Workshop on Next Steps in Studying Human Microbiome and Health in Prospective Studies

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Background
Purpose
Agenda
Workshop Summary
Steering Committee

Background

Interest in the role of the microbiome in disease has been increasing in the last year, as evidenced by the May 2016 announcement of the National Microbiome Initiative (NMI), a program which aims to advance microbiome science in order to aid in the development of useful applications in areas such as health care, food production, and environmental restoration. The National Institutes of Health (NIH) is planning to invest $20 million into microbiome research as part of the NMI in fiscal year 2016 and FY2017, with particular emphasis on multi-ecosystem comparison studies and the design of new tools to explore and understand microbiomes. More work needs to be done to understand how to move forward with epidemiologic studies of the human microbiome.

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Microbiome studies were put on the map with two major initiatives in 2007 and 2008, respectively: the NIH's Human Microbiome Project and the European Commission's Metagenomics of the Human Intestinal Tract (MetaHIT). Their aim was to generate research resources to enable comprehensive characterization of the human microbiota and to analyze their role in human health and disease.

Since then, a number of studies have been completed that have evaluated best practices for collection methods and efforts to comprehensively evaluate methods for measuring the human microbiome. These include the techniques and protocols for handling human microbiome samples as well as computational pipelines for microbial data processing. The evidence base of experimental data is growing and it may lead to development of consensus on the best methods for collecting biological samples for microbiome analyses. Furthermore, two large initiatives for standardization of DNA extraction and processing have been completed: in 2008 the International Human Microbiome Standards project for metagenomics began and in 2013 the Microbiome Quality Control Project for 16S rRNA sequencing was launched.

However, to date, there have been few epidemiological studies conducted on the role of the microbiome in human health. The standardization of methods necessary for translation to large-scale studies is still in its infancy. Unfortunately, variation at each step in the research pipeline is a concern. Variation may arise from sample collection, storage, DNA extraction, Polymerase Chain Reaction (PCR), DNA sequencing, bioinformatics, and statistical analyses. Drawing inferences from epidemiological studies of the human microbiome will require the replication of findings across multiple populations and, ideally, pooling data from many different cohorts.

To address this gap in research, investigators in the Metabolic Epidemiology Branch of the National Cancer Institute's (NCI) Division of Cancer Epidemiology and Genetics (DCEG) began working to establish cohorts with fecal and oral specimens to prospectively evaluate the association between the human microbiome and cancer risk. They also are pursuing a multi-pronged approach to address microbiome methodologic issues. Learn more about DCEG's research on the human microbiome and cancer.

Additionally, for the past few years, the Epidemiology and Genomics Research Program (EGRP) in NCI's Division of Cancer Control and Population Sciences (DCCPS) has funded a limited number of research projects by extramural investigators on the relation of the human microbiome and certain cancers. EGRP also convened a 2016 Workshop on Research Strategies for Nutritional and Physical Activity Epidemiology and Cancer Prevention. At this meeting emerged the need for a larger group of scientists studying the human microbiome to address critical issues regarding next steps in prospective studies. The efficient characterization of various human microbial ecologies using high-throughput sequencing has the potential to revolutionize research in chronic disease etiology. However, significant methodological challenges must be overcome before valid studies can be conducted in this exciting field.

Purpose

This two-day workshop was sponsored by NCI's Metabolic Epidemiology Branch in the Division of Cancer Epidemiology and Genetics (DCEG) and Epidemiology and Genomics Research Program in the Division of Cancer Control and Population Sciences (DCCPS). It focused on:

Bringing together diverse scientists to discuss and seek consensus on optimum methods for collecting oral, fecal, and tissue samples for multi-omics analyses;
Examining the degree of variation caused by DNA extraction, amplification, sequencing, and bioinformatics methods and the best methods to handle variation in future studies;
Evaluating the statistical methods for pooling microbiome data from multiple studies;
Addressing the best types of quality control samples to monitor variation in sample handling between sample batches, studies, and laboratories and which can assess stability during long-term storage; and
Reporting and data sharing standards for epidemiological studies of the human microbiome.

