Modeling the Role of the Microbiome in Evolution

There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones

Proteomics as a tool for the characterisation of nosocomial pathogens

The aim of the present investigation was to develop and assess the potential of various proteomic approaches for the characterisation of two major nosocomial pathogens, S. aureus and C. difficile and to further investigate the intraspecies diversity of C. difficile using a genotypic approach. The surface-associated proteins of S. aureus and intracellular stable ribosomal proteins of C. difficile were analysed by MALDI-TOF-MS and the resulting spectra interrogated using two databases viz. MMU (Waters®) and SARAMIS™ (AnagnosTec) respectively. A total of 134 clinical S. aureus isolates were tested using the MMU database and the MicrobeLynx™ software. All were successfully identified with minor contamination errors that corroborated with 16S rRNA sequencing. By contrast, C. difficile isolates were only partially identified (to the genus level) using the MMU database and protocol. Changes in the matrix solution and use of the new database (SARAMIS™) resulted in the correct identification of all C. difficile isolates and, detailed ultra-structural studies indicated that intracellular proteins were the new diagnostic biomarkers

Aging and Health

Aging is a major risk factor for chronic diseases, which in turn can provide information about the aging of a biological system. This publication serves as an introduction to systems biology and its application to biological aging. Key pathways and processes that impinge on aging are reviewed, and how they contribute to health and disease during aging is discussed. The evolution of this situation is analyzed, and the consequences for the study of genetic effects on aging are presented. Epigenetic programming of aging, as a continuation of development, creates an interface between the genome and the environment. New research into the gut microbiome describes how this interface may operate in practice with marked consequences for a variety of disorders. This analysis is bolstered by a view of the aging organism as a whole, with conclusions about the mechanisms underlying resilience of the organism to change, and is expanded with a discussion of circadian rhythms in aging

On the Origins and Control of Community Types in the Human Microbiome

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 and the degree of their distinctness have been highly debated. Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network. By controlling the presence or absence of these strongly interacting species we can steer the microbial ecosystem to any desired community type. This open-loop control strategy still holds even when the community types are not distinct but appear as dense regions within a continuous gradient. This finding can be used to develop viable therapeutic strategies for shifting the microbial composition to a healthy configurationComment: Main Text, Figures, Methods, Supplementary Figures, and Supplementary Tex

Host-pathogen interactions between the human innate immune system and Candida albicans—understanding and modeling defense and evasion strategies

The diploid, polymorphic yeast Candida albicans is one of the most important humanpathogenic fungi. C. albicans can grow, proliferate and coexist as a commensal on or within thehuman host for a long time. Alterations in the host environment, however, can render C. albicansvirulent. In this review, we describe the immunological cross-talk between C. albicans and thehuman innate immune system. We give an overview in form of pairs of human defense strategiesincluding immunological mechanisms as well as general stressors such as nutrient limitation,pH, fever etc. and the corresponding fungal response and evasion mechanisms. FurthermoreComputational Systems Biology approaches to model and investigate these complex interactionare highlighted with a special focus on game-theoretical methods and agent-based models. Anoutlook on interesting questions to be tackled by Systems Biology regarding entangled defenseand evasion mechanisms is given

Aging and Health

Aging is a major risk factor for chronic diseases, which in turn can provide information about the aging of a biological system. This publication serves as an introduction to systems biology and its application to biological aging. Key pathways and processes that impinge on aging are reviewed, and how they contribute to health and disease during aging is discussed. The evolution of this situation is analyzed, and the consequences for the study of genetic effects on aging are presented. Epigenetic programming of aging, as a continuation of development, creates an interface between the genome and the environment. New research into the gut microbiome describes how this interface may operate in practice with marked consequences for a variety of disorders. This analysis is bolstered by a view of the aging organism as a whole, with conclusions about the mechanisms underlying resilience of the organism to change, and is expanded with a discussion of circadian rhythms in aging

