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Diet, Microbiome and Health

Diet, Microbiome and Health

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Diet, Microbiome and Health

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Jan 2, 2018


Diet, Microbiome and Health, Volume 11, in the Handbook of Food Bioengineering series, presents the most up-to-date research to help scientists, researchers and students in the field of food engineering understand the different microbial species we have in our guts, why they are important to human development, immunity and health, and how to use that understanding to further promote research to create healthy food products. In addition, the book provides studies that clearly demonstrate how dietary preferences and social behavior significantly impact the diversity of microbial species in the gut and their numeric values, which may balance health and disease.

  • Highlights research discoveries on how gut microbiota influence and are impacted by health and disease
  • Includes information on and examples of healthy foods
  • Discusses gut microbiota in autism, GI disease, neuropsychiatric disorders, obesity and metabolic disease
  • Explores the barrier function of the gut
  • Examines how food preferences impact gut microbiota
Jan 2, 2018

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Diet, Microbiome and Health - Academic Press

Diet, Microbiome and Health

Handbook of Food Bioengineering, Volume 11

Edited by

Alina Maria Holban

Alexandru Mihai Grumezescu

Table of Contents


Title page


List of Contributors


Series Preface

Preface for Volume 11: Diet, Microbiome and Health

Section 1: State of the Art and Applications

Chapter 1: Gut Microbes: The Miniscule Laborers in the Human Body


1. Introduction

2. Major Players of the Gut Microbiome

3. Functions of the Gut Flora

4. Infant Gut Flora

5. Evolution of Gut Microbial Flora

6. Diet in Shaping Composition of Gut Flora

7. Gut Microbiota and Diseases

8. Gut Flora and Brain Functions

9. Effect of Antibiotics on the Gut Microbiome

10. Fortifying Gut Flora

11. Conclusions

Chapter 2: Role of Probiotics Toward the Improvement of Gut Health With Special Reference to Colorectal Cancer


1. Probiotics

2. Probiotics as Health Promoters

3. Probiotics and Colorectal Cancer

4. Conclusions

Section 2: Probiotics and Prebiotics

Chapter 3: Therapeutic Aspects of Probiotics and Prebiotics


1. Introduction

2. The Concept of Probiotics

3. Therapeutic Effects of Probiotics

4. Prebiotics and Synbiotics

5. Therapeutic Effects of Prebiotics

6. Synbiotics

7. Theuraptic Effects of Synbiotics

8. Conclusions

Chapter 4: Lactic Acid Bacteria Beverage Contribution for Preventive Medicine and Nationwide Health Problems in Japan


1. Introduction

2. Tolerance to Gastric Acid and Bile, and Viability in the Intestinal Tract

3. Modification of Gastrointestinal Function: Improvement of Diarrhea and Constipation

4. Metabolism: Changing Urinary Excretion of Nitrogen

5. Immunomodulation

6. Prevention of Cancer

7. Effect on Inflammatory Bowel Disease

8. Protection Against Infection

9. Global Burden Diseases in Japan

10. Concluding Remarks

Chapter 5: Gut Microbiota Alterations in People With Obesity and Effect of Probiotics Treatment


1. Obesity: A Multifactorial Disease

2. Human Microbiome

3. Conclusions

Chapter 6: Safety of Probiotics


1. Introduction

2. Regulatory Systems

3. Most Frequent and Important Adverse Events of Probiotics

4. Safety Assessment Studies

5. Proposed Evaluation of the Safety of Probiotics by FAO/WHO

6. Conclusions

Section 3: Nutritional Aspects

Chapter 7: Flavonoids in Foods and Their Role in Healthy Nutrition


1. Introduction

2. Chemistry and Classification of Flavonoids

3. Antioxidant Activity of Flavonoids

4. Bioavailability of Flavonoids

5. Physiological Role and Pharmacological Activities of Flavonoids

6. Flavonoid Content and Antioxidant Activity of Selected Bulgarian Plant Foods

7. Conclusions

Chapter 8: The Role of Milk Oligosaccharides in Host–Microbial Interactions and Their Defensive Function in the Gut


1. Introduction

2. Effect of Oligosaccharides on Pathogen Colonization

3. Effects of Oligosaccharides on Commensal Colonization

4. Immunomodulation by Oligosaccharides

5. Mucin Expression, Defensive Function, and Indirect Effects of Oligosaccharides

6. Developing Areas

7. Conclusions and Future Perspectives

Chapter 9: Nutritional Yeast Biomass: Characterization and Application


1. Introduction

2. Saccharomyces cerevisiae Preparations

3. Saccharomyces boulardii as a Probiotic Yeast

4. Yarrowia lipolytica as a Source of Bioactive Compounds

5. Nutritional Benefits of Other Yeast Strains

6. Conclusions

Section 4: Health, Disease, and Therapy

Chapter 10: Effect of Diet on Gut Microbiota as an Etiological Factor in Autism Spectrum Disorder


1. Introduction

2. Factors Affecting Infant Gut Microbiota

3. Gut Microbiota of Autistic Patients

4. Dietary Factors Affecting the Gut Microbiota

5. Manipulation of Imbalanced Gut Microbiota

6. Role of Probiotics, Prebiotics, and Symbiotics

7. Conclusions

Chapter 11: Dietary Fibers: A Way to a Healthy Microbiome


1. Introduction

2. Gut Microbiota

3. Dietary Fiber and Gut Microbiota

4. Types of Dietary Fiber

5. Interplay Between Gut Microbiota and Host Metabolism

6. Role of Dietary Fiber in Disease Prevention

7. Conclusions

Chapter 12: Effects of the Gut Microbiota on Autism Spectrum Disorder


1. Introduction

2. Gut Microbiota

3. Gut–Brain Axis and the Microbiota

4. The Microbiota–Gut–Brain Axis and Autism Spectrum Disorder

5. Treatments to Modify the Gut Microbiota in Order to Recover the Symptoms in Autism Spectrum Disorder

6. Summary

Chapter 13: Diet, Microbiome, and Neuropsychiatric Disorders


1. Introduction

2. Mechanisms in Which the Microbiome Effects the Brain and Central Nervous System

3. Major Depression Disorder (MDD)

4. Schizophrenia

5. Bipolar Disorder

6. Anxiety Disorders

7. Obsessive-Compulsive Disorder (OCD)

8. Autism Spectrum Disorders (ASD)

9. Conclusions

10. Conflict of Interest

Section 5: Function and Safety

Chapter 14: Gastrointestinal Exposome for Food Functionality and Safety


1. Gross Structure of Food-Associated Gastrointestinal Network

2. Mutual Interaction Between Food Components and Gut Microbiota

3. Crosstalk Between Food Contaminants and the Gut Microbiota: Potent Implications in Environmental IBD Etiology

4. Crosstalk Between Foodborne Toxins and Gut Pathogens: Cases in Mycotoxicoses

5. Food and Drug Metabolism in the Gastrointestinal Tract

6. Neuroendocrine Regulation in the Gastrointestinal Exposome

7. Impact of Foodborne Pathogens and Microbial Toxins on Gastrointestinal Immunity

8. Integrated Management of Food-Linked Gastrointestinal Exposome Networks


Chapter 15: Risk From Viral Pathogens in Seafood


1. Introduction

2. Risks From Pathogenic Microbes in Seafood

3. Risks From Pathogenic Viruses in Seafood

4. Historical Perspectives

5. Seafood as Vehicles for Viruses

6. Outbreaks and Prevalence

7. Viral Pathogens in Seafood

8. Risk Factors

9. Detection and Diagnosis

10. Risk Management

11. Conclusions




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List of Contributors

Navneet Agnihotri,     Panjab University, Chandigarh, India

Asif Ahmad,     Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Punjab, Pakistan

