Microbes and Metagenomics in Human Health An overview of recent publications featuring Illumina® technology TABLE OF CONTENTS 4 Introduction 5 Human Microbiome Gut Microbiome Gut Microbiome and Disease Inflammatory Bowel Disease (IBD) Metabolic Diseases: Diabetes and Obesity Obesity Oral Microbiome Other Human Biomes 25 Viromes and Human Health Viral Populations Viral Zoonotic Reservoirs DNA Viruses RNA Viruses Human Viral Pathogens Phages Virus Vaccine Development 44 Microbial Pathogenesis Important Microorganisms in Human Health Antimicrobial Resistance Bacterial Vaccines 54 Microbial Populations Amplicon Sequencing 16S: Ribosomal RNA Metagenome Sequencing: Whole-Genome Shotgun Metagenomics Eukaryotes Single-Cell Sequencing (SCS) Plasmidome Transcriptome Sequencing 63 Glossary of Terms 64 Bibliography This document highlights recent publications that demonstrate the use of Illumina technologies in immunology research. To learn more about the platforms and assays cited, visit www.illumina.com. An overview of recent publications featuring Illumina technology 3 INTRODUCTION The study of microbes in human health traditionally focused on identifying and 1. Roca I., Akova M., Baquero F., Carlet J., treating pathogens in patients, usually with antibiotics. The rise of antibiotic Cavaleri M., et al. (2015) The global threat of resistance and an increasingly dense—and mobile—global population is forcing a antimicrobial resistance: science for interven- tion. New Microbes New Infect 6: 22-29 1, 2, 3 change in that paradigm. Improvements in high-throughput sequencing, also 2. Shallcross L. J., Howard S. J., Fowler T. and called next-generation sequencing (NGS), allow a holistic approach to managing Davies S. C. (2015) Tackling the threat of anti- microbial resistance: from policy to sustainable microbes in human health. action. Philos Trans R Soc Lond B Biol Sci 370: 20140082 3. Sharland M., Saroey P. and Berezin E. N. In and on the human body, microbes outnumber human cells 10 to 1.4 These (2015) The global threat of antimicrobial resis- tance - The need for standardized surveillance microbial cells constitute the human microbiome. Uncovering the members of the tools to define burden and develop interven- human microbiome, and their collective genes and functions, defines the role of our tions. J Pediatr (Rio J) 91: 410-412 4. National Institutes of H. (2012) NIH Human microbial communities in health and disease. This goal can only be accomplished by Microbiome Project defines normal bacterial high-throughput sequencing technologies paired with powerful analytic tools.5 makeup of the body. 2015: www.nih.gov/ news/health/jun2012/nhgri-13.htm; accessed September 29, 2015 Metagenomics is one of the fastest growing scientific disciplines, and it is becoming 5. Cho I. and Blaser M. J. (2012) The human microbiome: at the interface of health and a central tool for improving the quality of life worldwide. Originally conceived as the disease. Nat Rev Genet 13: 260-270 collective genomes of nonculturable microorganisms,6 metagenomics now refers to 6. Handelsman J., Rondon M. R., Brady S. F., Clardy J. and Goodman R. M. (1998) the use of high-throughput DNA sequencing to provide taxonomic (“Who is there?”) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for and functional (“What are they doing?”) profiles of microbial communities without natural products. Chem Biol 5: R245-249 the need to culture the microbes in the laboratory.7 It is estimated that less than 7. Franzosa E. A., Hsu T., Sirota-Madi A., 8 Shafquat A., Abu-Ali G., et al. (2015) Sequenc- 2% of bacteria can be cultured in the laboratory. Our sudden ability to identify the ing and beyond: integrating molecular ‘omics’ previously unstudied 98% of microbes—whether they are prokaryotes, eukaryotes, for microbial community profiling. Nat Rev Microbiol 13: 360-372 or viruses—is revolutionizing and energizing the field of microbiology. 8. Wade W. (2002) Unculturable bacteria—the uncharacterized organisms that cause oral infections. Journal of the Royal Society of This document highlights recent publications that apply Illumina sequencing Medicine 95: 81-83 technologies to metagenomics research. 