The workshop format included opportunities for researchers to hear from public health leadership, interact and explore these topics in breakout sessions, and to network.

Agenda

Day 1 - May 16, 2017

Time	Topic
8:00 a.m.	Registration Opens
8:30 a.m. - 8:45 a.m.	Welcome and Introduction to the Workshop Stephen J. Chanock, MD Director, DCEG, NCI Kathy Helzlsouer, MD, MHS Associate Director, EGRP, DCCPS, NCI
8:45 a.m. - 10:00 a.m.	Session 1: What are the Fundamental Questions that Need to be Addressed in Relation to Microbiome in Health and Dysbiosis? Moderator: Robert N. Hoover, MD, ScD Director, Epidemiology and Biostatistics Program, DCEG, NCI Speakers: Rob Knight, PhD Professor, Department of Pediatrics & Department of Computer Science, University of California San Diego Curtis C. Harris, MD Chief, Laboratory of Carcinogenesis, Center for Cancer Research, NCI Kathy Helzlsouer, MD, MHS Associate Director, Epidemiology and Genomics Research Program, DCCPS, NCI
10:00 a.m. - 10:15 a.m.	Break
10:15 a.m. - 11:45 p.m.	Session 2: Collection, Stability, and Quality Control Moderator: Curtis Huttenhower, PhD Associate Professor, Department of Biostatistics, Harvard University Speakers: Fecal Collection - Rashmi Sinha, PhD Senior Investigator, Metabolic Epidemiology Branch, DCEG, NCI Oral Collection - Emily Vogtmann, PhD, MPH Research Fellow, DCEG, NCI Quality Controls - Joseph Russell Carmical, PhD Assistant Professor, Baylor College of Medicine
11:45 a.m. - 1:15 p.m.	Lunch
1:15 p.m. - 2:45 p.m.	Session 3: Variation Due to Extraction, Amplification, Sequencing, Bioinformatics & Best Methods for Future Studies Moderators: Hera Vlamakis, PhD Research Scientist, Broad Institute Owen White, PhD Professor, Epidemiology and Public Health; Associate Director, Institute For Genome Sciences; Director Of The Um Center For Health-Related Informatics And Bioimaging (Chib); University of Maryland School of Medicine Speakers: Microbiome Quality Control Study - Curtis Huttenhower, PhD Associate Professor, Department of Biostatistics, Harvard University Shot-Gun Sequencing - Diane Leigh Smith Hutchinson, PhD Research Associate, Baylor College of Medicine Automated Provenance Tracking in Microbiome Bioinformatics with QIIME 2 - Greg Caporaso, PhD Associate Professor, University of Northern Arizona
2:45 p.m. - 3:00 p.m.	Break
3:00 p.m. - 5:00 p.m.	Session 4: Statistical Methods Moderator: Mitchell H. Gail, MD, PhD Senior Investigator, Biostatistics Branch, DCEG, NCI Speakers: Biological Variability, Technical Artifacts and Reproducibility in the Study of the Microbiome Anthony Fodor, PhD Associate Professor, University of North Carolina at Charlotte Diversity, Composition and Dynamics in Microbiome Association Studies Hongzhe Li, PhD Professor, Perelman School of Medicine, University of Pennsylvania Replications, Confounding Effects and Overall Contribution of Microbiome in Large Scale Epidemiological Studies Jianxin Shi, PhD Senior Investigator, Biostatistics Branch, DCEG, NCI
5:00 p.m.	End of Day 1 Reconvene at 8:15am on May 17, 2017

