Tuohy / Del Rio Diet-Microbe Interactions in the Gut

Effects on Human Health and Disease
1. Auflage 2014
ISBN: 978-0-12-407941-0
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 268 Seiten

Drawing on expert opinions from the fields of nutrition, gut microbiology, mammalian physiology, and immunology, Diet-Microbe Interactions for Human Health investigates the evidence for a unified disease mechanism working through the gut and its resident microbiota, and linking many inflammation-related chronic diet associated diseases. State of the art post-genomic studies can highlight the important role played by our resident intestinal microbiota in determining human health and disease. Many chronic human diseases associated with modern lifestyles and diets - including those localized to the intestinal tract like inflammatory bowel disease and celiac disease, and more pervasive systemic conditions such as obesity, diabetes and cardiovascular disease - are characterized by aberrant profiles of gut bacteria or their metabolites. Many of these diseases have an inflammatory basis, often presenting with a chronic low-grade systemic inflammation, hinting at persistent and inappropriate activation of inflammatory pathways. Through the presentation and analysis of recent nutrition studies, this book discusses the possible mechanisms underpinning the disease processes associated with these pathologies, with high fat diets appearing to predispose to disease, and biologically active plant components, mainly fiber and polyphenols, appearing to reduce the risk of chronic disease development. - One comprehensive, translational source for all aspects of nutrition and diet's effect on gastrointestinal health and disease - Experts in nutrition, diet, microbiology and immunology take readers from the bench research (cellular and biochemical mechanisms of vitamins and nutrients) to new preventive and therapeutic approaches - Clear presentations by leading researchers of the cellular mechanisms underlying diet, immune response, and gastrointestinal disease help practicing nutritionists and clinicians (gastroenterologists, endocrinologists) map out new areas for clinical research and structuring clinical recommendations

Autoren/Hrsg.

