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Author: Liat Shenhav Publisher: ISBN: Category : Languages : en Pages : 102
Book Description
Microbial communities can undergo rapid changes, that can both cause and indicate host disease, rendering longitudinal microbiome studies key for understanding microbiome-associated disorders. However, most standard statistical methods, based on random samples, are not applicable for addressing the methodological and statistical challenges associated with repeated, structured observations of a complex ecosystem. Therefore, to elucidate how and why our microbiome varies in time, and whether these trajectories are consistent across humans, we developed new methods for modeling the temporal and spatial dynamics of microbial communities. We developed a method to identify 'time-dependent' microbes (Shenhav et al., PLoS Computational Biology 2019) and showed that their temporal patterns differentiate between the developing microbial communities of infants and those of adults. We also developed models to deconvolute the dynamics of microbial community formation. Using these methods, we found significant differences between vaginally- and cesarean-delivered infants in terms of initial colonization and succession of their gut microbial community (Shenhav et al., Nature Methods 2019) as well as the trajectories of these communities in the first years of life (Martino*, Shenhav* et al., Nature Biotechnology). These models, designed to identify and predict time-dependent patterns, will help researchers better understand the temporal nature of the human microbiome from the time of its formation at birth and throughout life.
Author: Liat Shenhav Publisher: ISBN: Category : Languages : en Pages : 102
Book Description
Microbial communities can undergo rapid changes, that can both cause and indicate host disease, rendering longitudinal microbiome studies key for understanding microbiome-associated disorders. However, most standard statistical methods, based on random samples, are not applicable for addressing the methodological and statistical challenges associated with repeated, structured observations of a complex ecosystem. Therefore, to elucidate how and why our microbiome varies in time, and whether these trajectories are consistent across humans, we developed new methods for modeling the temporal and spatial dynamics of microbial communities. We developed a method to identify 'time-dependent' microbes (Shenhav et al., PLoS Computational Biology 2019) and showed that their temporal patterns differentiate between the developing microbial communities of infants and those of adults. We also developed models to deconvolute the dynamics of microbial community formation. Using these methods, we found significant differences between vaginally- and cesarean-delivered infants in terms of initial colonization and succession of their gut microbial community (Shenhav et al., Nature Methods 2019) as well as the trajectories of these communities in the first years of life (Martino*, Shenhav* et al., Nature Biotechnology). These models, designed to identify and predict time-dependent patterns, will help researchers better understand the temporal nature of the human microbiome from the time of its formation at birth and throughout life.
Author: Aarthi Ravikrishnan Publisher: CRC Press ISBN: 0429946066 Category : Computers Languages : en Pages : 77
Book Description
Systems-Level Modelling of Microbial Communities: Theory and Practice introduces various aspects of modelling microbial communities and presents a detailed overview of the computational methods which have been developed in this area. This book is aimed at researchers in the field of computational/systems biology as well as biologists/experimentalists studying microbial communities, who are keen on embracing the concepts of computational modelling. The primary focus of this book is on methods for modelling interactions between micro-organisms in a community, with special emphasis on constraint-based and network-based modelling techniques. A brief overview of population- and agent-based modelling is also presented. Lastly, it covers the experimental methods to understand microbial communities, and provides an outlook on how the field may evolve in the coming years.
Author: Hyun-Seob Song Publisher: MDPI ISBN: 3038429759 Category : Science Languages : en Pages : 295
Book Description
This book is a printed edition of the Special Issue "Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics" that was published in Processes
Author: Kai Muffler Publisher: Springer ISBN: 3319096958 Category : Science Languages : en Pages : 264
Book Description
This book review series presents current trends in modern biotechnology. The aim is to cover all aspects of this interdisciplinary technology where knowledge, methods and expertise are required from chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science. Volumes are organized topically and provide a comprehensive discussion of developments in the respective field over the past 3-5 years. The series also discusses new discoveries and applications. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. In general, special volumes are edited by well-known guest editors. The series editor and publisher will however always be pleased to receive suggestions and supplementary information. Manuscripts are accepted in English.
