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![The United States Population’s Human Gut Microbiome
Has Diverged a Great Deal from Hunter-Gatherers
“The microbiome of uncontacted Amerindians,” J. C. Clemente, et al. Science Advances 1, e1500183 (2015).
[Amerindians in
Venezuela/Columbia]
[Africa]
U.S. Human
Microbiome
Project
Missing Microbes](https://image.slidesharecdn.com/ljcd-180323210236/75/Exploring-Your-Inner-Microbiome-35-2048.jpg)
Uploaded byLarry Smarr
Exploring Your Inner Microbiome
This document summarizes a lecture given by Dr. Larry Smarr on his research exploring the human microbiome. Some key points: - Dr. Smarr has been studying the microbial universe inside the human body for 40 years, since microbiology began as a frontier science. - Advances in DNA sequencing have enabled the sequencing of human and microbial genomes, revolutionizing our understanding of the microbiome. - The human microbiome is essential to health and disease, with 99% of our genes located in microbes rather than human cells. - Dr. Smarr's own microbiome was studied before and after colonoscopy and colon surgery, showing dramatic shifts and recovery periods. - Fecal microbiota trans
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Exploring Your Inner Microbiome
- 1. “Exploring Your InnerMicrobiome” Invited Lecture La Jolla Country Day School La Jolla, CA February 8, 2018 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technology Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD http://lsmarr.calit2.net
- 2. My Voyage ofDiscovery to Understand the Microbial Universe Inside Us Started 40 Years Ago
- 3. Forty Years Ago IDid Observational Research on Our Neighbor Galaxy
- 4. There are 100billion stars in the Andromeda galaxy… …and 100 billion galaxies in the known universe.
- 5. It’s a microbialworld… …there are 100 million times as many bacteria on Earth as stars in the universe. Microbiology is the ultimate Big Data science!
- 7. The Cost ofSequencing DNA Has Fallen Over 100,000x in the Last Ten Years This Has Enabled Sequencing of Both Human and Microbial Genomes
- 8. Marine Microbial EcologyGenome Sequencing Project – Anchor Dataset Launched March 13, 2007 Measuring the Genetic Diversity of Ocean Microbes Specify Ocean Data Each Sample ~2000 Microbial Species
- 10. 2007: 202 samples 21,752 sequences 2017: 27,000samples 2.2 billion sequences
- 11.
- 13. June 8, 2012June 14, 2012 Interest in the Human Microbiome Has Moved Quickly From Frontier Science to Public Awareness August 18, 2012June, 2012
- 14. To Understand Healthand Disease We Must Consider the Human Microbiome Inclusion of the “Dark Matter” of the Body Will Radically Alter Medicine 99% of Your DNA Genes Are in Microbe Cells Not Human Cells Your Body Has 10 Times As Many Microbe Cells As DNA-Bearing Human Cells
- 15. Most of Life’sEvolutionary Time Was in the Microbial World You Are Here Source: Carl Woese, et al Tree of Life Derived from 16S rRNA Sequences
- 16. When We ThinkAbout Biological Diversity We Typically Think of the Wide Range of Animals But All These Animals Are in One SubPhylum Vertebrata of the Chordata Phylum All images from Wikimedia Commons. Photos are public domain or by Trisha Shears, Richard Bartz, & Matt Clancy
- 17. Think of ThesePhyla of Animals When You Consider the Biodiversity of Microbes Inside You Phylum Annelida Phylum Echinodermata Phylum Cnidaria Phylum Mollusca Phylum Arthropoda Phylum Chordata Phylum Porifera All images from WikiMedia Commons. Photos are public domain or by Dan Hershman, Michael Linnenbach, Manuae, B_cool, Nick Hobgood
- 18. Treating the HumanSuperorganism: Your Body is an Ecology! Nature Reviews Microbiology v.9, p. 279 (2011)
- 19. The Human Microbiome HasVery Different Microbial Ecologies Slide from Rob Knight, UCSD
- 20. As Different as aCoral Reef’s and a Prairie's Microbiome Slide from Rob Knight, UCSD
- 21. Human Stool Containsa Vast Amount of Information: 1 Gram Contains ~1 Billion Microbes, Each With >1 Million DNA Bases 1 Teaspoon Stool Has the Information Content of 1 ton of DVDs
- 22. I Had SavedOver Three Years Of My Stool Samples When UCSD Hired Rob Knight Larry’s 40 Stool Samples Over 3.5 Years to Rob’s lab on April 30, 2015
- 23. Microbiome Ecology DiversityImmediately Drops After Colon Cleanse — Followed By Slow Recovery Source: Smarr, Hyde, McDonald, Sandborn, Knight
- 24. Large Jump InMicrobiome Ecology After Cleanse — Then “Wanders” for Two Weeks Back to Normal Source: Smarr, Hyde, McDonald, Sandborn, Knight
- 25. November 29, 2016I Had Robotic Surgery To Remove 8 Inches of Inflamed Colon
- 26. Larry Smarr’s SigmoidColon Resection UCSD’s Jacobs Medical Center November 29, 2016 Patient Smarr With Robot Arms Inside Him
- 27. Gut Microbiome Genus-LevelProfiles Daily Samples Before and After Abdominal Surgery Colonoscopy Surgery Source: Embriette Hyde, UCSD
- 28. Colonoscopy Surgery Much Larger Dropin Microbiome Ecology Diversity Following Surgery Than Following Colonoscopy Source: Embriette Hyde, UCSD
- 29. Pre-colonoscopy Post-colonoscopy Pre-surgeryPost-surgery Major Shift in Gut Microbiome Ecology Following Abdominal Surgery With Return to New Equilibrium State Source: Embriette Hyde, UCSD
- 30. The Colonoscopy Didn’tMake Me Look Like a New Person — But the Surgery Did! Pre-colonoscopy Post-colonoscopy Pre-surgery Source: Embriette Hyde, UCSD
- 31. From War toGardening: New Therapeutical Tools for Managing the Microbiome “I would like to lose the language of warfare,” said Julie Segre, a senior investigator at the National Human Genome Research Institute. ”It does a disservice to all the bacteria that have co-evolved with us and are maintaining the health of our bodies.” Will Medical Foods Provide New Tools for Altering Gut Microbiome?
