Principles In Microbiome Engineering

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

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.

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.

This book provides a straightforward and easy-to-understand overview of beneficial plant-bacterial interactions. It features a wealth of unique illustrations to clarify the text, and each chapter includes study questions that highlight the important points, as well as references to key experiments. Since the publication of the first edition of Beneficial Plant-Bacterial Interactions, in 2015, there has been an abundance of new discoveries in this area, and in recent years, scientists around the globe have begun to develop a relatively detailed understanding of many of the mechanisms used by bacteria that facilitate plant growth and development. This knowledge is gradually becoming an integral component of modern agricultural practice, with more and more plant growth-promoting bacterial strains being commercialized and used successfully in countries throughout the world. In addition, as the world’s population continues to grow, the pressure for increased food production will intensify, while at the same time, environmental concerns, mean that environmentally friendly methods of food production will need to replace many traditional agricultural practices such as the use of potentially dangerous chemicals. The book, intended for students, explores the fundamentals of this new paradigm in agriculture, horticulture, and environmental cleanup.

"This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. Resident microbes in healthy animals--including humans--can dictate many traits of the animal host. This animal microbiome is a second immune system conferring protection against pathogens; it can structure host metabolism in animals as diverse as reef corals and hibernating mammals; and it may influence animal behavior, from social recognition to emotional states. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet, and have contributed to animal diversification over long evolutionary timescales"--Publisher by publisher.

The most up-to-date reference on phytomicrobiomes available today The Plant Microbiome in Sustainable Agriculture combines the most relevant and timely information available today in the fields of nutrient and food security. With a particular emphasis on current research progress and perspectives of future development in the area, The Plant Microbiome in Sustainable Agriculture is an invaluable reference for students and researchers in the field, as well as those with an interest in microbiome research and development. The book covers both terrestrial and crop associated microbiomes, unveiling the biological, biotechnological and technical aspects of research. Topics discussed include: Developing model plant microbiome systems for various agriculturally important crops Defining core microbiomes and metagenomes in these model systems Defining synthetic microbiomes for a sustainable increase in food production and quality The Plant Microbiome in Sustainable Agriculture is written to allow a relative neophyte to learn and understand the basic concepts involved in phytomicrobiomes and discuss them intelligently with colleagues.

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.

Learn more about foundational and advanced topics in metabolic engineering in this comprehensive resource edited by leaders in the field Metabolic Engineering: Concepts and Applications delivers a one-stop resource for readers seeking a complete description of the concepts, models, and applications of metabolic engineering. This guide offers practical insights into the metabolic engineering of major cell lines, including E. Coli, Bacillus and Yarrowia Lipolytica, and organisms, including human, animal, and plant). The distinguished editors also offer readers resources on microbiome engineering and the use of metabolic engineering in bioremediation. Written in two parts, Metabolic Engineering begins with the essential models and strategies of the field, like Flux Balance Analysis, Quantitative Flux Analysis, and Proteome Constrained Models. It also provides an overview of topics like Pathway Design, Metabolomics, and Genome Editing of Bacteria and Eukarya. The second part contains insightful descriptions of the practical applications of metabolic engineering, including specific examples that shed light on the topics within. In addition to subjects like the metabolic engineering of animals, humans, and plants, you’ll learn more about: Metabolic engineering concepts and a historical perspective on their development The different modes of analysis, including flux balance analysis and quantitative flux analysis An illuminating and complete discussion of the thermodynamics of metabolic pathways The Genome architecture of E. coli, as well as genome editing of both bacteria and eukarya An in-depth treatment of the application of metabolic engineering techniques to organisms including corynebacterial, bacillus, and pseudomonas, and more Perfect for students of biotechnology, bioengineers, and biotechnologists, Metabolic Engineering: Concepts and Applications also has a place on the bookshelves of research institutes, biotechnological institutes and industry labs, and university libraries. It's comprehensive treatment of all relevant metabolic engineering concepts, models, and applications will be of use to practicing biotechnologists and bioengineers who wish to solidify their understanding of the field.