Author: Melissa Lynne Partyka Publisher: ISBN: 9780355461237 Category : Languages : en Pages :
Book Description
Microorganisms are fundamental members of aquatic and marine ecosystems capable of affecting the macroecology of these systems by serving as the foundation of complex food chains, biogeochemical processes, and disease dynamics. Though recognized as foundational, scientists continue to struggle to apply basic ecological concepts of like community, spatiotemporal variability, gradients, and disturbance regimes to microorganisms in meaningful ways due to the vast differences in scale between macrobial sampling designs and microbial existence. However, until new ecological concepts have been generated for understanding microbial populations, we must continue to sample varied habitats at multiple spatial and temporal scales with the hope of capturing both unique and common characteristics of these communities that will allow us to predict their responses to a changing environment. The ability to predict microbial behavior has particular importance for human health; for that reason, this research focused on bacterial members of the greater microbial community that have been associated with illness and disease in humans utilizing both culture and molecular techniques followed by multiple-regression analyses. In Chapter 1, the intention was to examine bacterial populations at broad spatial and temporal scales within 6 freshwater reservoirs in the foothills of the Sierra Nevada Mountains. We sought to understand whether microbial water quality within reservoirs was driven by upstream conditions and subsequently predictive of downstream outcomes. Specifically, this research sought to understand the variability of fecal indicator bacteria (Escherichia coli and fecal coliforms) and pathogens (E. coli O157:H7, Non-O157 shiga toxin-producing E. coli and Salmonella) along both horizontal and vertical profiles within California reservoirs as it related to upstream river sources and downstream irrigation water supplies. Continued monitoring and modeling of both bacterial indicators and enteric pathogens are critical to our ability to estimate the risk of surface irrigation water supplies and make appropriate management decisions. In this study, the extreme variability in microbial populations across both space and time made successful predictions largely impossible and underlined the extreme importance of sampling these dynamic communities at scales where their behavior can be observed, particularly where human health may be impacted. I sought to further refine the scale of examination in Chapter 2 which moved from the freshwater of the Sierras to the marine habits of coastal California. In these systems the bacterial genus Vibrio is both endemic and occasionally pathogenic. Thus, we strove for greater understanding of how four members of Vibrio, V. alginolyticus, V. parahaemolyticus, V. cholerae, and V. vulnificus, referred to as “the big four” of global human illness, interact with their environment and respond to changing conditions. We examined finer-scale spatial and temporal variability of the “big four” in one bay of Northern California, Tomales Bay, highly popular with tourists and known as a premier region for shellfish production. As with Chapter 1, bacterial populations were highly dynamic in both space and time. However, these data were more easily modeled by capturing weekly, daily, and occasionally hourly changes to the environment during seasonal storms and sub-meter differences in sediment characteristics during acute tidal cycles. As with the previous chapter, pathogen prevalence or concentration in water, sediment, or shellfish did not correlate (p>0.1) with concentrations of fecal indicator bacteria, suggesting the need for revisions to the current regulatory monitoring efforts. For the third and final chapter I chose to manipulate the environment experienced by microorganisms in a manner that is common to intertidal sand and mudflats along most coastlines, recreational clamming activity. The impact of physical disturbance by clamming activity on microbial communities of intertidal sand flats has received relatively little attention, though the state of California estimates that 20-40K clams are taken from California bays annually, suggesting many people are performing the behavior and a large volume of sediment is being moved. I examined these impacts through a replicated cross-factorial longitudinal experiment on two emergent islands at the mouth of Tomales Bay. By following these exact sites through time we were able to reveal a wealth diversity within a single species of Vibrio, V. alginolyticus, and examine how that diversity changed through recurring tidal cycles. Further, while it was apparent that our targeted species were not significantly (p>0.05) impacted by our experimental disturbances, there were clear differences in the responses of indicator bacteria (fecal coliforms and enterococci) and vibrios by location and across time. These data illustrate that a great deal remains to be discovered about human influence over microbial communities in coastal systems, opening the door for further refinement in study designs. Taken as a whole, this series of studies has helped to further highlight the need of studies that examine microbial populations not only at scales that are relevant to the organism under investigation, but to the humans that may encounter them and fall ill. I sought to provide suggestion to aid the regulatory community in modifying current guidelines in the interest of public health and to encourage the ecological community to continue to evaluate the impact of scale on our ability to make inferences and gain understanding of these unseen and complex microbial communities.
Author: T. Czaran Publisher: Springer Science & Business Media ISBN: 9780412575501 Category : Science Languages : en Pages : 312
Book Description
This book presents a comprehensive typology and a comprehensible description of spatiotemporal models used in population dynamics. The main types included are: reaction-diffusion systems, patch models, matapopulation approaches, host parasitoid models, cellular automata (interacting particle systems), tessellations and distance models. The models are introduced through examples and with informative verbal explanations to help understanding. Some of the cellular automation examples are models not yet published elsewhere. Possible extensions of certain model types are suggested.
Author: Institute of Medicine Publisher: National Academies Press ISBN: 0309264324 Category : Medical Languages : en Pages : 633
Book Description
Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.
Author: Martin G. Klotz Publisher: Frontiers Media SA ISBN: 288919793X Category : Microbiology Languages : en Pages : 264
Book Description
Microbial mat communities consist of dense populations of microorganisms embedded in exopolymers and/or biomineralized solid phases, and are often found in mm-cm thick assemblages, which can be stratified due to environmental gradients such as light, oxygen or sulfide. Microbial mat communities are commonly observed under extreme environmental conditions, deriving energy primarily from light and/or reduced chemicals to drive autotrophic fixation of carbon dioxide. Microbial mat ecosystems are regarded as living analogues of primordial systems on Earth, and they often form perennial structures with conspicuous stratifications of microbial populations that can be studied in situ under stable conditions for many years. Consequently, microbial mat communities are ideal natural laboratories and represent excellent model systems for studying microbial community structure and function, microbial dynamics and interactions, and discovery of new microorganisms with novel metabolic pathways potentially useful in future industrial and/or medical applications. Due to their relative simplicity and organization, microbial mat communities are often excellent testing grounds for new technologies in microbiology including micro-sensor analysis, stable isotope methodology and modern genomics. Integrative studies of microbial mat communities that combine modern biogeochemical and molecular biological methods with traditional microbiology, macro-ecological approaches, and community network modeling will provide new and detailed insights regarding the systems biology of microbial mats and the complex interplay among individual populations and their physicochemical environment. These processes ultimately control the biogeochemical cycling of energy and/or nutrients in microbial systems. Similarities in microbial community function across different types of communities from highly disparate environments may provide a deeper basis for understanding microbial community dynamics and the ecological role of specific microbial populations. Approaches and concepts developed in highly-constrained, relatively stable natural communities may also provide insights useful for studying and understanding more complex microbial communities.
Author: Liat Shenhav
Author: Liat Shenhav
Author: Aarthi Ravikrishnan
Author: Hyun-Seob Song
Author: Kai Muffler
Author: Bernhard Palsson
Author: Melissa Lynne Partyka
Author: T. Czaran
Author: Institute of Medicine
Author: Hyun-Seob Song
Author: Martin G. Klotz