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Biofilms in porous media critically influence hydraulic properties in environmental and engineered systems. However, a mechanistic understanding of how microbial life controls permeability remains elusive. By combining microfluidics,…

Biofilms inhabit a range of environments, such as dental plaques or soil micropores, often characterized by intricate, non-even surfaces. However, the impact of surface irregularities on the population dynamics of biofilms remains elusive…

We study the growth of a population of bacteria in a dynamical hostile environment corresponding to the immune system of the colonised organism. The immune cells evolve as subcritical open clusters of oriented percolation and are…

Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance in a bacterial population. We consider a minimal model of…

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…

Certain defense mechanisms of phages against the immune system of their bacterial host rely on cooperation of phages. Motivated by this example we analyse invasion probabilities of cooperative parasites in host populations that are…

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…

Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here we review some of the known aspects that modulate phage-bacteria interaction in a way…

Motile cells often explore natural environments characterized by a high degree of structural complexity. Moreover cell motility is also intrinsically noisy due to spontaneous random reorientation and speed fluctuations. This interplay of…

Despite the importance that fluid flow plays in transporting and organizing populations, few laboratory systems exist to systematically investigate the impact of advection on their spatial evolutionary dynamics. To address this problem, we…

The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the…

Bacteria populate the colon where they replicate and migrate in response to nutrient availability. Here I model the colon bacterial population as a sandpile model, the colon-pile. Sand addition mimics bacterial replication and grains…

In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via…

Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct…

We study colonies of non-motile, rod-shaped bacteria growing on solid substrates. In our model, bacteria interact purely mechanically, by pushing each other away as they grow, and consume a diffusing nutrient. We show that mechanical…

Cooperative behavior is widespread in nature, even though cooperating individuals always run the risk to be exploited by free-riders. Population structure effectively promotes cooperation given that a threshold in the level of cooperation…

Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…

The striking variety of macroscopic morphologies displayed by bacterial colonies depends on microscopic environmental and behavioural details in a manner that is currently not well understood. A surprising example is sibling inhibition,…

An organism that is newly introduced into an existing population has a survival probability that is dependent on both the population density of its environment and the competition it experiences with the members of that population.…

Bacteria commonly inhabit porous environments such as host tissues, soil, and marine sediments, where complex geometries constrain and redirect their motion. Although bacterial motility has been studied in porous media, the roles of cell…