Fasiha Ahsan,     National Institute of Food Science & Technology, University of Agriculture, Faisalabad, Pakistan

Hussain Al Dera

King Saud bin Abdulaziz University for Health Sciences

King Abdullah International Medical Research Center, Riyadh, Saudi Arabia

Rawan Aldahash,     King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia

Priyanka Bhadwal,     Panjab University, Chandigarh, India

Chetna Bhandari,     Panjab University, Chandigarh, India

Maira R. Segura Campos,     Autonomous University of Yucatan, Mérida, Yucatán, México

Petko Denev,     Institute of Organic Chemistry with Center of Phytochemistry, Bulgarian Academy of Sciences, Plovdiv, Bulgaria

Afaf El-Ansary

King Saud University

Autism Research and Treatment Center, Riyadh, Saudi Arabia

Masatoshi Hara,     The Japan Dietetic Association, Tokyo, Japan

Rita M. Hickey,     Teagasc Food Research Centre, Fermoy, Ireland

Jane A. Irwin,     University College Dublin, Dublin, Ireland

Monika E. Jach,     The John Paul II Catholic University of Lublin, Lublin, Poland

Daniel C. Javitt,     Columbia University Medical Center, New York, NY, United States

Gabriel A. Javitt,     Technion University, Haifa, Israel

Akira Kanda,     HANA Nutrition College, Tokyo, Japan

Sumaira Khalid

Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi

Government College University, Faisalabad, Punjab, Pakistan

Samanta S. Khora,     VIT University, Vellore, Tamil Nadu, India

Danuta Kołożyn-Krajewska,     Warsaw University of Life Sciences, Warsaw, Poland

Sandeep Kumar,     Panjab University, Chandigarh, India

Edwin E. Martínez Leo,     Autonomous University of Yucatan, Mérida, Yucatán, México

Sana Mahmood,     National Institute of Food Science & Technology, University of Agriculture, Faisalabad, Pakistan

Yuseok Moon

Department of Biomedical Sciences, Pusan National University, Yangsan

Immunoregulatory Therapeutics Group in Brain Busan 21 Project, Busan, South Korea

Sinead T. Morrin

Teagasc Food Research Centre, Fermoy

University College Dublin, Dublin, Ireland

Nalan H. Noğay,     Erciyes University, Kayseri, Turkey

Armando M. Martín Ortega,     Autonomous University of Yucatan, Mérida, Yucatán, México

Fanny Ribarova,     Medical College J. Filaretova, Medical University–Sofia, Sofia, Bulgaria

Suma Sarojini,     Department of Life Sciences, Christ University, Bangalore, Karnataka, India

Anna Serefko,     Medical University of Lublin, Lublin, Poland

Mian K. Sharif,     National Institute of Food Science & Technology, University of Agriculture, Faisalabad, Pakistan

Bhoomika Sharma,     Panjab University, Chandigarh, India

Prerna Sharma,     Panjab University, Chandigarh, India

Barbara Sionek,     Warsaw University of Life Sciences, Warsaw, Poland

Silvia Tsanova-Savova,     Medical College J. Filaretova, Medical University–Sofia, Sofia, Bulgaria

Dorota Zielińska,     Warsaw University of Life Sciences, Warsaw, Poland


In the last 50 years an increasing number of modified and alternative foods have been developed using various tools of science, engineering, and biotechnology. The result is that today most of the available commercial food is somehow modified and improved, and made to look better, taste different, and be commercially attractive. These food products have entered in the domestic first and then the international markets, currently representing a great industry in most countries. Sometimes these products are considered as life-supporting alternatives, neither good nor bad, and sometimes they are just seen as luxury foods. In the context of a permanently growing population, changing climate, and strong anthropological influence, food resources became limited in large parts of the Earth. Obtaining a better and more resistant crop quickly and with improved nutritional value would represent the Holy Grail for the food industry. However, such a crop could pose negative effects on the environment and consumer health, as most of the current approaches involve the use of powerful and broad-spectrum pesticides, genetic engineered plants and animals, or bioelements with unknown and difficult-to-predict effects. Numerous questions have emerged with the introduction of engineered foods, many of them pertaining to their safe use for human consumption and ecosystems, long-term expectations, benefits, challenges associated with their use, and most important, their economic impact.

The progress made in the food industry by the development of applicative engineering and biotechnologies is impressive and many of the advances are oriented to solve the world food crisis in a constantly increasing population: from genetic engineering to improved preservatives and advanced materials for innovative food quality control and packaging. In the present era, innovative technologies and state-of-the-art research progress has allowed the development of a new and rapidly changing food industry, able to bottom-up all known and accepted facts in the traditional food management. The huge amount of available information, many times is difficult to validate, and the variety of approaches, which could seem overwhelming and lead to misunderstandings, is yet a valuable resource of manipulation for the population as a whole.

The series entitled Handbook of Food Bioengineering brings together a comprehensive collection of volumes to reveal the most current progress and perspectives in the field of food engineering. The editors have selected the most interesting and intriguing topics, and have dissected them in 20 thematic volumes, allowing readers to find the description of basic processes and also the up-to-date innovations in the field. Although the series is mainly dedicated to the engineering, research, and biotechnological sectors, a wide audience could benefit from this impressive and updated information on the food industry. This is because of the overall style of the book, outstanding authors of the chapters, numerous illustrations, images, and well-structured chapters, which are easy to understand. Nonetheless, the most novel approaches and technologies could be of a great relevance for researchers and engineers working in the field of bioengineering.

Current approaches, regulations, safety issues, and the perspective of innovative applications are highlighted and thoroughly dissected in this series. This work comes as a useful tool to understand where we are and where we are heading to in the food industry, while being amazed by the great variety of approaches and innovations, which constantly changes the idea of the food of the future.

Anton Ficai, PhD (Eng)

Department Science and Engineering of Oxide Materials and Nanomaterials,

Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest,

Bucharest, Romania

Series Preface

The food sector represents one of the most important industries in terms of extent, investment, and diversity. In a permanently changing society, dietary needs and preferences are widely variable. Along with offering a great technological support for innovative and appreciated products, the current food industry should also cover the basic needs of an ever-increasing population. In this context, engineering, research, and technology have been combined to offer sustainable solutions in the food industry for a healthy and satisfied population.