Towards bioengineered ecosystems: Three studies in invasion biology

An important feature of ecosystems is their invasibility, i.e. their resistance to invasion by nonnative organisms. Invasion is a driver of change at scales as small as a bioreactor and as large as the scale of biogeography. Invasion can be either a desired outcome, for example in the use of probiotics to replace healthful gut microflora after a disturbance to the gut microbial ecosystem, or an undesired outcome, for example in the contamination of open culture systems such as algal raceway ponds. Biological invasion theory attempts to predict what makes a community vulnerable to invasion, what characteristics make an invader successful, and what consequences following invasion might arise. In this thesis, a review of recent literature on microbial invasion biology was conducted, and three separate studies in invasion biology were pursued. In Chapter 1, two overarching yet poorly understood factors determing microbial community invasibility were identified: environmental modulation, and community structure. The first factor, community structure, describes the set of species in an ecosystem and how they are trophically and otherwise related. While the majority of work in invasion biology has focused on the relationship between diversity and invasibility, we argue that it is imperative to move beyond simple diversity metrics towards more information-rich descriptors of community structure, by casting traditional ecological concepts like plasticity, redundancy, dormancy, and diversity into the language of networks. The second factor, environmental modulation, describes how communities can alter their own environment, deterring potential invaders by making the environment less consumable or habitable. We argue that this process has received too little attention in invasion biology and that insights can be drawn from the field of biopreservation, which utilizes beneficial microorganisms to preserve food environments from unwanted invaders. Chapter 2 introduces wild sourdough fermentations as a model system for the study of invasion biology through the lens of biopreservation. An experimental investigation of the robustness of traditional sourdough cultures to invasion was performed, exploring the role of environmental modulation of pH in deterring invaders. Two invader organisms were tested for their ability to invade, and a mathematical model was developed describing the bacterial fraction of a wheat flour dough. First, a simple experiment with a laboratory strain of Escherichia coli introduced into a traditionally propagated sourdough culture indicated that the production of organic acids is the primary mechanism of invasion resistance of sourdoughs against E. coli, which is ubiquitous in human environments. Second, experiments with the acidophile Alicyclobacillus acidoterrestris showed that while acid-tolerant invaders exist, the presence of environmental hurdles such as low temperature and high osmolarity are major factors in preventing their establishment in sourdough cultures. Finally, a mathematical model for the growth, metabolic output, and self-inhibition of the dominant sourdough organism Lactobacillus sanfranciscensis in wheat flour dough was developed. This model was able to predict population density, pH, lactate concentration, and maltose concentration in a manner consistent with experimental data. Chapter 3 considers the general problem of invasion in a three-species ecosystem, which was simulated mathematically assuming that the community structure of the ecosystem is completely defined. The aim of this chapter was to determine any relationships between the invasibility of a particular ecosystem and its community structure. We considered the scenario in which a rare species in an ecosystem suddenly becomes abundant as a result of a discrete mutation in one or more ecological parameters describing the system, representing either a sudden change in ecological strategy, an actual mutation, or a sudden change in the environment. The concepts of invasion distance and invasion direction were formulated, the former referring to the magnitude of the change in parameters required for a rare species to become abundant, and the latter referring to the direction of that parameter change. By performing simulations for 44 out of the 138 possible community structures in a simple 3-species ecosystem, we found that the invasion direction varied significantly with community structure but the invasion distance did not. This result set up future work investigating analytically how invasion direction varies with community structure. Chapter 4 introduces a mathematical model for a phage-bacterium ecosystem. From an invasion biology standpoint, either the phage or the bacterium can be considered as an invader, depending on the ecosystem they inhabit and also on one's point of view. A model was developed to describe an ecosystem containing three populations: phage-infected bacteria, uninfected bacteria, and an environmental reservoir of free bacteriophages. Five system parameters were used as inputs to the model: intrinsic host death rate, virus degradation rate, environmental transmission rate, lysis rate, and burst size. The model was set up to capture logarithmic growth of bacteria, as well as both both lytic and lysogenic life stages of the phage. All pairwise relationships between the five system parameters were investigated, by examining two payoff functions plotted as contour surfaces over each pair of parameters. We found that a high burst size, low virus degradation rate, and low host intrinsic death rate always resulted in the hiest payoff to the phage. In contrast, payoffs always reached a maximum when lysis rate and environmental transmission rate took on intermediate values. Moreover, a third payoff, the basic epidemiological reproduction number R0, was shown to be limited in expressivity as it could only capture monotonic payoff relationships. These results were relevant to the classic "trade-off" hypothesis in virulence theory, which states that lysis rate (virulence) and transmission rate are coupled. While no coupling relationship was assumed in our model, the relationship between lysis rate and transmission rate was markedly the most complex out of all pairwise relationships considered, thus validating the substantial amount of interest historically in this relationship as opposed to other relationships between system parameters. Finally, conditions were found for a stable steady-state solution representing a desirable outcome in a phage therapy context, which attempts to control unwanted bacterial populations by using bacterophages as therapeutic agents. These conditions were overlayed upon the phage payoff surfaces, and it was found that the phage therapy stability region was always located at higher lysis rate and host intrinsic death rate values than the payoff optima. Taken together, the work here contributes to the fields of biological and ecological engineering in the following ways. First, the role of ecosystem structure and environmental modulation were elucidated, and gaps in the literature in both of these areas were identified. Principles were then abstracted from both physical (e.g. sourdough fermentation) and simulated systems (e.g. phage-bacterium interaction) towards a greater understanding of robustness towards invasion and evolutionary trade-off relationships, respectively. Finally, several future directions for research were identified, including the generation of mathematical models to describe yeast-bacterium interactions in sourdoughs, further work on the effect of community structure on invasion direction, and additional experimental and theoretical work towards the realization of phage therapy

Programming microbes to treat superbug infection

Superbug infection is one of the greatest public health threat with grave implications across all levels of society. Towards a new solution to combat infection by multi-drug resistant bacteria, this thesis presents an engineering framework and genetic tools applied to repurpose commensal bacteria into “micro-robots” for the treatment of superbug infection. Specifically, a prototype of designer probiotic was developed using the human commensal bacteria Escherichia coli. The engineered commensal was reprogrammed with user-specified functions to sense superbug, produced pathogen-specific killing molecules and released the killing molecules via a lytic mechanism. The engineered commensal was effective in suppressing ~99% of planktonic Pseudomonas and preventing ~ 90% of biofilm formation. To enhance the sensing capabilities of engineered commensal, genetic interfaces comprising orthogonal AND & OR logic devices were developed to mediate the integration and interpretation of binary input signals. Finally, AND, OR and NOT logic gates were networked to generate a myriad of cellular logic operations including half adder and half subtractor. The creation of half adder logic represents a significant advancement of engineering human commensal to be biological equivalent of microprocessor chips in programmable computer with the ability to process input signals into diversified actions. Importantly, this thesis provides exemplary case studies to the attenuation of cellular and genetic context dependent effects through principles elucidated herein, thereby advancing our capability to engineer commensal bacteria.Open Acces