Related papers: Ecology theory disentangles microbial dichotomies
Quantitative predictions about the processes that promote species coexistence are a subject of active research in ecology. In particular, competitive interactions are known to shape and maintain ecological communities, and situations where…
Biodiversity widely observed in ecological systems is attributed to the dynamical balance among the competing species. The time-varying populations of the interacting species are often captured rather well by a set of deterministic…
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
We study a model ecosystem by means of dynamical techniques from disordered systems theory. The model describes a set of species subject to competitive interactions through a background of resources, which they feed upon. Additionally…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling frameworks. A long-standing hope of theoretical ecology is that…
Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…
How multicellular life forms evolved out from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations has shown that selection for…
In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…
The central goal of a dynamical theory of evolution is to abstract the mean evolutionary trajectory in the trait space by considering ecological processes at the level of the individual. In this work, we develop such a theory for a new…
This review focuses on microbiomes associated with residues within the context of other microbial habitats in cereal-producing agroecosystems such as phyllosphere or rhizosphere. We connect residue microbiome with the survival of…
Monod's law is a widely accepted phenomenology for bacterial growth. Since it has the same functional form as the Michaelis--Menten equation for enzyme kinetics, cell growth is often considered to be locally constrained by a single…
We develop and apply a learning framework for parameter estimation in initial value problems that are assessed only indirectly via aggregate data such as sample means and/or standard deviations. Our comprehensive framework follows Bayesian…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…
We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space making statistical…