9. Peacock S. (2014) Health care: Bring microbial sequencing to hospitals. Nature 509: 557-559 Reviews “The application of sequencing technology to microbial genomes will improve patient care and enhance public health. The feasibility and economics are clear.” – Peacock 20149 4 Microbes and metagenomics in human health HUMAN MICROBIOME The human microbiome encompasses the collection of microorganisms associated 10 10. Human Microbiome Project C. (2012) A frame- with the human body, including eukaryotes, archaea, bacteria and viruses. The work for human microbiome research. Nature National Institutes of Health (NIH) Common Fund Human Microbiome Project 486: 215-221 11. Foxman B. and Rosenthal M. (2013) Impli- was established in 2008, with the mission of generating resources to enable the cations of the human microbiome project for comprehensive characterization of the human microbiome and analyze its role in health epidemiology. Am J Epidemiol 177: 197-201 12. Morgan X. C., Segata N. and Huttenhower C. 11 and disease. This effort resulted in the characterization of microbial communities in (2013) Biodiversity and functional genomics different body parts, e.g., oral, gut, skin, and vaginal microbiomes. In parallel, research in the human microbiome. Trends Genet 29: 51-58 has also characterized multiple biomes associated with disease states, highlighting the 13. Penders J., Stobberingh E. E., Savelkoul P. H. 12 and Wolffs P. F. (2013) The human microbiome influence of microbiome dysbiosis in disease development. Some animal-associated as a reservoir of antimicrobial resistance. Front microbiomes have also been characterized in efforts to improve animal health and Microbiol 4: 87 understand the interactions between humans and the environment.13 Reviews DeWeerdt S. (2015) Microbiome: Microbial mystery. Nature 521: S10-11 Franzosa E. A., Hsu T., Sirota-Madi A., Shafquat A., Abu-Ali G., et al. (2015) Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol 13: 360-372 Koch L. (2015) Metagenomics: Shaping the gut microbiome. Nat Rev Genet 16: 2 Preidis G. A. and Hotez P. J. (2015) The newest “omics”--metagenomics and metabolomics--enter the battle against the neglected tropical diseases. PLoS Negl Trop Dis 9: e0003382 Zhou J., He Z., Yang Y., Deng Y., Tringe S. G., et al. (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio 6: Fricke W. F. and Rasko D. A. (2014) Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet 15: 49-55 Lasken R. S. and McLean J. S. (2014) Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet 15: 577-584 Peacock S. (2014) Health care: Bring microbial sequencing to hospitals. Nature 509: 557-559 References Franzosa E. A., Morgan X. C., Segata N., Waldron L., Reyes J., et al. (2014) Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A 111: E2329-2338 The majority of microbiome studies require that samples be taken at specific facilities by trained personnel, increasing costs and excluding some subjects from participation. The authors developed a protocol for self-collection of stool and saliva samples, and frozen shipping within 24 hours of collection. They used metagenome and metatranscriptome analysis to assess the accuracy and feasibility of this protocol against 2 other sample handling methods. There was strong within-subject correlation between all 3 methods at gene, species, and transcript levels, indicating that the developed protocol had minimal effect on metagenomic profiles. Oral microbes co-occurring in stool samples displayed a drop in abundance and transcript levels, suggesting that oral microbes that transit into the gut are not stable and do not play a role in gut ecology. Overall, the study provides a robust method for self-collection and distinguishes relationships between metatranscriptomes and metagenomes, highlighting the complementarity of both approaches in microbiome studies. Illumina Technology: HiSeq An overview of recent publications featuring Illumina technology 5 Lax S., Smith D. P., Hampton-Marcell J., Owens S. M., Handley K. M., et al. (2014) Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345: 1048-1052 14. Goodrich J. K., Waters J. L., Poole A. C., Humans imprint their residences with their specific microbial communities. These homes are a good proxy Sutter J. L., Koren O., et al. (2014) Human genetics shape the gut microbiome. Cell 159: to monitor indoor microbial profiles related to their inhabitants. The Home Microbiome Project monitored 789-799 skin and home-surface microbial communities by 16S rRNA V4 amplicon sequencing. A total of 10 15. Dominguez-Bello M. G., Costello E. K., houses were monitored for 6 weeks, including 3 families before and after moving to a new home. Microbial Contreras M., Magris M., Hidalgo G., et al. communities were specific to each home/family pair because human inhabitants were the main source of (2010) Delivery mode shapes the acquisition such microbiomes, which lead to acquisition of the family microbial community soon after a home move. and structure of the initial microbiota across Genetically