19: Microbiomes
- Page ID
- 159314
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)The human microbiome and the health of animals and the environment are increasingly recognized as essential components of public health. Microorganisms are not only agents of disease but also vital partners in maintaining the health of individuals and ecosystems. The growing burden of chronic and emerging infectious diseases, antibiotic resistance, and the effects of climate change have shown that human health cannot be viewed in isolation.
In this chapter, we will explore the connections between the microbiome and One Health, an interdisciplinary approach that links the health of people, animals, and the environment. We will examine how microbial communities support digestion, immunity, and development - and how disruptions to these communities can contribute to disease. We will also investigate how zoonotic diseases emerge, why antibiotic resistance spreads between sectors, and what global cooperation is needed to tackle these challenges. Advances in microbiome research and the One Health framework are reshaping how we understand, monitor, and promote health in a rapidly changing world.
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Figure \(\PageIndex{1}\): Skin metagenomics and defines relative abundance of viral, bacterial and fungal components of the microbial community. Credit: Darryl Leja, NHGRI.
- 19.1: An Introduction to Microbiomes
- This page covers the concepts of microbiome and microbiota, emphasizing the community of microorganisms and their genetic activities, and the host-microbe relationship's impact on health. It includes references to studies on human and plant microbiomes, examining their roles in health issues like mental health and ecological interactions.
- 19.2: The Human Microbiome
- This page summarizes the Human Microbiome Project's goals and phases, focusing on its role in understanding health and disease. It emphasizes the microbiome's impact on various conditions and its diversity based on body locations. Additionally, it highlights studies on gut microbiomes, plant microbiomes, and techniques in microbiome research.
- 19.3: Analyzing Microbiomes
- This page emphasizes the importance of selecting suitable methods for microbiome analysis tailored to specific research questions. It discusses various approaches such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, each with unique strengths and limitations.
- 19.4: Human Health and Disease
- This page discusses the importance of the human microbiome for health, highlighting its subcategories (gut, oral, skin) and influencing factors such as diet, age, and genetics. It explains that dysbiosis can lead to various diseases and emphasizes the role of host genetics in microbiome composition and disease susceptibility. The interplay between genetics, environment, and individual behaviors shapes the microbiome's diversity and function.
- 19.5: The Gut Microbiome
- This page emphasizes the critical role of the gut microbiome in human health, linking its composition and diversity to diseases such as obesity, diabetes, and IBD. Dysbiosis can indicate health issues and may be a treatment target. Factors influencing microbiome diversity include diet, genetics, and environment, with high-fat diets contributing to inflammation.
- 19.6: C diff Infection (CDI) and Fecal Microbiota Transplant (FMT)
- This page discusses the significant impact of chemotherapy and antibiotics on the gut microbiome, leading to increased risks of infections like C. difficile, which thrives in dysbiotic conditions. Alternative treatments such as probiotics and fecal microbiota transplants show promise, though safety and personalization challenges remain. The page also references studies on gut microbiome health, its relationship with various diseases (e.g.