Principles in Microbiome Engineering. Группа авторов

Singapore

       Series Editors

      Prof. Dr. Sang Y. Lee KAIST 373‐1, Guseong‐Dong 291 Daehak‐ro, Yuseong‐gu 34141 Daejeon South Korea

      Prof. Dr. Jens Nielsen Chalmers University Department of Chemical and Biological Engineering Kemivägen 10 412 96 Göteborg Sweden

      Prof. Dr. Gregory Stephanopoulos Massachusetts Institute of Technology Department of Chemical Engineering Massachusetts Ave 77 Cambridge, MA 02139 United States

      Cover Image: © shutterstock

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      Print ISBN: 978‐3‐527‐34725‐4 ePDF ISBN: 978‐3‐527‐82547‐9 ePub ISBN: 978‐3‐527‐82548‐6 oBook ISBN: 978‐3‐527‐82546‐2

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Preface

Though unseen to the naked eye, microbiomes represent an invisible universe with much yet to be explored. From the diverse microbial communities found within our own bodies all the way to the soil's depths, the omnipresence of these microbiomes underlies their vital role in mediating biological processes. By offering a means to harness these microbes for societal benefit, microbiome engineering can pave the way for crucial interventions in everything from disease treatment to agricultural productivity.

      Given the intricacy of interactions among microbes, it would be wise to comprehensively compile our state‐of‐the‐art knowledge on microbiome engineering. Written by leading experts, the volume's 10 chapters touch upon fundamental aspects – such as the microbiome's wide‐ranging influence on human health, disease, and agriculture; methods to engineer microbiomes for therapeutic and diagnostic applications, as well as insights into recent research directions that are shaping the field.

      With probiotics capturing public imagination in recent years, Chapter 1 aptly introduces our current understanding of the human microbiome through the lens of diet and nutrition. Chapter 2 builds upon this foundation by exploring how microbiome engineering can modulate common metabolic disorders from diabetes to cardiovascular disease.

      While microbes are popularly perceived as “villains” in the quest for health, Chapter 3 challenges this notion by describing the myriad ways microbes can be repurposed to sense, respond to, and even treat diseases. Rounding out the volume's initial focus on human health, Chapter 4 details specific considerations when engineering probiotics to be better adapted to the gut.

      Chapter 5 moves onto another equally fascinating – and important – application of microbiome engineering: precision agriculture, where minute variations in crop data are gathered and leveraged to improve yield and quality. Given the delicate balance of microbiomes, Chapter 6 provides an overview of the different biological sensors being developed to detect even the slightest of perturbations, such as riboswitches and transcription factors.

      Meanwhile, Chapter 7 focuses on how synergistic interactions among microorganisms can be further enhanced by engineering synthetic microbial consortia. Already ubiquitous in nature, advancing the design of microbial consortia could lead to breakthroughs in bioprocessing and bioremediation, among others. Proving that waste can indeed be turned into wonder, Chapter 8 describes the emerging treatment that is fecal microbiota transplantation, from the protocols involved to its clinical applications.

      With early‐life microbiota increasingly linked to long‐term health and disease, Chapter 9 shines a spotlight on the maternal microbiota and the many factors affecting its impact on newborn infants. Finally, this volume concludes in Chapter 10 by diving deep into a powerful technique in the microbiome engineering toolkit: transcription factor‐based biosensors, first introduced in Chapter 6.

      I would like to extend my deepest gratitude to the experts at the forefront of microbiome engineering for their contributions. By sharing their insights through the written word, I hope that this volume will be an indispensable resource that new generations of researchers can refer to as they add to the growing body of knowledge on microbiome engineering.

Singapore, April 2022

Matthew W. Chang National University of Singapore

1 Diet‐Based Microbiome Modulation: You are What You Eat

       Jiashu Li, Zeyang Qu, Feng Liu, Hao Jing, Yu Pan, Siyu Guo and Chun Loong Ho

       Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzehn 518055, China

1.1 Introduction

The microbiota refers to the total population of microbes that co‐exist with the host, whereas the microbiome is the regulated genomic composition of the microbiota. The microbiome was initially coined to study the co‐existing relationship between microbes and the hosting environment by Mohr in 1952 but only gained attention and recognition in the genomic era during the early 2000s [1, 2]. Microorganisms are present everywhere in our daily lives, establishing transient or permanent interactions with the human host. It is estimated that around 10–100 trillion microbes are present in the human body [3]. Although many different types of microbes co‐exist in human bodies such as viruses, fungi, and protozoa, bacteria are the most well studied and represented for their largest proportion and intimate relation with human health. The microbiota is shaped by the host's biochemistry, nutrition intake, and lifestyle pattern. In kind the microbiome influences human health through nutritional processes, immunomodulatory functions, manipulating the host behavior, and influencing disease pathogenesis.

      Thus, in this chapter, we will discuss how diet affects