ReviewAnalyzing the Human Microbiome: A “How To” guide for PhysiciansTyler, Andrea D PhD1, 2; Smith, Michelle I PhD2; Silverberg, Mark S MD, PhD1, 2Author Information 1 Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada 2 Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada Correspondence: Mark S. Silverberg, MD, PhD, Mount Sinai Hospital, 600 University Avenue, Rm 441, Toronto, Ontario M5G 1X5, USA. E-mail: firstname.lastname@example.org Received 13 November 2013; accepted 11 March 2014 published online 22 April 2014 American Journal of Gastroenterology: July 2014 - Volume 109 - Issue 7 - p 983-993 doi: 10.1038/ajg.2014.73 Buy Metrics Abstract The application of high-throughput next-generation sequencing to the analysis of the human microbiome has led to a shift in our understanding of the etiology of complex diseases. In consequence, a great deal of literature can now be found exploring this complex system, and reviewing recent findings. Observations of alterations in the intestinal microbiome associating with inflammatory bowel disease and other chronic conditions are well supported and have been widely accepted by the research community. Yet, it can be difficult to objectively evaluate the importance of these results, given the wide variety of methodologies applied by different groups in the field. The aim of this review is to focus attention on the basic principles involved in microbiome analyses, and to describe factors that may have an impact on the accurate interpretation of results. © The American College of Gastroenterology 2014. All Rights Reserved.