- 32. Manipulating Your MicrobiomeCan Work -- Fecal Microbiome Transfer Is a Rapidly Growing New Treatment for Clostridia Difficile Dr. Bill Sandborn, Chief UCSD GI Dr. Brigid Boland, UCSD GI C. diff is the nation’s most common hospital-acquired infection, affecting 500,000 and killing 30,000 Americans/year (CDC) Fecal transplants are 90% curative. OpenBiome supplies to over 500 hospitals in all 50 states, so far 10,000 transplants. www.cidrap.umn.edu/news-perspective/2015/02/cdc-puts-c-difficile-burden-453000-cases-29000-deaths
- 33. Fecal Transplants From HealthyDonor To C. Diff Patients Source: Knight Lab, UCSD Mouth Skin Vagina Stool
- 34. Massive Research isUnderway to Discover A Wide Range of New Techniques for Manipulating Your Microbiome www.huffingtonpost.com/entry/gut-bacteria-microbiome-disease_us_57068c55e4b053766188f383 www.synlogictx.com
- 35. The United StatesPopulation’s Human Gut Microbiome Has Diverged a Great Deal from Hunter-Gatherers “The microbiome of uncontacted Amerindians,” J. C. Clemente, et al. Science Advances 1, e1500183 (2015). [Amerindians in Venezuela/Columbia] [Africa] U.S. Human Microbiome Project Missing Microbes
- 36. We Must MoveFrom Combating Single Microbe Diseases to Developing the Human/Microbiome System Approach to Public Health Bach (2002) N Engl J Med, Vol. 347, 911-920 2014 For Public Health It is Still About Microbes, But from Single Species to Entire Ecologies
- 37. The Coupled Neural,Immune, and Microbiome Systems Provide a Model Explaining How Nutrition Can Alter Neurodevelopment
- 38. Gut Microbes RegulateSerotonin Production, 90% of Which is in the Large Intestine “It's almost unthinkable that the gut is not playing a critical role in mind states," says gastroenterologist Emeran Mayer, MD, director of the Center for Neurobiology of Stress at UCLA Cell 161 264-276 (2015)
- 39. The Microbiome–Gut–Brain Axis ProvidesNew Systemic Insights into Shifts in Behavior and Disease Source: Montiel-Castro, et al. Frontiers in Integrative Neuroscience 2013 Particularly Important for Healthy Aging
- 40. Many New ResearchStudies are Demonstrating Deep Relationships Between the Gut Microbiome and Behavioral Disorders
- 41. Center for Microbiome Innovation Seminars Faculty Hiring Education UCSD MicrobialSciences Initiative Instrument Cores Seed Grants Fellowships Chancellor Khosla Launched the UC San Diego Microbiome and Microbial Sciences Initiative October 29, 2015
- 42. …and over 120UCSD Faculty
- 43. Thanks to OurGreat Team! Calit2@UCSD Future Patient Team Jerry Sheehan Tom DeFanti Joe Keefe John Graham Kevin Patrick Mehrdad Yazdani Jurgen Schulze Andrew Prudhomme Philip Weber Fred Raab Ernesto Ramirez JCVI Team Karen Nelson Shibu Yooseph Manolito Torralba Ayasdi Devi Ramanan Pek Lum UCSD Metagenomics Team Weizhong Li Sitao Wu SDSC Team Michael Norman Mahidhar Tatineni Robert Sinkovits UCSD Health Sciences Team David Brenner Rob Knight Lab Justine Debelius Embriette Hyde Jose Navas Gail Ackermann Greg Humphrey William J. Sandborn Lab Elisabeth Evans John Chang Brigid Boland Dell/R Systems Brian Kucic John Thompson
Editor's Notes
- #28 Several taxa increase and remain increased after surgery: Blautia, [Ruminococcus](Lachnospiraceae), unclassified genus in family Rikenellaceae, unclassified genus in order YS2, Parabacteroides (minor) Some decrease or disappear and remain decreased after surgery: Akkermansia, [Prevotella](Paraprevotellaceae) Immediately after surgery, Providencia and an unclassified genus in family Enterobacteriaceae increase
- #30 The change due to surgery is much larger than the change due to colonoscopy, though changes due to both are apparent. Post-surgery samples move back to the same space on PC1, but not PC2. Likely due to continued elevation in abundance of select taxa after surgery (see taxa summary plots).