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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…

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,…

A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole.…

Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…

Growth in bacterial populations generally depends on the environment (availability and quality of nutrients, presence of a toxic inhibitor, product inhibition..). Here, we build a model to describe the action of a bacteriostatic antibiotic,…

We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…

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…

The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a…

Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…

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…

Human skin is a region of high metabolic activity where a rich variety of biomarkers are secreted from the stratum corneum. The skin is a constant source of volatile organic compounds (VOCs) derived from skin glands and resident microbiota.…

A review of recent investigations into pathogenesis of psoriasis summarizing data on the relationship between the presence {\beta}-streptococci in the organism and the cutaneous immune reaction. Results of the studies on gastrointestinal…

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,"…

Feature selection is indispensable in microbiome data analysis, but it can be particularly challenging as microbiome data sets are high-dimensional, underdetermined, sparse and compositional. Great efforts have recently been made on…

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…

Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…

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…

Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes…

The aim of this paper is to study two models for a bacterial population subject to antibiotic treatments. It is known that some bacteria are sensitive to antibiotics. These bacteria are in a state called persistence and each bacterium can…