1

Introduction

Many people think of the skin, or perhaps the lungs, as the principal barrier between human bodies and the outside world. Arguably, it is neither. Many would argue that our most intimate relationship with the outside world is in our gut. Our gastrointestinal (GI) tracts harbor a vast and still largely unexplored microbial world. Microbial cells on or in the human body, not just in the gut but elsewhere as well, outnumber human cells 10 to 1. Scientists are only just beginning to understand what is collectively known as the human microbiome—what it is, what it does, and how it benefits human health. They are recognizing the integral role of the microbiome in human physiology, health, and disease—with microbes playing critical roles in many host metabolic pathways—and the intimate nature of the relationships between, on the one hand, the microbiome and host physiology, and on the other, the microbiome and host diet. While there is still a great deal to learn, especially about the underlying mechanisms driving these relationships, the newfound knowledge already is being used to develop dietary interventions aimed at preventing and modifying disease risk by manipulating the microbiome.

The Food Forum convened a public workshop on February 22-23, 2012, to explore current and emerging knowledge on the human microbiome, its role in human health, its interaction with the diet, and the translation of new research findings into tools and products that improve the nutritional quality of the food supply. The purpose of the workshop was to (1) understand how diet influences the human microbiome, as well as how the microbiome influences the response to diet and dietary components; (2) become familiar with the acquisition of, and potential ways to modify,



The National Academies | 500 Fifth St. N.W. | Washington, D.C. 20001
Copyright © National Academy of Sciences. All rights reserved.
Terms of Use and Privacy Statement



Below are the first 10 and last 10 pages of uncorrected machine-read text (when available) of this chapter, followed by the top 30 algorithmically extracted key phrases from the chapter as a whole.
Intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text on the opening pages of each chapter. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.

Do not use for reproduction, copying, pasting, or reading; exclusively for search engines.

OCR for page 23
1 Introduction M any people think of the skin, or perhaps the lungs, as the principal barrier between human bodies and the outside world. Arguably, it is neither. Many would argue that our most intimate relationship with the outside world is in our gut. Our gastrointestinal (GI) tracts harbor a vast and still largely unexplored microbial world. Microbial cells on or in the human body, not just in the gut but elsewhere as well, outnumber human cells 10 to 1. Scientists are only just beginning to understand what is collectively known as the human microbiome—what it is, what it does, and how it benefits human health. They are recognizing the integral role of the microbiome in human physiology, health, and disease—with microbes playing critical roles in many host metabolic pathways—and the intimate nature of the relationships between, on the one hand, the microbiome and host physiology, and on the other, the microbiome and host diet. While there is still a great deal to learn, especially about the underlying mecha- nisms driving these relationships, the newfound knowledge already is being used to develop dietary interventions aimed at preventing and modifying disease risk by manipulating the microbiome. The Food Forum convened a public workshop on February 22-23, 2012, to explore current and emerging knowledge on the human microbi- ome, its role in human health, its interaction with the diet, and the trans- lation of new research findings into tools and products that improve the nutritional quality of the food supply. The purpose of the workshop was to (1) understand how diet influences the human microbiome, as well as how the microbiome influences the response to diet and dietary components; (2) become familiar with the acquisition of, and potential ways to modify, 23

