Bacteria live in highly diverse ecosystems inside the intestines of many organisms. How and at what pace they evolve in that ecosystem is not yet well understood. Here we address these questions using the power of mouse models and the wealth of functional knowledge on a human gut commensal, Escherichia coli. We demonstrate that the colonization success of a new invader E. coli strain depends...
Authors: Pierre A. Haas, Maria A. Gutierrez, Nuno M. Oliveira, and Raymond E. Goldstein
In complex microbial communities such as microbiomes, clonal bacteria switch between different phenotypes. This switching can be stochastic, but switching in response to other species is beginning to be appreciated as a feature of microbial populations because of the importance of competitive...
Authors: Julie Teresa Shapiro, Alvah Zorea, Aya Brown Kav, Itzik Mizrahi, Shai Pilosof
The microbiome is predominantly treated as the collection of microbes limited to a given space. However, all microbiomes are open communities that include, beyond microbes, mobile genetic elements. Of these, plasmids are major agents of microbial evolution, horizontally spreading genes within and between...
Microbial communities are highly dimensional, with many species and many variable environmental factors. Macroecology, which studies communities as statistical ensembles, is a promising way to connect these complex data to mechanistic models. In this talk, I will discuss a minimal set of macroecological patterns that characterize the statistical properties of species abundance fluctuations...
Authors: J Camacho-Mateu, Aniello Lampo, Matteo Sireci, Miguel A Muñoz, Jose A Cuesta
Microbial communities are ubiquitous in the entire biosphere, from seawaters and soils to animals’ guts, and have a great impact in many biological processes, for instance those involved in human health. Herein, a crucial role is played by interactions among species. It has been shown, indeed, that these...
Authors: João Valeriano, Ricardo Martínez-García
Cooperation is a social behavior that, despite being easily encountered in nature, is usually hard to explain, as it frequently appears to be evolutionarily unstable. Microbial communities provide a very rich playground to study the evolution of cooperation, as one can model these behaviors through simple rules and compare theoretical...
Authors: Seyfullah Kotil, Kalin Vetsigian
Diversity is abundant among microbial communities. Understanding the assembly of diverse microbial communities is a significant challenge. One of the recent plausible explanations for the assembly involves eco-evolutionary tunnels, where species interact in the same timescale with the mutational rate. A common framework to understand such tunnels...
Using models to understand microbiomes requires good data, generated from experiments designed to capture relevant information and having structure suitable for model fitting, analysis capable of dealing with the idiosyncracies in these data, and models capable of recapitulating the sometimes-weird features that we actually observe. Using small host-microbiome models, we can generate data...
Authors: Svenja Busche, Danielle Harris, Konrad Aden, Silvio Waschina
Auxotrophies are defined by the incapability of an organism to synthesize essential nutrients resulting in a dependence on the nutritional environment. Amino acids are vital nutrients for the human host and auxotrophic bacteria within the gut microbiome, which could result in competition for specific amino acids....
Most animals have a microbiome that affects their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. An open question is to what extent host-microbiomes can evolve through selection acting at the host-level. I will present a quantitative framework based on multi-level selection theory that addresses this question. Our model shows that...
The composition of a microbial community (microbiome) affects its stability and function and is shaped by selective and neutral processes that operate at different scales. For instance, environmental filtering typically operates at non-local scales while interactions (e.g., competition) operate locally. One way to study community composition is via microbe co-occurrence networks. The...
Authors: Jana C. Massing, Ashkaan Fahimipour, Carina Bunse, Jarone Pinhassi, Thilo Gross
Progress in molecular methods has enabled us to monitor bacterial community composition over time. Nevertheless, understanding community dynamics and its impact on ecosystem functioning is challenging due to the tremendous diversity. This highlights the need for conceptual frameworks to make sense of...
Constraint-based approaches are key concepts in modeling of metabolism. As key ingredient these approaches require the stoichiometric matrix of the metabolic network of an organism that can be readily derived from its genome. Using this stoichiometric matrix along with physiological constraints and an evolutionary objective, fluxes within such a network can be predicted using flux balance...
Authors: Ghjuvan Grimaud, Thomas Koffel, Elena Litchman, Christopher Klausmeier
Genome-scale metabolic models (GEMs) are a powerful tool to understand and predict the metabolic status of bacterial species in different environmental conditions (Terzer et al., 2009). GEMs simulated using constraint-based models such as Flux Balance Analysis (FBA) (Orth et al., 2010a) or Dynamical Flux...