Massive progress is constantly being made in this dynamic field, but most of the recent information remains poorly revealed to the large population. This series emerged out of our need, and that of many others, to bring together the most relevant and innovative available approaches in the intriguing field of food bioengineering. In this work we present relevant aspects in a pertinent and easy-to-understand sequence, beginning with the basic aspects of food production and concluding with the most novel technologies and approaches for processing, preservation, and packaging. Hot topics, such as genetically modified foods, food additives, and foodborne diseases, are thoroughly dissected in dedicated volumes, which reveal the newest trends, current products, and applicable regulations.

While health and well-being are key drivers of the food industry, market forces strive for innovation throughout the complete food chain, including raw material/ingredient sourcing, food processing, quality control of finished products, and packaging. Scientists and industry stakeholders have already identified potential uses of new and highly investigated concepts, such as nanotechnology, in virtually every segment of the food industry, from agriculture (i.e., pesticide production and processing, fertilizer or vaccine delivery, animal and plant pathogen detection, and targeted genetic engineering) to food production and processing (i.e., encapsulation of flavor or odor enhancers, food textural or quality improvement, and new gelation- or viscosity-enhancing agents), food packaging (i.e., pathogen, physicochemical, and mechanical agents sensors; anticounterfeiting devices; UV protection; and the design of stronger, more impermeable polymer films), and nutrient supplements (i.e., nutraceuticals, higher stability and bioavailability of food bioactives, etc.).

The series entitled Handbook of Food Bioengineering comprises 20 thematic volumes; each volume presenting focused information on a particular topic discussed in 15 chapters each. The volumes and approached topics of this multivolume series are:

Volume 1: Food Biosynthesis

Volume 2: Food Bioconversion

Volume 3: Soft Chemistry and Food Fermentation

Volume 4: Ingredients Extraction by Physicochemical Methods in Food

Volume 5: Microbial Production of Food Ingredients and Additives

Volume 6: Genetically Engineered Foods

Volume 7: Natural and Artificial Flavoring Agents and Food Dyes

Volume 8: Therapeutic Foods

Volume 9: Food Packaging and Preservation

Volume 10: Microbial Contamination and Food Degradation

Volume 11: Diet, Microbiome and Health

Volume 12: Impact of Nanoscience in the Food Industry

Volume 13: Food Quality: Balancing Health and Disease

Volume 14: Advances in Biotechnology for Food Industry

Volume 15: Foodborne Diseases

Volume 16: Food Control and Biosecurity

Volume 17: Alternative and Replacement Foods

Volume 18: Food Processing for Increased Quality and Consumption

Volume 19: Role of Material Science in Food Bioengineering

Volume 20: Biopolymers for Food Design

The series begins with a volume on Food Biosynthesis, which reveals the concept of food production through biological processes and also the main bioelements that could be involved in food production and processing. The second volume, Food Bioconversion, highlights aspects related to food modification in a biological manner. A key aspect of this volume is represented by waste bioconversion as a supportive approach in the current waste crisis and massive pollution of the planet Earth. In the third volume, Soft Chemistry and Food Fermentation, we aim to discuss several aspects regarding not only to the varieties and impacts of fermentative processes, but also the range of chemical processes that mimic some biological processes in the context of the current and future biofood industry. Volume 4, Ingredients Extraction by Physicochemical Methods in Food, brings the readers into the world of ingredients and the methods that can be applied for their extraction and purification. Both traditional and most of the modern techniques can be found in dedicated chapters of this volume. On the other hand, in volume 5, Microbial Production of Food Ingredients and Additives, biological methods of ingredient production, emphasizing microbial processes, are revealed and discussed. In volume 6, Genetically Engineered Foods, the delicate subject of genetically engineered plants and animals to develop modified foods is thoroughly dissected. Further, in volume 7, Natural and Artificial Flavoring Agents and Food Dyes, another hot topic in food industry—flavoring and dyes—is scientifically commented and valuable examples of natural and artificial compounds are generously offered. Volume 8, Therapeutic Foods, reveals the most utilized and investigated foods with therapeutic values. Moreover, basic and future approaches for traditional and alternative medicine, utilizing medicinal foods, are presented here. In volume 9, Food Packaging and Preservation, the most recent, innovative, and interesting technologies and advances in food packaging, novel preservatives, and preservation methods are presented. On the other hand, important aspects in the field of Microbial Contamination and Food Degradation are shown in volume 10. Highly debated topics in modern society: Diet, Microbiome and Health are significantly discussed in volume 11. Volume 12 highlights the Impact of Nanoscience in the Food Industry, presenting the most recent advances in the field of applicative nanotechnology with great impacts on the food industry. Additionally, volume 13 entitled Food Quality: Balancing Health and Disease reveals the current knowledge and concerns regarding the influence of food quality on the overall health of population and potential food-related diseases. In volume 14, Advances in Biotechnology for Food Industry, up-to-date information regarding the progress of biotechnology in the construction of the future food industry is revealed. Improved technologies, new concepts, and perspectives are highlighted in this work. The topic of Foodborne Diseases is also well documented within this series in volume 15. Moreover, Food Control and Biosecurity aspects, as well as current regulations and food safety concerns are discussed in the volume 16. In volume 17, Alternative and Replacement Foods, another broad-interest concept is reviewed. The use and research of traditional food alternatives currently gain increasing terrain and this quick emerging trend has a significant impact on the food industry. Another related hot topic, Food Processing for Increased Quality and Consumption, is considered in volume 18. The final two volumes rely on the massive progress made in material science and the great applicative impacts of this progress on the food industry. Volume 19, Role of Material Science in Food Bioengineering, offers a perspective and a scientific introduction in the science of engineered materials, with important applications in food research and technology. Finally, in volume 20, Biopolymers for Food Design, we discuss the advantages and challenges related to the development of improved and smart biopolymers for the food industry.

All 20 volumes of this comprehensive collection were carefully composed not only to offer basic knowledge for facilitating understanding of nonspecialist readers, but also to offer valuable information regarding the newest trends and advances in food engineering, which is useful for researchers and specialized readers. Each volume could be treated individually as a useful source of knowledge for a particular topic in the extensive field of food engineering or as a dedicated and explicit part of the whole series.

This series is primarily dedicated to scientists, academicians, engineers, industrial representatives, innovative technology representatives, medical doctors, and also to any nonspecialist reader willing to learn about the recent innovations and future perspectives in the dynamic field of food bioengineering.

Alina M. Holban

University of Bucharest, Bucharest, Romania

Alexandru M. Grumezescu

Politehnica University of Bucharest, Bucharest, Romania

Preface for Volume 11: Diet, Microbiome and Health

To define the ecological community of commensal, symbiotic, and potentially pathogenic microorganisms normally living on our skin and mucosa, the term of microbiota was proposed. Gut microbiota represents the most diverse and numerous part of the whole microbiota in mammals, including humans. As the microorganisms that compose the normal microbiota are very diverse (i.e., bacteria, fungi, archaea, and viruses) and many of them are uncultivable under laboratory conditions and difficult to identify, researchers have proposed a new term to better reflect the great diversity and huge impact of this microbial community on the host. Thus, the microbiome comprises all the genetic material within a microbiota (the entire collection of microorganisms in a specific niche, such as the human gut). Due to its diversity and importance, the microbiome is considered by some researchers as the second genome, and it seems that for every one human gene we have, there are at least 100 associated genes within our microbiome.

