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Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…
Run-and-tumble is a common but vital strategy that bacteria employ to explore environment suffused with boundaries, as well as to escape from entrapment. In this study we reveal how this strategy and the resulting dynamical behavior can be…
Under favourable conditions, many proteins can assemble into macroscopically large aggregate's, Parkinson's and other neurological and systemic diseases. The overall process of protein aggregation is characterized by initial lag time during…
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…
The tolerance of bacterial populations to biocidal or antibiotic treatment has been well documented in both biofilm and planktonic settings. However, there is still very little known about the mechanisms that produce this tolerance.…
An antibiogram is a periodic summary of antibiotic resistance results of organisms from infected patients to selected antimicrobial drugs. Antibiograms help clinicians to understand regional resistance rates and select appropriate…
Phages use bacterial host resources to replicate, intrinsically linking phage and host survival. To understand phage dynamics, it is essential to understand phage-host ecology. A key step in this ecology is infection of bacterial hosts.…
Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…
We experimentally investigate how aerotactic bacteria, confined within a thin liquid film between two solid substrates, respond to a controlled oxygen gradient. We find that the total bacterial number density dictates which mechanism…
Humans, domestic animals, orchard crops, and ornamental plants are commonly treated with antibiotics in response to bacterial infection. By curing infectious individuals, antibiotic therapy might limit the spread of contagious disease among…
Antimicrobial resistance is a threat to public health with millions of deaths linked to drug resistant infections every year. To mitigate resistance, common strategies that are used are combination therapies and therapy switching. However,…
The revival mechanism in dormant bacteria is a puzzling and open issue. We propose a model of information diffusion on a regular grid where agents represent bacteria and their mutual interactions implement quorum sensing. Agents may have…
We investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution called dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial…
This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the…
Bacteria live in environments that are continuously fluctuating and changing. Exploiting any predictability of such fluctuations can lead to an increased fitness. On longer timescales bacteria can "learn" the structure of these fluctuations…
We show that a bacteria and bacteriophage system with either a perfectly nested or a one-to-one infection network is permanent, a.k.a uniformly persistent, provided that bacteria that are superior competitors for nutrient devote the least…
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…