Authors: Jamie Lee, Takuya Miyano, and Reiko J. Tanaka
Atopic dermatitis (AD) is a chronic inflammatory skin disease of high socio-economic impact. An imbalanced skin microbiome is a common feature of AD patients, with Staphylococcus (S.) aureus colonising the skin. S. aureus damages the skin barrier, and its killing has been hypothesised as a promising treatment for AD. However, clinical...
Authors: Xiaoyu Shan, Otto X. Cordero
Recent studies have shown that microbiomes are composed of groups of functionally cohesive taxa, whose abundance is more stable and better associated with metabolic fluxes than that of any individual taxon. However, identifying these functional groups in a manner that is independent from error-prone functional gene annotations remains a major open...
Our work on gut microbiota centers on two main themes. The first topic is about quantitative inference from experimental data of the dynamics of the bacterial gut population. One tool to study the populations which dynamics cannot be directly observed is to use tagged neutral subpopulations. The distribution of the different tags in the population are measured at several points, and from the...
Authors: Thibaut Morel-Journel, François Blanquart
Despite the extensive literature on the epidemiology, pathogenesis and virulence of Escherichia coli, much less is known about the ecological interactions between non-pathogenic strains within the gut microbiome. In general, strains are considered in terms of `residency', i.e. the ability of certain strains, once established, to remain...
The human gut harbors a highly dynamical microbiota shaped by the rapid turnover of bacterial biomass: While food intake by the host regularly supports fast growth of new bacteria, a substantial fraction of the bacterial population is also lost with every major bowel movement. The dynamics of the turnover depend strongly on the consumed diet and the speed with which bacteria grow. But the...
Authors: Caitlin Guccione, Cameron Martino, Antonio Gonzalez, Rob Knight, Kit Curtius
Microbes are abundant in human cancers and specific cancer types have unique microbiomes. Understanding the role of microbes in cancer development, progression, and metastasis could transform clinical cancer diagnostics and prognostics.(1) Although research on the cancer microbiome is expanding, previous...
The human gut microbiome harbors astronomical quantities of genetic diversity across evolutionarily distant species. However, it is becoming increasingly apparent that not all contributors towards said diversity are subject to evolutionary dynamics. Rather, genetic variants can be present in a host due to the co-occurrence of multiple genetically diverged lineages of a given species, a form of...
How ecological interactions can shape community assembly and maintenance is of particular interest for microbial communities, which are generically highly diverse, and where even closely related strains can have distinct ecologies. Statistical physics offers mathematical tools to deal with the complexity of diverse communities. In recent years, considerable progress has been made in the study...
Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host-microbe-microbe interactions. The intestinal microbiota of salmonids may offer a solution since it is often characterized by few dominating species. Healthy fish coexist with a mutualistic Mycoplasma sp. species, while stress allows the...
The immense diversity observed in natural microbial communities is surprising in light of the competitive exclusion principle and the numerous weapons microbes have evolved to inhibit each other's growth. In this work, we study patterns of antibiotic-mediated interactions between microbes using classical models from theoretical ecology. Building on previous work, we analyse the ecological...
The existence of an Evolutionarily Stable State (ESS) in a host-symbiont interaction at ecologically stable coexistence is studied in the framework of eco-evolutionary dynamics. Our basic objective is to obtain an evolutionary insight into the transmission behaviour of symbionts (which can be either parasitic or mutualistic depending on effects on mortality and fecundity) which are obligate...
Marine phytoplankton is composed of unicellular algae and their associated bacteria. These algal communities are highly variable in species composition, but their patterns tend to recur seasonally. This diversity suggests the existence of ecological niches for the associated bacteria. To clarify the role of the bacterial community on the phytoplankton, we co-cultured several bacterial species...
Commensal bacteria are also often major opportunistic pathogens with important public health consequences. For example, Escherichia coli colonises the gut of all humans and occasionally causes intestinal and extra-intestinal infections responsible for ~1M deaths worldwide each year. The colonization of hosts by E. coli is a highly dynamical process with strain turnover in the gut over...
Bacteria live in highly diverse ecosystems inside the intestines of many organisms. How and at what pace they evolve in that ecosystem is not yet well understood. Here we address these questions using the power of mouse models and the wealth of functional knowledge on a human gut commensal, Escherichia coli. We demonstrate that the colonization success of a new invader E. coli strain depends...
Habitat degradation, including the change of natural habitats into agricultural areas, alters natural communities all over the world. Land-use change may affect the host and its microbiome composition and structure, thus influencing the host's function and health, and the potential transmission and spread of microbes and disease. However, the relative effect of land-use change in shaping the...