It is well known that our physical and mental well-being depends on our diet, and the gut microbiota plays a key role in processing and converting food into usable nutrients. Along with a major role in digestion, our microbiota is responsible for other important processes, such as immunity, detoxification, absorption, infection protection, and even in the occurrence of some diseases, such as metabolic disorders, obesity, diabetes, and some cancers. The composition of microbiome largely changes after a diet switch or a particular therapy, especially antibiotic therapies and this change somehow impacts on our general health and well-being.

At present, the human microbiome project, and the elucidation of the functions of microbiome genes, represents one of the prioritized areas. Researchers believe that these studies would have a great impact on the elucidation of mechanisms and development of therapeutic approaches of numerous currently incurable diseases.

This volume reveals the main roles of human microbiota and discusses how these inhabitants of the human body could influence the development or therapy of some diseases. The impact of diet and some particular dietary ingredients on the composition of microbiota, as well as potential risks associated with the utilization of some elements that could interfere with normal microbiota, such as probiotics, are also highlighted.

The volume contains 15 chapters prepared by outstanding authors from India, Japan, Ireland, Poland, Bulgaria, Mexico, USA, Saudi Arabia, Pakistan, Korea, and Turkey.

The selected manuscripts are clearly illustrated and contain accessible information not only for a wide audience, especially food scientists, microbiologists, biotechnologists, biochemists, molecular biologists, geneticists, healthcare representatives, but also for any reader interested in learning about the most interesting and recent advances on the correlations among diet, microbiome and health.

Chapter 1 of this volume was prepared by Sarojini and is entitled Gut Microbes: The Miniscule Laborers in the Human Body. The chapter reveals the role of the gut microbes in the proper functioning of the human body, emphasizing on the digestive and nervous systems and implications of microbiota in balancing health and disease.

Sharif et al., in Chapter 2, Role of Probiotics Toward the Improvement of Gut Health With Special Reference to Colorectal Cancer, discuss various types of probiotics, their selection criteria, and functional roles in the improvement of overall health. A special reference toward the potential impact of probiotics on the progression of colorectal cancer is made.

Ahmad and Khalid, in Chapter 3 entitled Therapeutic Aspects of Probiotics and Prebiotics, highlight the potential of various prebiotics in relation to microflora and key health benefits. Probiotics and prebiotics are gaining interest as therapeutic food ingredients in the current era of complementary medicine due to their supporting therapeutic roles against different ailments, such as decreasing symptoms of lactose intolerance, improving intestinal heath and bioavailability of nutrients, reducing the susceptibility to the prevalence of allergy and risk of certain cancers, and acting as a functional food in treatment of diarrhea-predominant irritable bowel syndrome.

Chapter 4, Lactic Acid Bacteria Beverage Contribution for Preventive Medicine and Nationwide Health Problems in Japan, prepared by Kanda and Hara, discusses how lactic acid bacteria–containing beverages has contributed and still have the potential to contribute to health and a longer life span of Japanese people by maintaining a healthy intestinal tract.

In Chapter 5, Gut Microbiota Alterations in People With Obesity and Effect of Probiotics Treatment, Martínez Leo et al. review the main microbiome modifications in patients with obesity, how they are a risk factor for obesity, and finally the role that probiotics play in the dietetic treatment for obesity, the weight management, and the microbiome balance reestablishment.

Zielińska et al., in Chapter 6, Safety of Probiotics, discuss documented cases of side effects of some probiotics, such as infections caused by probiotics and epidemiological data, assessment of the risk connected with intake of food probiotic products, and other safety concerns of these generally recognized as safe products.

Chapter 7, Flavonoids in Foods and Their Role in Healthy Nutrition, written by Tsanova-Savova et al., presents the current scientific knowledge on the importance of flavonoids for human health. It also presents original results on flavonoid content and composition in various fruits and vegetables, as well as data about their antioxidant activities.

Morrin et al., in Chapter 8, The Role of Milk Oligosaccharides in HostMicrobial Interactions and Their Defensive Function in the Gut, describe the mechanisms by which oligosaccharides reduce infection, increase commensal microbiota numbers, induce mucin expression, progress neurodevelopment status, and decrease the likelihood of allergic manifestation. Elucidating the specific functions of individual oligosaccharides and determining their contribution to intestinal health are required to obtain a greater knowledge of their potential benefits to infant formula and subsequently infant health.

Chapter 9, entitled Nutritional Yeast Biomass: Characterization and Application, prepared by Jach and Serefko, discusses preclinical and clinical studies that indicate that nutritional yeast biomass is important for prophylactic and/or therapeutic purposes. It is a rich source of amino acids, single-cell proteins, minerals (e.g., chromium, selenium, zinc, iron, magnesium, copper, and manganese), and vitamin B, which promote normal functioning of the immune system.

El-Ansary et al., in Chapter 10, Effect of Diet on Gut Microbiota as an Etiological Factor in Autism Spectrum Disorder, show that understanding the mechanism of diet–microbiota interaction may help to avoid the increasing prevalence of autism. Strategies to decrease the overgrowth of pathogenic bacteria and thus improve the composition of gut microbiota of autistic patients through dietary intervention may help to ameliorate gastrointestinal disorders commonly seen in them.

Chapter 11, Dietary Fibers: A Way to a Healthy Microbiome, prepared by Sharma et al., highlights the effect of dietary fiber consumption on the quality and diversity of gut microbiome and the interplay of these two in providing health and nutritional benefits to humans.

In Chapter 12, Effects of the Gut Microbiota on Autism Spectrum Disorder, Noğay explains that autism is responsive to the composition of gut microbiota, and understanding the early interaction between the intestinal microbiota and autism for nutritional interventions in a risk population would impact the development of this disorder.

Javitt and Javitt, in Chapter 13, Diet, Microbiome, and Neuropsychiatric Disorders, review dietary/microbiomal contributions to neuropsychiatric illness, as well as emergent dietary-based prevention and management approaches. In addition, this chapter shows critical approaches by which the study of the microbiome can help elucidate mechanisms underlying severe and highly prevalent neuropsychiatric disorders, as well as mechanisms by which dietary and microbiomal interventions can replace or minimize the need for neuropharmacological intervention.

Chapter 14, Gastrointestinal Exposome for Food Functionality and Safety, prepared by Moon, describes a gastrointestinal exposome-linked comprehension of food functionality, toxicity, and related biomarkers in terms of disease prevention or progression. The gastrointestinal exposome is the internal microenvironment that contains foodborne xenobiotics (dietary components and food contaminants) and microbiome, which cross talk with host sentinel components, including the immune and neuroendocrine systems. In the luminal parts of the mucosa, food functional components or contaminants are mixed with the gut microbiota and host-derived biomolecules, all of which cross talk, resulting in complex outcomes in the body.

