusion principle asserts that coexisting species must occupy distinct ecological niches (i.e. the number of surviving species can not exceed the number of resources). An open question is to understand if and how different resource dynamics affect this bound. Here, we analyze a generalized consumer resource model with externally supplied resources and show that -- in contrast to self-renewing resources -- species can occupy only half of all available environmental niches. This motivates us to construct a new schema for classifying ecosystems based on species packing properties.
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