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Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact not only with each other but indirectly through environmental effects, however…
This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge…
Our view of the microbial world and its impact on human health is changing radically with the ability to sequence uncultured or unculturable microbes sampled directly from their habitats, ability made possible by fast and cheap next…
Certain invasive plants may rely on interference mechanisms (allelopathy, e.g.) to gain competitive superiority over native species. But expending resources on interference presumably exacts a cost in another life-history trait, so that the…
Metapopulation models have been instrumental in demonstrating the ecological impact of landscape structure on the survival of a focal species in complex environments. However, extensions to multiple species with arbitrary dispersal networks…
Microbes thrive in diverse porous environments -- from soil and riverbeds to human lungs and cancer tissues -- spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal…
Microbial communities routinely have several possible species compositions or community states observed for the same environmental parameters. Changes in these parameters can trigger abrupt and persistent transitions (regime shifts) between…
The colonization of Mars presents extraordinary challenges, including radiation exposure, low atmospheric pressure, and toxic regolith. Recent advancements in synthetic biology and genetic engineering offer unprecedented opportunities to…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
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,…
Persistence is an important characteristic of many complex systems in nature, related to how long the system remains at a certain state before changing to a different one. The study of complex systems' persistence involves different…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
Cancer cells can be described as an invasive species that is able to establish itself in a new environment. The concept of niche construction can be utilized to describe the process by which cancer cells terraform their environment, thereby…
While fields like Artificial Life have made huge strides in quantifying the mechanisms that distinguish living systems from non-living ones, particular mechanisms remain difficult to reproduce in silico. Known as open-endedness, we've been…
The role of species interactions in controlling the interplay between the stability of an ecosystem and its biodiversity is still not well understood. The ability of ecological communities to recover after a small perturbation of the…
Spatial structure and species interactions jointly shape the dynamics and biodiversity of ecological systems, yet most theoretical models either neglect spatial heterogeneity or sacrifice analytical tractability. Here, we provide a unified…
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 intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can…