Khora, in Chapter 15, Risk From Viral Pathogens in Seafood, discusses the main pathogenic viruses that cause severe gut-related disorders and dysbiosis in consumers, also highlighting main contamination routes and associated risks.

Alina M. Holban

University of Bucharest, Bucharest, Romania

Alexandru M. Grumezescu

Politehnica University of Bucharest, Bucharest, Romania

Section 1

State of the Art and Applications

Chapter 1: Gut Microbes: The Miniscule Laborers in the Human Body

Chapter 2: Role of Probiotics Toward the Improvement of Gut Health With Special Reference to Colorectal Cancer

Chapter 1

Gut Microbes: The Miniscule Laborers in the Human Body

Suma Sarojini    Department of Life Sciences, Christ University, Bangalore, Karnataka, India


Our physical and mental being largely depends on our dietary intake and the manipulations done on food by the gut bacterial flora in the digestive tract. Scientists have discovered a lot of previously unknown facts about the gut microbiota. They have been found to play a role in manifold processes, such as digestion, nutrient conversion, absorption, detoxification, and so on. In fact, people who consume plant-based and animal-based diets will have separate array of gut microbes. The composition of these microbiota will drastically change during a switch to a new diet. Deficiencies of adequate beneficial gut bacterial flora have been associated with many ailments. As there are billions of such microbes in our body, the number of bacterial genes could far outnumber the human genes in our body. The role of gut microbes in the proper functioning of the human digestive and nervous systems and its implications will be discussed in this chapter.


gut microbiota




lactic acid bacteria

brain-gut-microbiota axis


fecal microbiota transplant

1. Introduction

If there is anything that is of paramount and ultimate importance to mankind, then it is none other than health. The best way and how long one can lead a healthy life is the ultimate quest of human beings. Scientists have been looking into various routes to achieve this target for many centuries. Finally, they have come to a realization that the key for proper health lays not outside the body, but within. The miniscule living organisms that reside in our body—the gut bacteria—hold the key for a healthy state of the body and mind. The trillions of microbes living in association with the digestive tract of animals are collectively termed as gut microbiota. The past 2 decades saw many discoveries by scientists realizing the highly significant roles of these microbes in animal health. The chapter attempts to give an outlook into the evolution of these microbes, benefits offered to the host, problems caused when the gut microbial diversity is tampered with, and the potential benefits of replenishing the beneficial microflora.

Joshua Lederberg had originally coined the term microbiome to define the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space (Lederberg and McCray, 2001). The study of all these bacteria that comprises the gut microbiome was a daunting task. The reason could be attributed to the uncultivable nature of about 20%–60% of the microbiome associated with the human beings (Bik et al., 2006; Pei et al., 2004). The culture of individual species of bacteria that was the major hurdle in this process (Walker et al., 2011) became insignificant with the advent of high end sequencing methods. This has led to an information explosion in this arena of biology. A lot of questions regarding the diversity and functions of these miniscule warriors in our body were considered during the human microbiome project (HMP). This project was funded by the NIH (Peterson et al., 2009).

2. Major Players of the Gut Microbiome

Human cells comprise only one tenth of the number of human microflora cells. About 10¹⁴ bacteria reside in the human body (Berg, 1996). The number of human cells is estimated to be around 3.72 × 10¹³ (Bianconi, 2013). The collective mass of these microbes comprises about 2% of the body weight of a person. The microbes occupy almost all niches in our body ranging from the gut, skin, eyes, mouth and nose. The large intestine forms the greatest niche of these microbes (MacDougall, 2012). In fact, the genes of these tiny microbes encode about a 100-fold more genes than the human species (Ley et al., 2006).

The human gastrointestinal tract does not have a uniform chemistry throughout. The differences at the physical and chemical level in turn give rise to a different population of diversity of microbiota in different regions of the gastrointestinal tract. Factors, such as age, illness, antibiotic intake, stress, diet, and lifestyle affect the composition of the gut microflora (Gerritsen et al., 2011; Woodmansey, 2007). It is estimated that the gut flora is composed of more than thousand different species. In the complex gut microflora, the most common ones comprise about 150–200 species and the less common ones come to about 1000 species. The genes encoded by the gut microbiota, known as the microbiome, are 100-fold more abundant than the genes of the human genome (Hamady and Knight, 2009). The gene pool of the gut bacteria contributes more than three million unique microbial genes in humans (Proctor, 2011). Most of the members of this community live in symbiotic association with the host and some of them may become opportunistic pathogens when there are changes in the host physiology. This intricate microbial system includes bacteria that live in a symbiotic relationship with their host and some microbes that have potentially pathogenic characteristics. The balance between the two ultimately decides whether the individual remains healthy or may be prone to diseases.

In the past few years, a lot of information was generated on the gut microbiome primarily due to high throughput genome sequencing methods. The vast majority of the human gut microbiota is comprised of the four phyla: Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, with the former two being the most abundant in most of the normal healthy individuals (Belenguer et al., 2011). In a human being, at any given time, between 500 and 1000 different species of gut bacteria reside in the gastrointestinal tract. Firmicutes alone constitute more than 60% of the microbiota. Bacteroidetes account for more than 20% of the normal microbiota (Eckburg and Relman, 2007; Khor et al., 2011) The composition of the gut flora has been found to be different in individuals consuming plant- and animal-based food. Members of the genus Prevotella are seen mostly in people consuming a plant based diet whereas Bacteroides and Ruminococcus are predominant in people consuming animal based food (Damman et al., 2012).

Results of the sequencing of about 22 faecal metagenomes of individuals from four different countries led to the classification of the human gut microbiome into three enterotypes. It was found that these three enterotypes were not dependent on the geography of the region. Bacteroides dominated type I whereas type II had a lesser number of the same. Type II showed a preponderance of Prevotella; and type III, of Ruminococcus (Armougom et al., 2011). In the past 3–4 years this domain of microbiology has been progressing at a rapid pace and each month more and more microbes are being discovered as potential players in the gut microbiome.

3. Functions of the Gut Flora

The association between human beings and their gut flora can be categorized mostly into a symbiotic one, the latter getting shelter and food from humans and the former returning the favor in a bunch of ways, benefiting both the body and the mind of human beings. A plethora of functions are attributed to these warriors day by day, the most significant and the earliest discovered ones were the roles played in the breakdown of carbohydrates that is normally impossible by the human cell machinery. The immune system and these gut microbes are constantly looking out for each other. The main duty of the immune system is to control pathogens, hence they should keep a close watch on these microbiota and treat them as friends and not enemies of the host. The immune system also has a role in checking whether these individuals are becoming opportunistic pathogens too.

The most important prerequisite to the exploration of the effects of the gut bacteria on the host physiology was the development of germ free animal models. One such system is the gnotobiotic mice. These are germ free mice into which we can introduce microbes individually or sequentially (Gordon and Pesti, 1971). These can be used as potential tools to study the effects of a single species of bacterium or a population of mixed species of microbes. The interplay of thousands of these gut bacteria could be studied using these tools. The interactions could be mutually beneficial or antagonistic ones. Critical analysis of these interactions on the hosts due to the introduction of a new member of gut bacterium can be carried out in this manner (Reigstad and Kashyap, 2013).

