Related papers: Friend or Foe
We present a mathematical model based on a system of partial differential equations (PDEs) with cross-diffusion and reaction terms to describe ecological interactions between multiple bacterial species and substrates within microaggregates,…
Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
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…
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…
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…
The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…
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.…
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…
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…
We present a proof-of-concept of a model comparison approach for analyzing spatio-temporal observations of interacting populations. Our model variants are a collection of structurally similar Bayesian networks. Their distinct Noisy-Or…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
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…
An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…
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…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these…