ILSI NA Gut Microbes Consensus Workshop: Defining a Healthy Gut Microbiome

Transcription

1 2012 ILSI North America Scientific Session Human Gut Microbiome January 24, 2012, Phoenix, AZ ILSI NA Gut Microbes Consensus Workshop: Defining a Healthy Gut Microbiome Johanna W. Lampe, PhD, RD Fred Hutchinson Cancer Research Center

2 Sponsored by: Gut Microbes and Health Committee Chair: Steve Davis, PhD, Abbott Nutrition COMMITTEE MEMBERS Abbott Nutrition BENEO Group Cargill, Incorporated Dannon Company General Mills National Starch, Corn Products International Tate & Lyle T M

3 Gut Microbes & Health Subcommittee Defining a Healthy Gut Microbiome Steve Davis Abbott Nutrition JoMay Chow Abbott Nutrition Artem Khlebnikov Dannon Company Douwina Bosscher Cargill, Incorporated Gunhild Kozianowski Beneo Group Mary Ellen Sanders Dairy & Food Culture Technologies Kathy Ellwood KE Nutrition Janet King Children s Hospital, Oakland Research Institute Sarah Waybright ILSI North America Sharon Weiss Eric Hentges T M

4 Attendees Abbott Nutrition Beneo Cargill, Inc. National Starch, Corn Product International Dannon General Mills NIH (NCCAM) FDA (CFSAN) USDA/ARS IOM ASN ADA AGA ASM ILSI EU

5 ILSI NA Conference December 6, 2011 Defining a Healthy Gut Microbiome Conference goals: To help guide development of scientific information describing what constitutes a healthy gut microbiome, by working toward development of points of scientific agreement, to be published in a peer-reviewed journal. Format: Short presentations and ensuing discussion on 3 themes: How is a healthy gut microbiome defined? How should healthiness of a gut microbiome be assessed? What is the current evidence that regulating or manipulating the microbiota/microbiome is beneficial? T M

6 Consensus Workshop Panelists Fredrik Bäckhed, PhD, University of Gothenberg Brett Finlay, PhD, University of British Columbia Claire Fraser-Liggett, PhD, University of Maryland Yehuda Ringel, MD, University of North Carolina R. Balfour Sartor, MD, University of North Carolina Philip Sherman, MD, Hospital for Sick Children, Univ. of Toronto James Versalovic, MD, PhD, Baylor College of Medicine Vincent Young, MD, PhD, University of Michigan Moderator: Mary Ellen Sanders, PhD, Dairy & Food Culture Technologies T M

7 Putting It Into Perspective ~ trillion microorganisms in the gastrointestinal tract (10 times more than human cells in the body) Microbiome (collective genomes of the gut microbial community) has 100 x as many genes as the human genome An estimated species present in the human gut Symbiosis between human host and microorganisms

8 Comparison of the Microbial Diversity from Different Ecosystems Gut is a unique, harsh, anaerobic environment Most of the diversity in human gut microbiota occurs in sequences that are >97% similar

9 Bacterial Diversity in the Adult Human Gut 6 divisions of Eubacteria are found in the human gut Bacteroidetes and Firmicutes dominate. Low % culturable Bäckhed et al. Science 2004

10 Characterizing the Gut Microbiome: Molecular Approaches DNA { Which microbes are there? -16S rrna genes Fingerprinting Sequencing What is the genetic potential? - Metagenomics { RNA Proteins Metabolites What are the microbes doing? - Metatranscriptomics - Metaproteomics - Metabolomics

11 Comparison of Taxanomic and Functional Variations in the Human Gut Microbiome 18 fecal microbiomes from MZ twins and their mothers Suggests a core microbiome at the level of metabolic function with high redundancy Turnbaugh et al. Nature :480-4

12 Session 1a: How is a healthy microbiome defined? Chair: Vincent Young, University of Michigan Co-Chair: Philip Sherman, Hospital for Sick Children, Univ. of Toronto QUESTIONS What is health in reference to the GI microbiome? Absence of disease? Maintenance of physiological function(s) or optimal health? Resistance to infection? What are the important community characteristics? Diversity, richness, evenness What distinguishes the microbiota of healthy individuals with those of patients with disease?

13 Session 1b: How is a healthy microbiome defined? Chair: Fredrik Bäckhed, University of Gothenberg Co-Chair: Claire Fraser-Liggett, University of Maryland QUESTIONS What is a healthy GI microbiome? Absence of pathogens? Is there a core microbiome? Multiple enterotypes? Maintenance of homeostasis? Over what time span? Protection against or restoration after pertubation?

14 Sessions 2a & 2b: How should the healthiness of a gut microbiome be assessed? Chair: James Versalovic, Baylor College of Medicine Co-Chair: Claire Fraser-Liggett QUESTIONS What are the important aspects of sampling? Are current sampling and storage conditions sufficient? Will fecal samples vs other samples enable answering relevant questions on gut microbiota and health? What other samples are needed? What level of characterization of the entire GI microbiome is necessary to address the question of gut microbiota and health Level? Phyla vs Genera vs Species vs Strain Omics and systems biology approaches

15 Sessions 2c & 2d: How should the healthiness of a gut microbiome be assessed? Chair: Yehuda Ringel, University of North Carolina Co-Chair: Vincent Young QUESTIONS What types of human study designs are needed to evaluate the impact of the gut microbiome on health? Are observational studies sufficient? If so, what type? Are intervention studies required? What biomarkers and endpoints are appropriate to assess gut microbiome health?

16 Session 3a & 3b: What is the current evidence that regulating or manipulating the microbiome is beneficial? Chair: R. Balfour Sartor, University of North Carolina Co-Chair: James Versalovic Chair: Brett Finlay, University of British Columbia Co-Chair: Yehuda Ringel QUESTIONS What is the current evidence that maintaining homeostasis of the GI microbiome is beneficial? What is the current evidence that targeting dysbiosis of the GI microbiome is beneficial?

17 Summary and Where do we go from here? How is a healthy gut microbiome defined? Much of the current focus has been on disease. Health of gut microbiome is more than lack of overt disease. Although need to catalog who is there, also need to ascertain impact on function (i.e., metabolic activities). How should healthiness of a gut microbiome be assessed? Fecal samples are representative of distal GI tract, but may be insufficient to characterize the small intestine. Need observational and intervention trials, & new study designs. What is the current evidence that regulating or manipulating the microbiota/microbiome is beneficial? Sparse; some evidence for some diseases, but not consistent. Conference outcomes to be submitted to peer-reviewed journal in early 2012.

18 Biomarkers to Define a Healthy GI Microbiome: New project seeking other industry members Consensus conference revealed paucity of accepted biomarkers with which to define a healthy microbiome. Goal: Identify biomarkers that will be generally accepted for use in identifying and confirming the benefits of foods, food ingredients, and supplements that promote human health through the GI microbiota/microbiome. What biomarkers are useful and how can they be analyzed? What are reference levels for defining healthy GI microbiome? CONTACT: Sarah Waybright, ILSI NA swaybright@ilsi.org ext. 134

19 Human Gut Microbiome: SESSION OUTLINE Overview: Update on NIH Human Microbiome Project Lita Proctor, PhD National Human Genome Research Institute, NIH, Bethesda Microbiota and Human Health: Lessons Learned Fergus Shanahan, MD University College Cork, Ireland Three Enterotypes of Gut Microbiota Marie Joossens, PhD VIB, Vrije Universiteit, Brussels, Belgium Human Microbiome: Emerging Technologies and New Methodologies Karen Nelson, PhD J Craig Venter Institute, Maryland