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Principles in Microbiome Engineering Provides an overview of the techniques and applications insight into the complex composition and interactions of microbiomes Microbiomes, the communities of microorganisms that inhabit specific ecosystems or organisms, can be engineered to modify the structure of microbiota and reestablish ecological balance. In recent years, a better understanding of microbial composition and host-microbe interactions has led to the development of new applications for improving human health and increasing agricultural productivity and quality. Principles in Microbiome Engineering introduces readers to the tools and applications involved in manipulating the composition of a microbial community to improve the function of an eco-system. Covering a range of key topics, this up-to-date volume discusses current research in areas such as microbiome-based therapeutics for human diseases, crop plant breeding, animal husbandry, soil engineering, food and beverage applications, and more. Divided into three sections, the text first describes the critical roles of systems biology, synthetic biology, computer modelling, and machine learning in microbiome engineering. Next, the volume explores various state-of-the-art applications, including cancer immunotherapy and prevention of diseases associated with the human microbiome, followed by a concluding section offering perspectives on the future of microbiome engineering and potential applications. Introduces a variety of applications of microbiome engineering in the fields of medicine, agriculture, and food and beverage products Presents current research into the complex interactions and relationships between microbiomes and biotic and abiotic elements of their environments Examines the use of technologies such as Artificial Intelligence (AI), Machine Learning (ML), and Big Data analytics to advance understanding of microbiomes Discusses the engineering of microbiomes to address human health conditions such as neuro psychiatric disorders and autoimmune and inflammatory diseases Edited and authored by leading researchers in the rapidly evolving field, Principles in Microbiome Engineering is an essential resource for biotechnologists, biochemists, microbiologists, pharmacologists, and practitioners working in the biotechnology and pharmaceutical industries.
Principles in Microbiome Engineering Provides an overview of the techniques and applications insight into the complex composition and interactions of microbiomes Microbiomes, the communities of microorganisms that inhabit specific ecosystems or organisms, can be engineered to modify the structure of microbiota and reestablish ecological balance. In recent years, a better understanding of microbial composition and host-microbe interactions has led to the development of new applications for improving human health and increasing agricultural productivity and quality. Principles in Microbiome Engineering introduces readers to the tools and applications involved in manipulating the composition of a microbial community to improve the function of an eco-system. Covering a range of key topics, this up-to-date volume discusses current research in areas such as microbiome-based therapeutics for human diseases, crop plant breeding, animal husbandry, soil engineering, food and beverage applications, and more. Divided into three sections, the text first describes the critical roles of systems biology, synthetic biology, computer modelling, and machine learning in microbiome engineering. Next, the volume explores various state-of-the-art applications, including cancer immunotherapy and prevention of diseases associated with the human microbiome, followed by a concluding section offering perspectives on the future of microbiome engineering and potential applications. Introduces a variety of applications of microbiome engineering in the fields of medicine, agriculture, and food and beverage products Presents current research into the complex interactions and relationships between microbiomes and biotic and abiotic elements of their environments Examines the use of technologies such as Artificial Intelligence (AI), Machine Learning (ML), and Big Data analytics to advance understanding of microbiomes Discusses the engineering of microbiomes to address human health conditions such as neuro psychiatric disorders and autoimmune and inflammatory diseases Edited and authored by leading researchers in the rapidly evolving field, Principles in Microbiome Engineering is an essential resource for biotechnologists, biochemists, microbiologists, pharmacologists, and practitioners working in the biotechnology and pharmaceutical industries.
The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.
Honey bees are critically important commercial pollinators and model systems for insect physiology and behavior. Honey bees are also suffering dramatic declines worldwide due to many factors, including agricultural practices, parasites, and pesticide use. These bees house a simple, conserved gut microbiome that is important for their health. Can we use this gut microbiome to protect bees in new ways? Synthetic biology combines recombinant DNA technology and rational design principles to redesign biological processes. Microbiome engineering applies synthetic biology and engineering principles to microbial communities to improve or expand their functions. Because of their agricultural importance, history as a model organism, and simple gut microbiome, honey bees are a promising testbed for the nascent field of microbiome engineering. In Chapter 1 I provide a brief introduction to the host-associated microbiomes, honey bees, and synthetic biology. In Chapter 2, I develop broad-host-range tools for genetic manipulation of bacteria from honey bees and show that genetically engineered bacteria can recolonize and function in bees. This lays the groundwork for follow-on efforts to both study and further engineer the bee gut microbiome. In Chapter 3, I describe the application of these genetic tools to engineer core microbiome member Snodgrassella alvi to produce double-stranded RNA (dsRNA) and thereby induce RNA-interference (RNAi) in bees. Activating RNAi enables bee researchers to study specific bee genes. In the future this technique may be used to protect honey bee hives from viruses and parasitic mites. In Chapter 4, I describe a computational approach for designing and evaluating defined bacterial communities and discuss using these defined communities in honey bees. These chapters together demonstrate how the bacterial community native to an organism can be modified and address several technical limitations of microbiome engineering in honey bees. Finally, I discuss the next steps for continuing this work