Studies conducted by the members of the HMP suggest that the gut bacterial genes contributed more in the arena of human evolution and survival than the human genes. The human genome carries roughly 22,000 protein-coding genes whereas the human microbiome contributes some 8 million unique protein-coding genes. The number of genes is more than 300 times the number of human genes. These miniscule workers break down proteins, lipids, and carbohydrates in our diet into absorbable forms that can be easily taken up by the body. They also produce many compounds, such as vitamins and antiinflammatories, which the human genes cannot synthesize (MacDougall, 2012).

The most abundant and diverse group of microbiota in the human colon are the bacteria that sum up to about 10¹⁴ citizens. A total of about 70 different genera of bacteria are depicted by the studies on their 16S rRNA genes to play a role in this (Xu and Gordon, 2003). Of the three predominant groups, Firmicutes and Actinobacteria are Gram-positive whereas Firmicutes are Gram-negative. The Bacteroidetes phylum mainly produces acetate and propionate, whereas the Firmicutes phylum has butyrate as its primary metabolic end product (Macfarlane and Macfarlane, 2003).

Specific enzymes are required to digest the bulk of dietary fibers in human food. Consequently, these carbohydrates pass through the upper part of the gastrointestinal (GI) tract undigested. Later they are fermented in the cecum. Most of the enzymes required for this process are not synthesized by the human protein machinery and are therefore dependant on gut bacteria. The predominant products of this microbial digestion with the help of gut bacteria are the short-chain fatty acids (SCFAs) (Nicholson et al., 2012; Roy et al., 2006).

The daily intake and type of food consumed by different people are reflected in the differential composition of the nondigestible carbohydrates that reach the large intestine. Plant cell-wall polysaccharides, oligosaccharides, and resistant starches comprise the primary components of fiber that pass the upper gastrointestinal tract (Flint et al., 2008). About 25 g of daily dietary fiber gets into the digestive tract by way of diet in Western societies (Bingham et al., 2003). Diets that predominantly constitute fruit and vegetables will have a fiber content of 60 g/day (Musso et al., 2011).

Butyrate, a short-chain fatty acid, is a main end product of the intestinal microbial fermentation of dietary fibers. Butyrate is an important energy source for intestinal epithelial cells and plays a role in the maintenance of colonic homeostasis. The proximal colon is the venue of maximum bacterial diversity as the substrate availability is the highest in that zone. This nutrient richness becomes progressively lesser toward the distal end of the colon and hence one can find a lesser gut floral population there. These factors tend to make the proximal part of the colon the principal site of fermentation. The bacterial fermentation results in the production of SCFAs and also gases, such as hydrogen and carbon dioxide (Topping and Clifton, 2001).

Short chain fatty acids, such as butyrate, propionate, acetate, and so on, have been shown in experimental models to have antineoplastic properties. Among these, butyrate was found to be the most potent (Waldecker et al., 2008). Butyrate is also a highly preferred energy source. This indeed is yet another advantage of the molecule in maintaining the proper health of the colon mucosa. A number of independent experiments have proven the inhibitory effect of butyrate on tumorigenesis. The best-hypothesized mechanisms for this inhibitory effect are its antiinflammatory and immunomodulatory effects. Various components of the host defense barrier could be boosted by this effect. Availability of butyrate has also been found to reduce oxidative stress and give a feeling of satiety (Greer and O’Keefe, 2011; Vipperla and O’Keefe, 2012).

One of the most important butyrate producers is Faecalibacterim prausnitzii, which is a member of Clostridium cluster IV. This microbe has also been shown to have independent antiinflammatory properties related to secreted metabolites, which in turn was found to block nuclear factor κB activation and IL-8 production (Sokol et al., 2008). This is an important finding since it has correlations to the carcinogenesis events in the mammalian system.

The antiinflammatory, antitumorigenic, and pathogen exclusion properties of the innumerable number of lactic acid bacteria in the gut benefit the host in multiple ways (Cummings et al., 1987; Marteau, 2013). Microbiota diversity of each individual is influenced by the genotype and physiology of the host, history of colonization, environmental factors, and diet and medicine intake (Zoetendal et al., 2001). The proper functioning of the metabolic pathways were not found to have any major deviations in a group of individuals under study as many biochemical pathways are redundant between alternative members of the microbiome. This was the finding of the Human Microbiome Consortium (Abubucker et al., 2012).

A major chunk of fecal matter is made up of bacteria in the gastrointestinal tract. The number and composition of these different microbes decide the bowel health of an individual. Researchers have shown that a fiber-rich diet reduces the risk of colorectal cancer. This correlation is due to the dilution and elimination of toxins (Bingham et al., 2003) through fecal bulk, which in turn is decided by the fiber content of the dietary intake. High water holding capacity, action of fermentative bacteria, and the presence of water-holding fibers decide the efficiency of this process (Birkett et al., 1997; Cummings et al., 1992).

Mate selection is another function that is directly shown to have correlation with gut bacteria. This finding was done using experiments conducted on insects. The fruit fly, Drosophila pseudoobscura, fed with starch, preferred to mate with other flies on a starch diet, rather than flies that were on a maltose sugar diet. The maltose-fed flies also preferred similar ones for mating. This research finding was proposed after continuous monitoring and data recording for about a decade (Dodd, 1989). Administration of antibiotics was shown to upset these preferences and mating was found to be at random in such cases. This suggested that the changes in gut microbes brought about by diet drove the mating behavioral pattern. As a continuation of the experiment, the researchers inoculated the antibiotic-treated flies’ food with Lactobacillus plantarum cultured from starch-raised flies. The mating preferences were then found to reverse the findings that were the case before antibiotic treatment. This experiment supports the hypothesis that gut bacteria can even affect sexual behavior. The researchers also hypothesize that this kind of selective mating is an early step toward splitting one species into two and hence the gut bacterial inhabitants are major contributors shaping not only behavior but also evolution (Rosenberg and Zilber-Rosenberg, 2011).

In another study involving termites, it was found that antibiotic-treated termites showed a reduced diversity in their gut bacteria and produced fewer eggs. The antibiotic rifampicin was administered to two termite species Zootermopsis angusticollis and Reticulitermes flavipes. This was attributed to the change in the gut bacterial composition as a result of antibiotic administration. The nourishment status and fecundity were affected in such termites. These bacterial species were found to help in digestion and absorption of nutrients (Rosengaus et al., 2011).

Thus, the gut microbiota are responsible for the smooth functioning of metabolic pathways involved in digestion and absorption of carbohydrates and lipids, providing signals for renewal of intestinal epithelium, preserving the gut integrity, production of vitamins, destruction of harmful xenobiotics, and development of a potent intestinal immune system. It is also responsible for the secretion of antimicrobial products, which has dual beneficial jobs, such as favoring the growth of beneficial microbes and preventing the growth of pathogenic bacteria by a mechanism of colonization resistance (Bearfield et al., 2002; Jiménez et al., 2008). Some of the products of the gut microbiota and their potential functions are depicted in Table 1.1.

