Related papers: Quantification of metabolic niche occupancy dynami…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource…
The human niche represents the intersection of biological, ecological, cultural, and technological processes that have co-evolved to shape human adaptation and societal complexity. This paper explores the human niche through the lens of…
The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
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…
From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to…
Nutrient limitation is one of the most common triggers of antibiotic tolerance and persistence. Here, we present two microfluidic setups to study how spatial and temporal variation in nutrient availability lead to increased survival of…
The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of…
Bacteria commonly live in structured communities that affect human health and influence ecological systems. Heterogeneous populations, such as motile and non-motile populations, often coexist in bacteria communities. Motile subpopulations…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…