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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…
The intricate interplay between host organisms and their gut microbiota has catalyzed research into the microbiome's role in disease, shedding light on novel aspects of disease pathogenesis. However, the mechanisms through which the…
Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…
Microbial communities display extreme diversity. A variety of strains or species coexist even when limited by a single resource. It has been argued that metabolite secretion creates new niches and facilitates such diversity. Nonetheless, it…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
Microbes produce metabolic resources that are important for cell growth yet leak across membranes into the extracellular environment. Other microbes in the same environment can use these resources and adjust their own metabolic production…
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose…
A spacially extended model of the collective behavior of a large number of locally acting organisms is proposed in which organisms move probabilistically between local cells in space, but with weights dependent on local morphogenetic…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…
Multicellular collective migration is a ubiquitous strategy of cells to translocate spatially in diverse tissue environments to accomplish a wide variety of biological phenomena, viz. embryonic development, wound healing, and tumor…