OCR for page 23
24 THE HUMAN MICROBIOME, DIET, AND HEALTH the human microbiome to reduce risk and prevent or modify disease; (3) explore the societal and policy implications of applying research findings to the food supply; and (4) identify opportunities for future research and food product and technology development on the interaction between the human microbiome and diet or dietary components and how this interac- tion influences health outcomes. This report summarizes the presentations and discussions that took place during the workshop. It summarizes only the statements of partici- pants at the workshop over the course of the two consecutive days. It is not intended to be an exhaustive exploration of the subject matter, nor does it represent the findings, conclusions, or recommendations of a consensus committee process. The goal was to illuminate issues, not resolve them. The workshop served as a mechanism for individuals from a variety of academic, industry, government, marketing research, and other groups to discuss and debate issues openly and to identify possible approaches for ad- dressing some of the more pressing issues pertaining to microbiome-related research and product development. ORGANIZATION OF THIS REPORT The organization of this report parallels the organization of the work- shop itself (see Appendix A). This introductory chapter sets the stage by summarizing the keynote presentation by Karen Nelson and providing an overview of major workshop themes. Chapter 2 summarizes the presenta- tions and discussion on the wealth of sequencing data that have been ac- cumulating rapidly as a result of advances in sequencing technology. It also covers what researchers have already learned about what microbes inhabit which parts of the body and the trend toward seeking to understand not just what microbes are present, but what those microbes are doing and how their activity influences host health (i.e., session 1). Chapter 3 summarizes the presentations and discussion that focused on associations between the microbiome and health and disease, with a focus on pediatric, oral, and GI tract health and disease (i.e., part of session 2). Toward the end of the first day, speakers began addressing in greater depth not just how the microbiome interacts with its host, but how those interactions are medi- ated by diet. Chapter 4 summarizes the presentations and discussion that focused on how the microbiome influences host response to diet and dietary components (i.e., parts of sessions 2 and 3). Chapter 5 summarizes the pre- sentations and discussion that focused on how host diet, in turn, impacts the microbiome, the implications of that impact for human health, and the opportunities and scientific challenges to translating this knowledge into tools and products for use in building and maintaining health (i.e., parts of session 3 and all of session 5).

OCR for page 23
INTRODUCTION 25 As the workshop progressed, participants began exploring the social and policy challenges, especially around regulation of food claims, to trans- lating all of these new research findings into tools and products for building and maintaining health. Chapter 6 summarizes those presentations and discussions (i.e., session 6). Finally, Chapter 7 summarizes the discussion that took place during the final session of the workshop, when participants were challenged to identify opportunities for future research and product development related to diet-mediated interactions between the microbiome and human health. KEYNOTE ADDRESS: THE FUTURE IMPACT OF BENEFICIAL MICROBES AND GUT HEALTH1 Microbial cells that populate the human body outnumber human cells by an order of magnitude, with the most densely populated areas being the nasal, oral, skin, gastrointestinal, and urogenital environments. Scientists are only just beginning to understand what these microbes do, how they function, and how they can be manipulated to benefit human health. Re- search on the human microbiome has benefited tremendously from other recent advances in microbiology, not the least of which is a growing rec- ognition of the vast microbial diversity that exists. Keynote speaker Karen Nelson mentioned Craig Venter and colleagues’ circumnavigations of the globe to collect seawater samples and study oceanic microbial diversity (Rusch et al., 2007; Venter et al., 2004; Wu et al., 2011; Yooseph et al., 2007). According to Nelson, that work led to a doubling of the number of predictive protein signatures2 “essentially overnight.” The lesson learned, she said, was “that there is a tremendous amount of microbial diversity in the environment that we have not tapped … we really don’t know how much diversity is out there.” Advances in Sequencing Technologies In addition to spawning a realization of how vast the microbial world is, studies of microbial diversity in other (non–human body) environments also helped the development of advanced sequencing technologies that are now driving research on the microbiome. Nelson recalled how exciting it was when she and colleagues (Eckburg et al., 2005) used Sanger sequenc- ing of the 16S ribosomal RNA (rRNA) gene to evaluate microbial diversity in six major subdivisions of the GI tract even though they were unable to interpret the significance of their results at the time. Shortly thereafter, 1  This section summarizes Karen Nelson’s keynote presentation. 2  Nucleotide sequence signatures that indicate the presence of a particular protein.

