WGO Handbook on Gut Microbes

World Digestive Health Day WDHD May 29, 2014 WGO Handbook on Gut Microbes World Gastroenterology Organisation (WGO) The WGO Foundation (WGO-F) 555 East Wells Street, Suite 1100 Milwaukee, WI USA 53202 Tel: +1 (414) 918-9798 • Fax: +1 (414) 276-3349 Email: [email protected] Websites: www.worldgastroenterology.org • www.wgofoundation.org Table of Contents Message from the Chair ..............................................................................................................................................4 Francisco Guarner, MD, Spain From the Chair and Vice Chair of the WGO Foundation ............................................................................................5 Eamonn Quigley MD, FRCP, FACP, FACG, FRCPI, USA, Chair, WGO Foundation Richard Hunt, FRCP, FRCPEd, FRCPC, MACG, AGAF, MWGO, Canada, Vice Chair, WGO Foundation WDHD 2014 Supporter and Partners .........................................................................................................................6 Microbial Communities ...............................................................................................................................................7 Claudia Herrera, MD, Spain Francisco Guarner, MD, Spain Functions of the Gut Microbiota ..................................................................................................................................9 Francisco Guarner, MD, Spain Techniques to Characterize the Gut Microbiota ......................................................................................................12 Joël Doré, PhD, France Chaysavanh Manichanh, PhD, Spain Composition and Structure of the Human Gut Microbiota ......................................................................................16 Virginia Robles-Alonso, MD, Spain Francisco Guarner, MD, Spain Dusko Ehrlich, PhD, United Kingdom Acquisition of the Human Gut Microbiota ................................................................................................................19 Yanjiao Zhou, MD, PhD, USA Barbara B. Warner, MD, USA Phillip I. Tarr, MD, USA Impact of Diet on Gut Microbes .................................................................................................................................24 Francisco Guarner, MD, Spain Lindsey G. Albenberg, DO, USA Gary D. Wu, MD, USA Antibiotics and Gut Microbes ....................................................................................................................................27 Chaysavanh Manichanh, PhD, Spain The Gut Microbiota in Functional Bowel Disorders .................................................................................................31 Giovanni Barbara, MD, Italy Cesare Cremon, MD, Italy Vincenzo Stanghellini, MD, Italy The Gut Microbiota in Inflammatory Bowel Disease ...............................................................................................33 Harry Sokol, MD, PhD, France Gut Microbiota, Obesity and Associated Metabolic Disorders ...............................................................................36 Patrice D. Cani, PhD, Belgium Nathalie M. Delzenne, PhD, Belgium Probiotics: the Concept .............................................................................................................................................39 Mary Ellen Sanders, PhD, USA Probiotics in Diarrheal Diseases ..............................................................................................................................43 María Julieta Argüero, MD, Argentina Juan Andrés De Paula, MD, Argentina Probiotics in Functional Bowel Disorders ...............................................................................................................47 Eamonn M M Quigley, MD, FRCP, FACP, FACG, FRCPI, USA Amy E Foxx-Orenstein, DO, FACP, FACG, USA World Digestive Health Day WDHD May 29, 2014 WGO HANDBOOK ON GUT MICROBES 2 Probiotic Therapy for Induction and Remission in Inflammatory Bowel Diseases ..............................................53 Richard N Fedorak, MD, Canada Probiotics in Pediatrics .............................................................................................................................................56 Michael D. Cabana, MD, MPH, USA Prebiotics ...................................................................................................................................................................58 GR Gibson, PhD, United Kingdom Fecal Microbiota Transplant (FMT) ..........................................................................................................................61 Elizabeth Broussard, MD, USA Christina Surawicz, MD, USA Harvesting the Microbiome for the Future ..............................................................................................................64 