Tuohy, Kieran

Del Rio, Daniele

Inhaltsverzeichnis

1;Front Cover;1
2;Diet-Microbe Interactions in the Gut;4
3;Copyright Page;5
4;Contents;6
5;Foreword;10
6;Acknowledgements;12
7;List of Contributors;14
8;1 The Microbiota of the Human Gastrointestinal Tract: A Molecular View;16
8.1;Introduction;16
8.2;Gut Microbiota Metabolism in Health and Disease;16
8.3;Methodologies for Studying the Human Gut Microbiota;18
8.3.1;Measuring Species Richness and Variability;18
8.3.2;Estimating Microbial Relative Abundance within the Gut Microbiota using Culture-Independent Methods;19
8.3.3;Measuring Microbial Activity;20
8.4;Spatial Distribution of the Gut Microbiota and Interactions with Diet;21
8.4.1;The Stomach;21
8.4.2;The Small Intestine (Jejunum and Ileum);22
8.4.3;The Colon (Large Intestine);23
8.5;Models to Study Microbial Ecology;25
8.6;Conclusions;26
8.7;References;26
9;2 A Nutritional Anthropology of the Human Gut Microbiota;32
9.1;Human Diet or Microbiota, Which Came First?;32
9.2;Metagenomics and Cultivation-Independent Assessment of Human Gut Microbiota;33
9.3;Microbiome and Human Nutritional Phenotype;33
9.4;The Gut Microbiota in Human Evolution;34
9.5;Population Metagenomic Variation within the Human Microbiota;36
9.5.1;Populations can be Separated by Characteristic Differences in the Gut Microbiota;36
9.6;The Western Diet Metagenome is Obesity Prone;39
9.7;Conclusions;40
9.8;References;40
10;3 Probiotic Microorganisms for Shaping the Human Gut Microbiota – Mechanisms and Efficacy into the Future;42
10.1;Introduction;42
10.2;Let’s Start With the Definition of Probiotics;42
10.3;Shaping the Microbiota;43
10.4;The Neonatal Period;44
10.5;Adult Life and the Proposed Enterotype Classification;46
10.6;The Aged Period;47
10.7;Mechanisms and Efficacy;48
10.8;Efficacy in Healthy People;48
10.9;Conclusions;52
10.10;References;52
11;4 Bifidobacteria of the Human Gut: Our Special Friends;56
11.1;Taxonomy of Bifidobacteria;56
11.2;Bifidobacterial Ecology;58
11.3;Bifidobacterial Populations in the Human Gut;58
11.4;Bifidobacteria as Probiotics;59
11.5;Bifidobacterial Genomics;60
11.6;Comparative Genomics and Bifidobacteria;61
11.7;Interaction Between Bifidobacteria and Their Hosts;62
11.7.1;Exopolysaccharides (EPS);62
11.7.2;Pilus-Like Structure;62
11.7.3;Serine Protease Inhibitor;63
11.7.4;Bacteriocins;63
11.8;Conclusions;63
11.9;References;64
12;5 Shaping the Human Microbiome with Prebiotic Foods – Current Perspectives for Continued Development;68
12.1;Introduction;68
12.2;Linking Microbiome Structure and Function;69
12.3;Probiotics;70
12.4;Prebiotics;71
12.5;Testing Prebiotics;74
12.6;Conclusion;80
12.7;References;81
13;6 Bioactivation of High-Molecular-Weight Polyphenols by the Gut Microbiome;88
13.1;Introduction;88
13.2;Proanthocyanidins;88
13.2.1;Structures and Nomenclature;88
13.2.2;Distribution in the Plant Kingdom: From Ecological Role to Behavior during Gastrointestinal Transit;89
13.2.3;Variability and Proanthocyanidin Determination in Foods;91
13.2.4;Dietary Sources, Intake and Health Benefits;91
13.2.5;Fate of Proanthocyanidins through the Digestive Tract;92
13.2.5.1;In Vitro Biotransformation;94
13.2.5.2;In Vivo Biotransformation;99
13.3;Hydrolyzable Tannins (Gallotannins and Ellagitannins);100
13.3.1;Chemistry of Hydrolyzable Tannins (Gallotannins and Ellagitannins);101
13.3.2;Occurrence and Dietary Sources;102
13.3.3;Metabolism of Hydrolyzable Tannins in Humans;105
13.3.4;Protective Effects of Hydrolyzable Tannins Intake in Human Subjects;111
13.4;Conclusions;113
13.5;References;113
14;7 Gut Microbial Metabolism of Plant Lignans: Influence on Human Health;118
14.1;Introduction;118
14.2;Conversion of Plant Lignans to Enterolignans by Gut Bacteria;119
14.3;Associations Between Lignan Exposure and Human Health;122
14.3.1;Cancer;122
14.3.1.1;Colorectal Cancer;123
14.3.1.2;Breast Cancer;123
14.3.1.3;Prostate Cancer;124
14.3.2;Cardiovascular Disease;125
14.3.3;Other Health Effects;125
14.4;Interindividual Differences in Lignan Metabolism;125
14.4.1;Diet;126
14.4.2;Sex Differences in Enterolignan Production;128
14.4.3;Other Factors Associated with Enterolignan Production;128
14.5;Conclusions;129
14.6;Acknowledgements;129
14.7;References;129
15;8 Gut Microbiome Modulates Dietary Xenobiotic Toxicity: The Case of DON and Its Derivatives;134
15.1;Introduction;134
15.2;Gastric Stability of DON Derivatives;136
15.3;Bacterial Transformation and Intestinal Absorption of DON and its Derivatives;136
15.4;DON and DON-Conjugates Impact on the Human Gut;138
15.5;References;139
16;9 Gut Microbiota–Immune System Crosstalk: Implications for Metabolic Disease;142
16.1;Gut Microbial Recognition by the Immune System;142
16.1.1;Immune Effectors of Intestinal Microbiota–Host Crosstalk;143
16.2;Intestinal Barrier, Gut Permeability and Metabolic Inflammation;144