OCR for page 23
26 THE HUMAN MICROBIOME, DIET, AND HEALTH Gill et al. (2006) conducted the first metagenomic study of the human gut microbiome. Metagenomics describes the ability to sequence all the genetic material in a sample without initially having to cultivate the microbial species that are present. The development of these methods was a huge step forward over sequencing methods that were focused on a single phy- logenetic marker (as was the case with 16S rRNA) and other methods that were dependent on a PCR (polymerase chain reaction) amplification step that is now known to potentially introduce significant bias. For the Gill et al. (2006) study, even though the researchers sampled from only two indi- viduals, all that microbial diversity again elicited much excitement. At that time, the J. Craig Venter Institute (JCVI) had one of the largest sequenc- ing centers in the world, running about 100 Sanger sequencing machines around the clock that generated about 1-2 megabases per day. Today, the newest high-throughput sequencing technology is capable of generating an entire human genome in about 4 hours.3 Nelson noted that her first microbial genome sequence project involving the genome of Thermotoga maritime took approximately 2 years and cost about $2 million. Today, the same project could probably be done in an afternoon for less than $200. She predicted that sequencing technology will continue to advance. “I be- lieve that sequencing is going to become like PCR,” she said. “Every grad student is going to have their own sequencing machine on their desktop.” The largest human microbiome sequencing study to date is the National Institutes of Health (NIH)-funded Human Microbiome Project (HMP), whose focus is on generating a metagenomic reference database for “nor- mal” individuals to serve as a resource for researchers studying microbiome- disease associations and other phenomena. The reference dataset is based on a human cohort of 300 individuals, with microbial genome data being collected from five major body sites (nasal, oral, skin, GI, and urogenital environments). When the project started, the goal was to sequence 1,000 reference genomes. Today, the goal is to sequence 3,000 reference genomes. Results from the first 178 genomes sequenced were published in 2010 (Hu- man Microbiome Jumpstart Reference Strains Consortium, 2010). In ad- dition to its mostly bacteria-focused work, the HMP also has an initiative to sequence several viruses and microeukaryotes that are associated with the human body. The Microbiome and Disease In parallel to the HMP, a number of other organizations have been funding microbiome work focused on specific diseases, with many research- ers taking systems biology approaches and integrating multiple -omics 3  The human genome contains an estimated 3,000 megabases.

OCR for page 23
INTRODUCTION 27 technologies (e.g., transcriptomics, proteomics, glycomics, metabolomics). Nelson perceives the field as moving away from “just sequencing” toward “integrating all these different -omics approaches.” In addition to its involvement with the HMP, JCVI itself has about 20 disease-focused metagenomic studies funded not just by NIH but also by the National Science Foundation (NSF), the Bill & Melinda Gates Foundation, the National Aeronautics and Space Administration, and others. For ex- ample, the National Institute of Diabetes and Digestive and Kidney Diseases recently awarded JCVI a $5 million grant to study the gut microbiome and virome, along with the urinary proteome and metabolome, in an effort to identify a panel of biomarker candidates for type 1 diabetes. JCVI will be recruiting children with type 1 diabetes and using their healthy siblings as controls. NIH also funded JCVI in collaboration with researchers from New York University to examine how the microbiome and virome change over time in individuals with esophageal cancer. Investigators are following 80 individuals over 4 years; the study is currently entering its final year. Already they have detected microbial signatures associated with different stages of esophageal cancer. It is unclear whether the microbial changes are caus- ing the cancer or the cancer is causing the microbial changes. Either way, N ­ elson said, “You can imagine new therapies that are based on … restoring what the normal [microbial] population looks like.” A third example of disease-focused JCVI research is a study being conducted in collaboration with Dr. David Brenner at the University of California, San Diego, on liver damage and alcoholism. Using different mouse models, the researchers have demonstrated a correlation between certain changes in microbial metabolites and disease onset (Fouts et al., 2012; Yan et al., 2011). The Health and Wellness Potential of Microbiome Manipulation Also at JCVI, Dr. Roger Lasken has created what Nelson described as a “high-throughput pipeline” for generating genomes of microbial species that cannot be cultivated. The methodology is based on cell sorting mecha- nisms and multiple displacement amplification (MDA). Nelson noted that this type of nontraditional approach is necessary for accessing genomes of the 98 to 99 percent of microbes that cannot be cultivated. As scientists learn more about the role of the microbiome in human health and wellness, accessing that genomic space will become increasingly desirable. Nelson foresees this once-inaccessible genomic information being used to develop novel therapeutic and nutritional (e.g., probiotic) tools in the future. Yet before the health and wellness potential of microbiome manipula- tion can be realized, the field faces some key challenges. Nelson identified informatics as one of the “big gaps.” She said, “I think we are getting ahead of ourselves in terms of being able to interpret the data that are be-