Table 1.1

Gut microbial products and their potential functions.

DCA, Deoxycholic acid; LCA, lithocholic acid; LPS, lipopolysaccharides; PSA, polysaccharide A; SBA, secondary bile acids; SCFA, short-chain fatty acids.

Physiological and phenotypic differences have been observed between germ-free and control animals in lab conditions with respect to their microbiome and thereby the host health (Turnbaugh et al., 2006). In germ-free animals, lymph nodes were found to be smaller in size and they had lesser body temperatures, absence of urease and β-glucuronidase activities, and lower organ weights when compared to the control animals (Berg, 1996; Tannock, 1999). Morphological, structural, and functional abnormalities were found to be present in germ-free animals. These included lower levels of digestive enzyme activity, reduced vascularity, thin muscle walls, lower rates of cytokine and serum immunoglobulin production, lesser number of intraepithelial lymphocytes, and Peyer’s patches (Compare et al., 2002).

One of the first lines of defense against microbes in our body is the mucus layer overlying the intestinal epithelium. This consists primarily of glycoproteins secreted by goblet cells. Bacterial pathogens, such as Helicobacter pylori (Windle et al., 2000), Entamoeba histolytica (Moncada et al., 2000), and Pseudomonas aeruginosa (Aristoteli et al., 2003) have evolved cellular mechanisms that allow them to utilize the mucus associated nutrients. They do so by the reduction of mucin disulfide bonds or utilizing proteases. When pathogenic microbes do these kinds of damages, there is another set of bacteria, the commensals, which reinforce the barrier provided by the intestine. This job is done by both the resident gut microbiota and the ones that the host procures by way of having probiotics in the diet. Species of Lactobacillus present in probiotics have been shown to increase expression of mucin glycoproteins MUC2 and MUC3 in vitro in human intestinal cell lines (Mack et al., 2003; Mattar et al., 2002). However, convincing data from in vivo studies is lacking. Probiotics exert many beneficial effects on the health of the gastro intestinal tract, including increased mucus production, augmentation of secretory IgA in the mucus layer, synthesis of antimicrobial peptides, and tight junction integrity of intestinal epithelial cells (Ohland and Macnaughton, 2010). All these mechanisms put together will offer several advantages for the functioning of the gastrointestinal tract as an effective barrier against invasion by pathogenic microbes.

The mammalian gut has an inbuilt mechanism to prevent colonization of pathogenic bacteria. This is accomplished by two methods—mechanical barriers and immunochemical barriers. A healthy gut bacterial population can further strengthen these barriers. This can be achieved by the consumption of probiotics. The beneficial gut microbiota competes with the pathogenic ones by putting forth competition for the attachment sites on the mucosal surface in the gut and also for nutrients (Stecher and Hardt, 2008). One of the species of gut flora, namely Oxalibacterium formigenes, helps to regulate the homeostasis of oxalic acid. This has a role to play in preventing the formation of kidney stones (Jalanka-Tuovinen et al., 2011). All these functions are of high physiological significance, because in the absence of gut bacteria, significant consequences, such as improper development of the gut immune system and the development of Clostridium difficile, antibiotic-associated colitis, can happen. One of the causes for this alteration in gut microbial diversity is the consumption of broad-spectrum antibiotics without replenishing the gut flora later by way of intake of vitamin B complex or probiotics. Probiotic microbes, such as Bacillus spp., Bifidobacterium spp., Lactobacillus spp., Lactococcus spp., Leuconostoc cremoris, Saccharomyces spp., or Streptococcus spp., alone or in combination, have shown a protective effect in preventing pediatric antibiotic-associated diarrhea (Johnston et al., 2011).

Gut microbiota help to protect the intestinal lining by allowing nutrients into the bloodstream and preventing disease-causing pathogens and toxins from passing through. The gut bacteria have carried out this function as a dynamic group. The members existing in the population would have been established through thousands of years of coevolution, elimination, and selection. Therefore, it can be argued that the imbalances found in the microbial composition of the gut may be catastrophic. It can result in emergence of multiple diseases and can make individuals less responsive to drugs. The hypothesis from the early days of research in this field was that the composition of the intestinal microbiota was relatively stable from early childhood. A phenomenon called gut dysbiosis has been pinpointed to induce carcinogenesis. Gut dysbiosis refers to the alteration of the composition of the gut flora and the consequent failure of the microbiome to sync up with the rest of the immune system. The inflammatory responses due to gut dysbiosis can trigger a chain of events in the different metabolic pathways of the body, which in turn will start affecting the different organ systems of the body. Mice lacking toll-like receptor 5, a transmembrane protein expressed in the intestinal mucosa that binds bacterial flagella, develop metabolic syndrome, and were found to exhibit gut dysbiosis and low-grade inflammation (Vijay-Kumar et al., 2010).

4. Infant Gut Flora

The discovery that infants are born without gut microbiota and that infants get their share of the microflora rapidly after birth from the mother and the surrounding environment is a relatively new one. The composition of the microbiota was found to be constantly changing until about the infant reached 3 years of age. Later it becomes mature and will have a composition almost matching that of the adult one. Colonization of the gut by these microbes resulted in two potential benefits. The more important benefit is that these gut bacteria educate the immune system and increase the tolerance to microbial immunodeterminants. The second benefit comes by virtue of the microbiota acting as a big metabolic organ that can break down otherwise indigestible food components, degrade potentially toxic compounds in the diet, such as oxalate, and produce some amino acids and vitamins (Xu and Gordon, 2003). Several studies have shown that infants possess a signature microbiota by the end of the first year of life and between 2–5 years of age, the microbiota fully resembles that of an adult structurally and functionally (Backhed, 2011; Koenig et al., 2011; Palmer et al., 2007). This has led to a theory that the gut flora acquired in the first 3 years of life plays a crucial role in determining an individual’s health later in life.

Even in the ayurvedic medical practices of ancient India, a major thrust was given to the diet of pregnant women, with emphasis on what to eat and what not to consume during the term of the pregnancy. With recent advances in medical science, now it has been proven that the mother’s diet and microflora have an impact on microbial colonization of the infant body. The child acquires his microbiome initially during the passage through the vaginal canal of the mother. In case of a cesarean delivery, this kind of vaginal contact is absent and hence the maternal vaginal flora has less of a role to play than the nonmaternally derived environmental bacteria in the infant’s intestinal colonization (Biasucci et al., 2008). It has been known from the mid-1980s that breaking the fecal and vaginal transmission route by Cesarean sections have a major impact on the infant gut microbiota (Bennet and Nord, 1987). The gut bacterial diversity has been on the lower side in C-section babies when compared to those delivered by the vaginal mode (Jakobsson et al., 2014).

Meconium was also found to play a role in the acquisition of gut microbiota. It was earlier thought that meconium was sterile. In a recent experiment conducted on meconium samples of preterm babies, it was found that the meconium harbors a complex array of microbes (Moles et al., 2013). Meconium formation related events could play a major role in the infant gut colonization. This has a big role in shaping the immunity of the child (Jost et al., 2013).