16.3;Effects of Intestinal Bacterial Short-Chain Fatty Acids (SCFAs) on Inflammation and Metabolism;145
16.4;Dietary Fat Metabolism, Bile Acids and Gut Microbiota;146
16.5;Diet, Tmao, Gut Microbiota and Atherosclerosis;147
16.6;Immune Versus Metabolic Functions in Intestinal Epithelial Cells Gene Networks;148
16.7;Conclusion;149
16.8;References;150
17;10 The Interplay of Epigenetics and Epidemiology in Autoimmune Diseases: Time for Geoepigenetics;154
17.1;The Etiology and Pathogenesis of Autoimmune Disease;154
17.2;The Rationale for Geoepigenetics;155
17.3;Geoepigenetics of Systemic Lupus Erythematosus (SLE);156
17.4;Geoepigenetics of Rheumatoid Arthritis (RA);158
17.5;Geoepigenetics of Systemic Sclerosis;159
17.6;Conclusions;160
17.7;References;160
18;11 Obesity-Associated Gut Microbiota: Characterization and Dietary Modulation;164
18.1;The Obesity Pandemic;164
18.2;Genetic Determinants of Obesity;164
18.3;Obesity Associated Gut Microbiota;165
18.3.1;Gut Microbiota and Obesity: Evidence from Mice;166
18.3.1.1;Differences in Bacterial Composition at a Phylum Level;166
18.3.1.2;Differences in Bacterial Composition at a Genus/Group Level;166
18.3.2;Gut Microbiota and Obesity: Evidence from Human Studies;166
18.3.2.1;Difference in Bacterial Composition at Phylum Level;166
18.3.2.2;Difference in Bacterial Composition at Genus/Groups Level;167
18.3.3;Archaea Methanogens;167
18.3.4;Cause or Consequence;168
18.4;Interactions between Gut Microbes and Obesity: “The Energy Extraction Theory”;169
18.4.1;Gut Microbiota and Dietary “Energy-Harvest”;169
18.4.2;Role of SCFA and their Receptors in Dietary “Energy-Harvest”;171
18.5;Interactions between Gut Microbes and Obesity: “The Appetite Control Theory”;172
18.6;Interactions between Gut Microbes and Obesity: “The Inflammation Theory”;173
18.7;Gut Microbiota AS A Therapeutic Target of Probiotics, Prebiotics and Synbiotics;176
18.8;Conclusions;181
18.9;References;181
19;12 An Apple a Day Keeps the Doctor Away – Inter-Relationship Between Apple Consumption, the Gut Microbiota and Cardiometabo...;188
19.1;Introduction;188
19.2;Apple Components;188
19.2.1;Simple Carbohydrates;189
19.2.2;Vitamins and Minerals;190
19.2.3;Fiber;190
19.2.4;Polyphenols;190
19.2.4.1;Polyphenols Bioavailability;192
19.3;The Human Gut Microbiota;193
19.3.1;Modulation of the Gut Microbiota Composition – Impact of Apples and Apple Components;194
19.4;Cardiometabolic Disease Risk – Epidemiological Studies;195
19.5;Cardiometabolic Risk Factors;196
19.5.1;Lipid Metabolism;196
19.5.2;Mechanisms Explaining the Potential Lipid Lowering Effects;199
19.5.2.1;Inhibition of Enterohepatic Circulation;199
19.5.2.2;Modulation of Lipid Metabolism;199
19.5.2.3;Digestive Enzyme Inhibition;199
19.5.2.4;Polyphenol–Pectin Synergistic Effect;199
19.5.3;Blood Pressure and Vascular Function;200
19.5.4;Inflammation;200
19.5.5;Antioxidant Role;201
19.6;Diabetes Risk;202
19.7;Conclusion;202
19.8;References;203
20;13 Whole Plant Foods and Colon Cancer Risk;210
20.1;Introduction;210
20.2;Diet and Colorectal Cancer;210
20.3;Biological Activity and Anticancer Properties of Whole-Grain Cereals;212
20.3.1;Biomarkers for CRC;213
20.4;Biological Activity and Anticancer Properties of Brassica Vegetables;214
20.5;Human Studies;214
20.6;Biological Activity and Anticancer Properties of Berry Fruits;216
20.7;Conclusion;218
20.8;References;219
21;14 Population Level Divergence from the Mediterranean Diet and the Risk of Cancer and Metabolic Disease;224
21.1;Mediterranean Diet as the Traditional Diet of Southern Europe;224
21.1.1;Historical Overview;224
21.1.2;Expression of Culture and Lifestyle – UNESCO’s Recognition;225
21.1.3;Scientific Definition and Description;225
21.2;The Evidence-Based Health Protection by Mediterranean Diet;226
21.2.1;First Epidemiological Evidence;226
21.2.2;Level of Adherence: Is there any Measure?;226
21.2.3;The Moli-Sani Experience;227
21.2.4;Mediterranean Diet – From Epidemiology to Clinical Trials;228
21.3;Mediterranean Diet as a Health Protection Model;229
21.3.1;Preventing Cardio-Metabolic Disease;229
21.3.2;Protection against Different Types of Cancer;230
21.4;Mediterranean Food Consumption and Human Gut Microbiota;231
21.4.1;Mediterranean Food Intake and Impact on Human Gut Microbiota;231
21.4.2;Concluding Remarks;234
21.5;References;234
22;15 Diet and the Gut Microbiota – How the Gut:Brain Axis Impacts on Autism;240
22.1;Background;240
22.2;Gut Microbiota and ASD;241
22.3;Amino Acid Metabolism;243
22.4;Lipid Metabolism and the Brain;245
22.5;Short-Chain Fatty Acids (SCFA) and the Brain;246
22.6;Gut Microbiota and Digestive Function;248
22.6.1;Dietary Patterns, Gut Microbiota and Brain Development;250
22.6.2;Dietary Modulation of the Gut Microbiota for Improved Brain Function;250
22.7;Probiotics, Gut Microbiota Successional Development and Brain Function;252
22.8;Conclusions;253
22.9;References;253
23;Index;262