OCR for page 23
28 THE HUMAN MICROBIOME, DIET, AND HEALTH ing generated.” Another key challenge is the lack of communication and collaboration among experts in microbiology, nutrition, and other relevant fields. She encouraged more dialogue across disciplinary groups and more industry participation in the dialogue. Challenges with Experimental Design During the question-and-answer period following Nelson’s talk, most of the discussion revolved around experimental design, including tissue sampling, sample size, and the definition of “normal.” An audience member suggested that sampling from the small intestine would be more informative than sampling from fecal samples or from the esophagus. Nelson agreed that the field needs to move in a direction where scientists are sampling from other parts of the GI tract, but researchers have done as well as they have been able in the early stages. Sampling from the small intestine would be more invasive than fecal sampling. She suggested that more cross-­ disciplinary dialogue, in this case with medical researchers, could help move the field in that direction. Another question was raised about the value of a study based on a sample size of 300, let alone 2, individuals (the person ask- ing the question was referring to Nelson’s mention of the N = 300 sample size of the HMP reference database and the N = 2 sample size of the Gill et al., 2006, study). Nelson agreed that the field needs to move in that direc- tion, that is, toward sampling large host populations, but again she said, “We did what we could do at that point in time.” Another audience mem- ber asked how HMP investigators define “normal.” Lita Proctor agreed that the question is “nontrivial.” Defining normal was a struggle. They finally decided that for the purpose of the HMP, “normal,” or “healthy,” meant verification of no overt disease based on clinical examination. MAJOR OVERARCHING THEMES The microbiome is integral to human physiology, health, and disease. • Scientists are beginning to recognize the microbiome as an extra level of biological complexity that is integral to human physiology, health, and disease. Some workshop participants perceived the microbiome as an extension of human metabolism, with gut bacteria playing key roles in host metabolism. Native bacteria impact not only which di- etary components their host is able to extract from its diet, but also how those dietary components are converted into biological signals. Gut microbes also impact host energetics. Neither chronic nor in- fectious disease risk can be understood without also taking into ac- count the microbiome. Indeed, the microbiome is increasingly being

OCR for page 23
INTRODUCTION 29 viewed as a target for diagnostic, prognostic, and even therapeutic approaches to predicting or managing various disease conditions. • As much as scientists are learning about associations between the microbiome and physiology, health, and disease, the microbial world inside us remains a vast and largely untapped world. As Peter Turnbaugh asked, “What additional functions or metabolic capabili- ties are provided us by these communities, and how does that impact our health and disease?” The microbiome is arguably the most intimate connection that humans have with their external environment, mostly through diet. • A major recurring theme of the workshop discussion was the very intimate connection that the human microbiome has with both its human host and its host’s external environment. Diet appears to be the most important environmental modulator of the microbiome, with significant implications for human health and disease. As sci- entists continue to learn about the impact of diet on the microbiome and the consequences of that impact for human health and disease, the food industry is using that newfound knowledge to develop novel products for building and maintaining health via their impact on the microbiome. Given the emerging nature of research on the microbiome, some important methodological issues still have to be resolved with respect to undersam- pling (i.e., some workshop participants expressed concern not just about underpowered studies, but also about tissue undersampling) and a lack of causal and mechanistic studies. • In almost every open discussion, individual workshop participants or audience members expressed concern about the danger of mak- ing predictions about diet-microbiome-health relationships based on studies with small samples sizes. For example, Ellen Silbergeld said, “I think the comments that have been raised throughout this meeting about how we’re really dealing with a very small edge of knowledge when we talk about the microbiome in any specific do- main should give us pause when we make predictions as to what is going to happen.” She remarked that small studies are helpful for formulating new hypotheses, but they are not sufficient for translat- ing science into public health. She and others cautioned that “large- N” studies will be needed in the future. Johan van Hylckama Vlieg and other participants agreed that more large-N studies are needed but emphasized that small-N studies serve an essential exploratory