The microbes that live in and on plants (the plant microbiome) are critical for plant health, and exert their influence by facilitating nutrient acquisition, regulating plant hormone levels, and helping to withstand pathogen attack. Due to these potential benefits, the plant microbiome has become an appealing target for engineering sustainable improvements in crop productivity. However, the lack of a mechanistic understanding for plant-microbiome interactions at the molecular level has impeded engineering efforts. In this dissertation, I address the role of plant-derived specialized molecules in shaping the composition of the root microbiome, and that of microbe-produced molecules in influencing plant health. Using broadly-applicable experimental platforms that allow for hypothesis-driven mechanistic studies, along with previously developed reverse genetic tools in the model plant Arabidopsis, I discovered a novel mechanism of action for coumarins (root-exuded, specialized small molecules) in assembling the microbiome of plant roots. Additionally, I describe a role for Pseudomanas-derived pyrroloquinoline quinone (a redox-active small molecule) in improving plant growth under iron-limiting conditions -- a nutrient deficiency prevalent in one-third of the world's soils. Finally, I highlight a serendipitous discovery made while engineering plants to modulate the root microbiome using opines -- unusual conjugates of two common plant metabolites that can be catabolized by select microbes. The microbes inciting the production of opines, Agrobacterium species, hijack the plant cell's splicing machinery as part of its pathogenic lifestyle. This novel finding could be exploited to improve transgene expression in plants, and to survey bacterial genomes for genes that are horizontally transferred across the kingdoms of life. These contributions, which provide mechanistic roles for both plant and microbe-derived small molecules within the phytobiome, offer concrete strategies for engineering phytobiomes to improve agricultural systems.
Human and Animal Microbiome Engineering provides both basic and detailed information about microbiome engineering for the health enhancement of humans and animal populations. Contents provide updated information about current research topics in this emerging field including microbiome gene therapy, engineered probiotics and smart living biotic machines for the release of therapeutics. The book is divided into 4 sections covering microbiome engineering application with a focus on future perspectives in human health and enhancement; microbiome engineering in human health and disease including real-world case studies; animal microbiome engineering essentials; and microbiome engineering for livestock improvement. This is the perfect reference for researchers and scientists to further explore the relationship between host and microbiome and discover novel ideas about the concepts of microbiome engineering in the health enhancement of humans and animal populations.
This book reports on the ecological engineering of granular sludge processes for a high-rate removal of carbon, nitrogen, and phosphorus nutrients in compact wastewater treatment plants. It provides novel insights into microorganisms and metabolisms in wastewater microbiomes and the use of microbial ecology principles to manage wastewater treatment processes. It covers a very comprehensive and inter-disciplinary research of systems microbiology and environmental biotechnology. From the initial economic assessment of the aerobic granular sludge technology, concepts of microbiome science and engineering are developed to uncover and manage the microbial ecosystem of granular sludge. Mixed-culture biotechnological processes, multifactorial experimental designs, laser scanning microscopy, molecular microbial ecology and bioinformatics methods, numerical ecology workflows, and mathematical modelling are engaged to disentangle granulation phenomena, microbial selection, and nutrient conversions across scales. The findings are assembled in a guideline for microbial resource management in granular sludge processes to support knowledge utilization in engineering practice. Outputs are integrated in the state of the art of biological wastewater treatment. This book addresses both scientists and engineers who are eager to get insights into and engineer microbiomes for environmental biotechnologies. It makes a valuable contribution to methods for strengthening the role of wastewater treatment plants for recovering safe water and resources, in the context of circular economy and for sustaining health and the environment in an ecologically balanced society.
The human microbiome is home to diverse bacteria that are critical in maintaining normal function and human health. It is primarily shaped by environmental factors, such as stress, diet, and geographical location. An unbalanced microbiome due to disease or prolonged antibiotic use can have significant, long-term health impacts. There is a need for a therapeutic intervention that can meaningfully re-engineer the microbiome in response to imbalances. In this work, the fabrication and efficacy of peptide-carbohydrate capsules will be discussed. These biocapsules are loaded with commensal bacteria and have an antimicrobial coating which show promise in being able to inhibit local pathogenic growth while precisely releasing commensal bacteria in the GI tract. This biomaterial has the potential to become a powerful tool in supporting the diverse human microbiome and sets the groundwork for future development of this biome-engineering tool which can successfully create an ecological niche for delivered commensal bacteria to integrate into the microbiome.
A great number of diverse microorganisms inhabit the human body and are collectively referred to as the human microbiome. Until recently, the role of the human microbiome in maintaining human health was not fully appreciated. Today, however, research is beginning to elucidate associations between perturbations in the human microbiome and human disease and the factors that might be responsible for the perturbations. Studies have indicated that the human microbiome could be affected by environmental chemicals or could modulate exposure to environmental chemicals. Environmental Chemicals, the Human Microbiome, and Health Risk presents a research strategy to improve our understanding of the interactions between environmental chemicals and the human microbiome and the implications of those interactions for human health risk. This report identifies barriers to such research and opportunities for collaboration, highlights key aspects of the human microbiome and its relation to health, describes potential interactions between environmental chemicals and the human microbiome, reviews the risk-assessment framework and reasons for incorporating chemicalâ€"microbiome interactions.