Day 2 - May 17, 2017

Time	Topic
8:15 a.m. - 8:45 a.m.	Session 5: Microbiome-related NCI Extramural/Intramural Grants and Projects NCI Extramurally-funded Microbiome Epidemiology Grants – Gabriel Lai, PhD Program Director, Environmental Epidemiology Branch, EGRP, DCCPS, NCI NCI Intramurally-funded Microbiome Epidemiology Projects – Christian Abnet, PhD, MPH Branch Chief and Senior Investigator, Metabolic Epidemiology Branch, DCEG, NCI
8:45 a.m. - 9:15 a.m.	Martin J. Blaser, MD Muriel and George Singer Professor of Medicine; Professor of Microbiology; Director, Human Microbiome Program, NYU School of Medicine
9:15 a.m. - 10:45 a.m.	Session 6: Collection, Storage/Stability, QC - Cohort Experience Moderator: Somdat Mahabir, PhD, MPH Program Director, Environmental Epidemiology Branch, EGRP, DCCPS, NCI Speakers: Shanghai Men's and Women's Health Studies - Wei Zheng, MD, PhD, MPH Co-Leader, Cancer Epidemiology Research Program; Anne Potter Wilson Professor of Medicine; Director, Vanderbilt Epidemiology Center; Vanderbilt-Ingram Cancer Center Multi-Ethnic Cohort - Loic LeMarchand, MD, PhD Professor and Full Member, Epidemiology Program, University of Hawaii Cancer Center and Clinical Professor, John A. Burns School of Medicine, University of Hawaii at Manoa Adventist Health Study-2 – Michael J. Orlich, MD, MPH Assistant Professor, School of Medicine and School of Public Health, Loma Linda University Health Effects of As Longitudinal Study (HEALS) Cohort - Habibul Ahsan, MD, MMedSc Professor, Department of Public Health Sciences, Department of Medicine; Associate Director, Cancer Research Center, University of Chicago Nurses Health Studies and Health Professional Follow-Up Study - Andrew T. Chan, MD, MPH Associate Professor, Harvard Medical School, Massachusetts General Hospital, and Brighamn and Women's Hospital
10:45 a.m. - 11:00 a.m.	Break
11:00 a.m. - 11:45 a.m.	Recommendations from Participants *Break-out sessions* Sample collection, storage, QCs Sample processing Statistical analyses Moderator: John Michael Gaziano, MD, MPH Professor, Harvard Medical School
11:45 a.m. - 1:15 p.m.	Lunch
1:15 p.m. – 2:00 p.m.	Session 7: Reporting & Data Sharing Standards for Epidemiological Studies of the Human Microbiome Moderator: Walter Willett, MD, DrPH Fredrick John Stare Professor of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health Speakers: Christian Abnet, PhD, MPH Branch Chief and Senior Investigator, Metabolic Epidemiology Branch, DCEG, NCI Jacques Ravel, PhD Professor and Associate Director, Institute for Genome Sciences, University of Maryland
2:00 p.m. – 3:00 p.m.	Closing Panel Session: Human Microbiome and Cancer in Epidemiology Studies: Next Steps Moderator: Somdat Mahabir, PhD, MPH Program Director, Environmental Epidemiology Branch, EGRP, DCCPS, NCI Panelists: Rashmi Sinha, PhD Senior Investigator, Metabolic Epidemiology Branch, DCEG, NCI Heidi Kong, MD, MHSc Investigator, Dermatology Branch, Center for Cancer Research, NCI Walter Willett, MD, DrPH Fredrick John Stare Professor of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health
3:00 p.m.	End of Day 2

Workshop Summary

Sinha R, Ahsan H, Blaser M, Caporaso JG, Carmical JR, Chan AT, Fodor A, Gail MH, Harris CC, Helzlsouer K, Huttenhower C, Knight R, Kong HH, Lai GY, Smith Hutchinson DL, Le Marchand L, Li H, Orlich MJ, Shi J, Truelove A, Verma M, Vogtmann E, White O, Willett W, Zheng W, Mahabir S, Abnet C. Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017. Microbiome. 2018; 6: 210.

Steering Committee

Rashmi Sinha, PhD, Metabolic Epidemiology Branch, DCEG, NCI (Chair)
Christian Abnet, PhD, Metabolic Epidemiology Branch, DCEG, NCI
Somdat Mahabir, PhD, MPH, Environmental Epidemiology Branch, Epidemiology and Genomics Research Program (EGRP), DCCPS, NCI
Mukesh Verma, PhD, Methods and Technologies Branch, EGRP, DCCPS, NCI

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