OCR for page 23
30 THE HUMAN MICROBIOME, DIET, AND HEALTH role, enabling researchers to generate testable hypotheses for those larger studies. In addition, well-designed and small sample studies can contribute to building a mechanistic understanding of clinical observations obtained in larger studies. • With respect to fecal sampling, participants expressed concern that making inferences about what is happening inside the gut based on what is detected in feces can be dangerous given that the microbiome is a dynamic, complex system that is highly individual and easily perturbed. Jeremy Nicholson said, “For me, it is like trying to sniff an exhaust pipe of a Ferrari and tell you what color [the car] is. You have this very complex ecology which you have compressed into a piece of feces.… I think we need to develop new technologies to be able to study the microbes in situ and what they are doing locally.” Again, however, given its noninvasive nature, fecal sampling has been the only choice in many of these early studies. • There were some calls for more mechanistic research. Even when sequencing data are complemented with functional annotation, pur- ported functions are just that—purported. They still need to be validated with mechanistic study—thus, the importance of animal models or even non-animal models. • Some workshop participants also called for more longitudinal stud- ies as a way to examine causality. Much of what is being learned about diet-microbiome-health relationships is correlational, not cau- sational (e.g., that a particular microbial strain or microbial metabo- lite is associated with a disease risk, but with no clear understanding of which came first). Dietary interventions intended to have an impact on host biology via their impact on the microbiome are being developed, and the market for those products is seeing tremendous success. However, the current regulatory framework threatens to slow industry interest and investment. • Much of this early research on the microbiome focuses on associa- tions between the microbiome and disease, not health, and most dietary interventions intended to have an impact on host biology via their influence on the microbiome (e.g., probiotics) are being studied for their potential to prevent disease, not promote health. However, current regulatory constraints on food claims prohibit communicat- ing to consumers many of the effects that studies focused on dis- ease prevention demonstrate. Some workshop participants noted the challenges and value of conducting more studies in healthy popula- tions versus changing the regulatory landscape to accommodate the science.

OCR for page 23
INTRODUCTION 31 REFERENCES Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson, and D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308(5728):1635-1638. Fouts, D. E., M. Torralba, K. E. Nelson, D. A. Brenner, and B. Schnabl. 2012. Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease. Journal of Hepatology 56(6):1283-1292. Gill, S. R., M. Pop, R. T. Deboy, P. B. Eckburg, P. J. Turnbaugh, B. S. Samuel, J. I. Gordon, D. A. Relman, C. M. Fraser-Liggett, and K. E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312(5778):1355-1359. Human Microbiome Jumpstart Reference Strains Consortium. 2010. A catalog of reference genomes from the human microbiome. Science 328(5981):994-999. Rusch, D. B., A. L. Halpern, G. Sutton, K. B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J. A. Eisen, J. M. Hoffman, K. Remington, K. Beeson, B. Tran, H. Smith, H. Baden- Tillson, C. Stewart, J. Thorpe, J. Freeman, C. Andrews-Pfannkoch, J. E. Venter, K. Li, S. Kravitz, J. F. Heidelberg, T. Utterback, Y. H. Rogers, L. I. Falcon, V. Souza, G. Bonilla-Rosso, L. E. Eguiarte, D. M. Karl, S. Sathyendranath, T. Platt, E. Bermingham, V. Gallardo, G. Tamayo-Castillo, M. R. Ferrari, R. L. Strausberg, K. Nealson, R. Friedman, M. Frazier, and J. C. Venter. 2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biology 5(3):e77. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers, and H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667):66-74. Wu, D., M. Wu, A. Halpern, D. B. Rusch, S. Yooseph, M. Frazier, J. C. Venter, and J. A. Eisen. 2011. Stalking the fourth domain in metagenomic data: Searching for, discover- ing, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS ONE 6(3):e18011. Yan, A. W., D. E. Fouts, J. Brandl, P. Starkel, M. Torralba, E. Schott, H. Tsukamoto, K. E. Nelson, D. A. Brenner, and B. Schnabl. 2011. Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology 53(1):96-105. Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, and J. C. Venter. 2007. The Sorcerer II Global Ocean Sampling Expedition: Expanding the uni- verse of protein families. PLoS Biology 5(3):e16.

OCR for page 23