Research in the past few years has shown that gut bacteria can cross previously unsuspected barriers too. Pyrosequencing studies on the maternal feces, breast milk, and corresponding neonatal feces were carried out with a view to finding out the microflora composition in these three samples. It pointed to the fact that the mother and the neonate had a shared population of gut-associated obligate anaerobic genera (Bifidobacterium, Bacteroides, Parabacteroides), butyrate-producing members (Coprococcus, Faecalibacterium, Roseburia, and Subdoligranulum) and members of the Clostridia (Blautia, Clostridium, Collinsella, and Veillonella). A research group (Jost et al., 2014) put forth a theory of a novel way of communication between the newborn baby and the mother. They suggested that the mother’s gut flora reaches the breast milk via an enteromammary pathway. Such bacteria crossing these barriers were found to influence the neonatal gut colonization and immune system maturation.

A multitude of evidences was obtained in the past few years that stresses the significance of breast-feeding on the initial neonatal gut colonization in the physical and mental health of an individual. Breast milk is known to provide a plethora of nutrients and bioactive immunological compounds. Apart from these it also supplies a substantial load of commensal bacteria, including the beneficial anaerobic bacteria, Bifidobacterium sp. It is with the goal of enhancing such commensal population that infant formulas are increasingly supplemented with probiotic bacteria. Though many attempts have been made to fortify infant formula by these various probiotic bacterial species, it can never compete with the richness offered by the breast milk.

Earlier, doctors recommended Cesarean section delivery only in cases where some complication was expected. But in the past 20 years the rate of cesarean delivery (CD) has risen tremendously. In China, the country with the highest population, the rate of C-section is as high as 50%. In the case of Brazil, it is even higher, touching a whopping 80% (Lumbiganon et al., 2010). Though some of the C-section deliveries are preformed for obstetrical indications, a majority of them is done without the actual need. This increased rates of C-section deliveries has been found to be correlating with increasing incidences of autoimmune diseases, such as type 1 diabetes, Crohn’s disease, multiple sclerosis and allergic diseases, such as asthma, allergic rhinitis, dermatitis, and so on, especially in Western, industrialized countries (Bach, 2002; Okada et al., 2010).

The study conducted by Dominguez-Bello et al. (2010) noted a difference in fetal colonization based on mode of delivery. A predominance of pathogenic bacteria typically found on the skin and in hospitals (such as Staphylococcus and Acinetobacter) was found in babies born by cesarean delivery, whereas a preponderance of Lactobacillus was found in babies born vaginally. But before reaching any conclusions, one has to think about another factor, too—the vaginally delivered patients in the study did not receive any antibiotics and the cesarean cases were administered antibiotics, such as cephalosporin prior to the delivery, which is not a standard norm in the United States. A conclusive statement can be made only after ruling out the possibility that the exposure to antibiotics could account for the difference in the gut colonization pattern.

Probiotics provide an easy way of introducing and replenishing beneficial gut bacteria. Microbiota modulation by probiotics early in life is receiving great interest. During the first few months of life, where the microbial colonization and immune system maturation are still in progress, administration of probiotics can go a long way in shaping the gut microbiome. Taken together, the long-term health benefits for mothers and children may be conferred by balanced maternal nutrition during pregnancy, influencing the infant microbiota and immune system development, which have an impact on early and late health.

5. Evolution of Gut Microbial Flora

Scientists study the evolution of the microbiome in two ways—the first is through coprolites, which are fossilized fecal matter. And the second method is through study of teeth enamel. Teeth preserve and fossilize very well, and the tooth surface bacteria are often calcified (called dental calculus). The evolution of diet, health, diseases, and overall genetics of primitive humans can be obtained from dental calculus (Weyrich et al., 2015). How and to what extent one species adjusts to a new diet is of paramount importance to the survival of that species on this planet Earth. If one looks at the history of life on this planet, examples of many such successful adaptations can be found—for example, the way the teeth and gut of the ruminants evolved in response to the significant amount of C4 plants (mainly grasses) available during the period of low CO2 in the atmosphere (Stevens and Hume, 2004).

Over the course of evolution, human beings have struck a symbiotic relationship with the gut microbes. A constant source of nutrition is provided to these bacteria in the gut of humans. They return the favor in a multitude of ways by helping in the functioning of the human digestive and nervous systems (Chen et al., 2013; Geurts et al., 2013). Many human genes have their counterparts in bacteria. These are mainly derived by descent, but some by gene transfer from bacteria (McFall-Ngai et al., 2013). The cognitive performance of the human brain today owes a lot to the gut bacteria (Montiel-Castro et al., 2013). Coevolution has been hypothesized to occur in animal species whose parental care enables vertical transmission of whole gut communities, and where the properties of the community as a whole confer a fitness advantage to the host (Ley et al., 2006).

A comparison between the genomes across different species of animals has revealed that 37% of the ∼23,000 human genes have homologs in bacteria and archaea and 28% originated in unicellular eukaryotes. Thus, most life forms share approximately one third of their genes, including those encoding central metabolic pathways (Domazet-Loso and Tautz, 2008). These genes, which could have been brought to the human genome by gut bacteria (Keeling and Palmer, 2008), might have accumulated mutations, a subset of which would have been lost from the genome and another subset would have persisted, as it would have conferred some selective advantage to the host. The products of some of these homologous genes would have provided the foundation for signaling between extant animals and bacteria (Hughes and Sperandio, 2008).

When compared to the primitive human beings, the ever-increasing meat content in the hominin diets, beginning about 3 million years ago, has led to the progressive reduction in the gut length because they could extract more expeditious calories in shorter lengths. In a study conducted on wild African apes (chimpanzees, bonobos, and gorillas) and modern humans (Moeller et al., 2014), it was found that humans had lost some of their ancestral microbial diversity as compared to apes. This was attributed to the hominin’s animal-based diets. Environment also was found to play a major role in an individual’s gut flora diversity. The microbiomes of humans in America (USA) were slightly different from those of the African (Malawi) adults. The study found that the humans across three continents had significantly less microbiome diversity than extant wild apes. The authors have suggested that the meat-based diets could be the culprits.

6. Diet in Shaping Composition of Gut Flora

Diet is the primary determinant of the composition of the gut floral associations in an individual. This dietary influence starts very early in an individual’s life—right from infancy. Infants dependent only on breast milk had higher levels of Bifidobacterium spp., whereas infants dependent on formula had higher levels of Bacteroides spp., C. coccoides, and Lactobacillus spp. (Brown et al., 2012; Fallani et al., 2010; Harmsen et al., 2000). Significantly greater levels of amino acid fermentation products and lower levels of carbohydrate fermentation products were observed in people having animal based diets when compared to those having plant based diets (David et al., 2014). This is reflected in the gut microfloral composition. In Thailand, a research study tried to enumerate the composition of gut bacteria in vegetarian and nonvegetarian subjects found that nonvegetarians had a much higher abundance of Bacteroides while vegetarian subjects had a preponderance of Prevotella genera (Ruengsomwong et al., 2014).

An abundance of Bacteroides and Firmicutes

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