Emma Allen-Vercoe, PhD, Canada World Digestive Health Day WDHD May 29, 2014 WGO HANDBOOK ON GUT MICROBES 3 Message from the Chair Dear Colleagues, Our knowledge of the microbial communities that inhabit the human gut has grown exponentially over the last few years and there is a profusion of novel information flowing from basic science laboratories into the clinical scenarios. Gut Microbes function like an organ within the gastrointestinal tract, and Gastroenterologists are the health professionals who should bring the new knowledge into practice. The human host provides a habitat and nutrition to a large and diverse ecosystem of microbial communities and they play key roles in digestion, metabolism and immune function and have a significant impact beyond the gastrointestinal tract. Changes in the diversity and function of those communities are associated with far reaching consequences on host health and have been linked with a number of disorders, including functional bowel disorders, inflammatory bowel diseases and other immune mediated diseases (coeliac disease, allergies), metabolic conditions (type 2 diabetes, NASH), and perhaps, behavioral disorders such as autism and depression. The emerging data on the microbiota and its interaction with the host may provide novel diagnostic and prognostic tests for clinician, and also lead to the development of new and effective therapeutic interventions (functional foods, probiotics, prebiotics, microbiota transplants) to relieve symptoms, as well as treat and prevent illness. The World Gastroenterology Organisation (WGO) seeks to raise awareness of this novel organ and bring the latest fundamental and clinically relevant knowledge to the Gastroenterologist and, through the Gastroenterologist, to the lay public. The “Gut Microbes - Im- portance in Health and Disease” campaign for World Digestive Health Day 2014 seeks to undertake the challenge of translating science into practice by developing educational and training platforms and materials around the world through a concerted collaboration with WGO Member Societies. Such actions include a WGO Gut Microbes Manual, “Meeting in a Box” tools to share with Member Societies, an update of the Probiotics and Prebiotics WGO Guideline, sponsored meetings and more. We look forward to a fruitful campaign throughout 2014 and beyond. Sincerely, Francisco Guarner Professor Francisco Guarner, MD Chair, WDHD 2014 Barcelona, Spain World Digestive Health Day 2014 Steering Committee The World Digestive Health Day Campaign is led by the following individuals representing a global view and expertise in the area of gut microbiota and health. They guide the course of the campaign, and lead in the development of tools and activities throughout 2014 and beyond. Member Chair, WDHD 2014 Member Juan Andrés de Paula, Francisco Guarner, MD Amy Foxx-Orenstein, MD MD University Hospital Vall Mayo Clinic Hospital Italiano of Bue- d’Hebron Phoenix, USA nos Aires Barcelon, Spain Buenos Aires, Argentina Chairman, WGO Foun- Member dation Member Justin Wu, MD Richard Fedorak, MD Eamonn Quigley, MD The Chinese University of University of Alberta The Methodist Hospital Hong Kong Edmonton, Canada Houston, USA Shatin, Hong Kong Member Member Uday Ghoshal, MD Giovanni Barbara, MD Sanjay Gandhi Post University of Bologna Graduate Institute of Bologna, Italy Medical Sciences Lucknow, India World Digestive Health Day WDHD May 29, 2014 WGO HANDBOOK ON GUT MICROBES 4 From the Chair and Vice Chair of the WGO Foundation World Digestive Health Day (WDHD) was initiated several years ago by the World Gastroenterology Organisation in order to high- light important global issues in digestive diseases. As WDHD has evolved over the years it has developed from a one day event to a year-long campaign which engages with gastroenterologists, doctors, health care professionals and the general public on many aspects of the prevalence, prevention, diagnosis and management of common gastrointestinal and liver symptoms and disorders. Through direct collaboration with our member societies in 111 countries around the world and with the support of other professional societies with similar interests, non-governmental agencies, governments and industry, we have helped to promote understanding and raise awareness on these issues. This year we address one of the “hottest” topics in medicine and medical science: gut microbes. Rapid developments in technology have permitted the detailed description of the bugs that normally inhabit our gastrointestinal tracts and are beginning to reveal their many functions in heath and disease. With such progress have come new challenges: in comprehending new terminology, in distinguishing

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