Leseproben

Chapter 2

A Nutritional Anthropology of the Human Gut Microbiota

Carlotta De Filippo and Kieran M. Tuohy,    Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy

Undoubtedly, modern humankind is an omnivorous species. Nevertheless, types of diet changed radically over the course of human evolution, from hunter–gatherers, through the birth of agriculture and culminating with the modern Western-style diet. The Upper Paleolithic period is the crucial time because of the appearance of anatomically modern humans in Europe.

The human gut “metagenome” is a complex consortium of trillions of microbes, whose collective genomes contain at least 100-times as many genes as our own eukaryote genome. This essential “organ” provides the host with enhanced metabolic capabilities, protection against pathogens, education of the immune system and modulation of gastrointestinal development.

Historically, the microbial ecosystem of the gastrointestinal tract was specific for an environmental niche, as much as the flora and fauna of an ecosystem are geographically distinct. A clear example of this richness and diversity is that currently in Africa, the microbial composition is very different from that described in the Western world. Globalization of the microbial population of our digestive tracts is due to industrialization and standardization of food chain products that homogenizes the microorganisms that we ingest. Understanding the evolution of human–microbe ecosystems greatly benefits from a baseline reflecting an ancestral state of the human microbiome. The study of our closest living cousins, the other great apes, provides one path to reconstruct ancestral microbiomes. Retrieving human microbiome information from samples left behind by our distant ancestors would provide an ideal approach to understanding the coevolution of humans and microbes.

Keywords

Gut microbiota; Metagenomics; Diet; Microbial communities

Human Diet or Microbiota, Which Came First?

The feeding strategy of appears to be characterized by an extraordinary omnivorism, which has no equal among mammals with the exception to some extent of the Suidae and the brown bear. This strategy allows him to have a diet that is able to capture all substances and nutrients necessary for its energy and structural needs, according to the best sources, such as foods, available in the ecosystem of origin and from a certain point in its evolution, adapted to remote ecosystems. We can therefore say that diet is one of the main factors that differentiates and drives evolution of human populations. Dietary differences originated from cultural evolution and geographic differences in availability of crops and cultivation and animal husbandry. It is widely recognized that a varied and balanced diet is essential to an individual’s health. The adverse effects of nutrient deficiency are numerous and well documented.1–4 Because nutritionally related problems continue to be the cause behind many diseases that hinder progress towards universally adequate health, all countries should be actively pursuing the improvement of their people’s nutritional status. Recently we witnessed an explosion of food consumption studies in both urban and rural areas of developing countries.5–7 These types of studies are vital to our understanding of more “transitional” and/or “traditional” diets vs. the modern-day Western-style diet. Furthermore, food-consumption in rural communities in particular generally involves a large proportion of the food coming from home-production or gathering or, at the very least, having been grown, produced and purchased locally. Therefore, diets are usually monotonous and simple because they are dependent on the availability of foods in the home or local markets as well as the prices of those foods. However, the foods themselves, often consumed with little processing or using traditional fermentation technologies, represent complex mixtures of non-digestible carbohydrates and fibers, polyphenols and live fermentative microorganisms, thereby representing both complex nutritional support for the gut microbiota and an important source of passenger microorganisms with immune-modulatory and metabolic potential. The relative invariability of these traditional diets may potentially be reflected in gut colonization by relatively homogeneous and characteristic microbiomes. Recent discoveries highlighting the importance of gut microbiota have demonstrated how the availability of the nutrients present in the foods comprising everyone’s diet is highly dependent on the human gut microbiota. The question then becomes, to what extent is the human gut microbiota dependent on changes in diet and how robust is the human microbiota from birth to death? To propose potential answers to these questions first of all we have to understand what is the human microbiota.

Metagenomics and Cultivation-Independent Assessment of Human Gut Microbiota

The human gut microbiota is composed of commensal microorganisms inherited largely from our mothers at birth, passengers’ microorganisms, mainly environmental, with which we come into continuous contact via the food we eat, and potential pathogens, exogenous invaders which try to overcome the body’s defenses and cause disease. In the 20th century our knowledge of the human microbiota was constrained by the ability to describe and study the biological functions of less than a hundred cultivable bacteria. The species we described until the year 2000 were also the most easily cultivated, and given the special attention of funding agencies towards pathogens, we fundamentally ignored the genome to function relation for the vast majority of our commensal organisms which do not cause disease and a handful of bacterial species used in food production and shown to dominate the gut microbiota of breast-fed infants, the lactobacilli and bifidobacteria, respectively.

Furthermore, for a century the study of microorganisms has been limited by the ability to cultivate them. The established view is that only a subset of the microbial species which make up our microbiome can be easily cultivated. Recently, the scientific revolution driven by high-throughput sequencing techniques (Next Generation Sequencing, NGS), has made possible the unraveling of the evolutionary history of human gut microbiome. Key to this endeavor has been the emergence of bioinformatics tools necessary to describe the microbial ecology-encoded high-resolution NGS data derived from diverse microbiomes.

Large-scale projects such as the European Metagenomics of the Human Intestinal Tract MetaHIT8 and the US Human Microbiome Project, HMP9,10 have made substantial progress towards this goal and the amount of metagenomic information is exponentially increasing, especially that obtained for individuals living in industrialized countries. The first EU-funded MetaHIT consortium produced Illumina sequences of fecal samples of 124 European individuals, including healthy, overweight and obese adults, as well as patients with inflammatory bowel disease (IBD).8 When extended to Japanese and American populations, MetaHIT also established that the worldwide population could be classified into three distinct enterotypes.11 The NIH-funded Human Microbiome Project, HMP Consortium, is also developing and indexing another fundamental reference set of microbial genome sequences from a population of 242 healthy adults, sampled at different body sites, generating 5177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far.9,10 In parallel, they have sequenced approximately 800 reference strains isolated from the human body, generating data that represent the largest resource describing the abundance and variety of the human microbiome. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome.9,10 The information deposited in these resources promises to be a goldmine for pathway and network inference, reconstructing the super-meta-pathway subtending the interaction between humans and their microbiomes.

Microbiome and Human Nutritional Phenotype

The role of the gut microbiota in provision of nutritionally relevant molecules for human health and nutrition is still largely unknown, but indeed these organisms do contribute metabolic and digestive functions absent from the human genome.12 A glimpse of the metabolic pathway complexity contained in metagenomics datasets first emerged from the study of Gill et al.13: the human genome lacks most of the enzymes required for degradation of plant polysaccharides and they are supplied by the human gut microbiome which can metabolize cellulose, starch and unusual sugars such as arabinose, mannose, and xylose, thanks to at least 81 different glycoside hydrolase families. With the aim of understanding the dietary modulation of gut microbiota, Zhu et al.14 undertook a large-scale analysis of 16S rRNA gene sequences to profile the microbiota inhabiting the digestive system of giant pandas using a metagenomic approach. They performed predicted gene functional classification, finding the presence of putative cellulose-metabolizing symbionts in this little-studied microbial environment, explaining how giant pandas are able to partially digest bamboo fiber, despite a genome lacking enzymes that can degrade cellulose. This study showed the...