An MRI Showed My Sigmoid Colon Wall Was Thickened and Inflamed

1. An MRI Showed My Sigmoid Colon Wall Was Thickened and Inflamed

2. I Got a Copy of My MRI Data &Used Calit2 Software to Enable Me to Fly Through My Internal Organs

3. I Searched for Clues AmongMy 150 Blood and Stool Variables, Each Graphed Over 5-10 Years Calit2 64 megapixel VROOM

4. Only One Variable Was Far Out of Norm-Complex Reactive Protein From Blood Sample 27x Upper Limit Normal Range <1 mg/L Normal CRP Indicates Chronic Episodic Inflammation

5. By Looking at Stool Samples Over Time I Discovered My Lactoferrin Was Very Far Above Normal 124x Upper Limit Normal Range <7.3 µg/mL Lactoferrin Is an Indicator of White Blood Cells Attacking Your Colon

6. High Lactoferrin Biomarker Values Led Me to HypothesizeI Had Inflammatory Bowel Disease (IBD) Scand J Gastroenterol. 42, 1440-4 (2007) My Values 2009-10 My Values May 2011 IBD is an Autoimmune Disease Which Comes in Two Subtypes: Crohn’s Disease and Ulcerative Colitis

7. Tracking Multiple Immunological Biomarkers Over Time Lets Me Record the Immune System “Dance” Gut Microbiome Samples Sign Symptom Source: Calit2 Future Health Expedition Team

8. Exploring the Dance Inside Your SuperorganismBetween Your Microbiome and Human Immune System Your Body Has 10 Times As Many Microbe Cells As Human Cells Inclusion of Microbiome Will Radically Change Medicine

9. Computing and Visualizingthe Genomic Dance of the Microbes Calit2 VROOM-FuturePatient Expedition Sequencing by JCVI or Human Microbiome Program Required 25 CPU-Years on SDSC Gordon Supercomputer

10. Almost All Abundant Species (≥1%) in Healthy SubjectsAre Severely Depleted in LS Gut Source: Sequencing JCVI; Analysis Weizhong Li, UCSD; HMP, NIH; UCSD SOM LS December 28, 2011 Stool Sample

11. Rare Species Take Over the Altered Microbial EcologyIn LS vs. Average Healthy Number Above LS Blue Bar is Multiple of LS Abundance Compared to Average Healthy AbundancePer Species 152x 765x 148x 849x 483x 220x 201x 169x 522x Source: Sequencing JCVI; Analysis Weizhong Li, UCSD, HMP, NIH LS December 28, 2011 Stool Sample

12. When We Think About Biological DiversityWe 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

13. Think of These Phyla of AnimalsWhen You Consider the Biodiversity of Microbes Inside You Phylum Chordata Phylum Annelida Phylum Cnidaria Phylum Echinodermata Phylum Mollusca Phylum Arthropoda All images from WikiMedia Commons. Photos are public domain or by Dan Hershman, Michael Linnenbach, Manuae, B_cool

14. We Found Major Shifts in Microbial Ecology PhylaBetween Healthy and Two Forms of IBD Most Common Microbial Phyla Microbiome “Dysbiosis” or “Mass Extinction”? Collapse of Bacteroidetes Explosion of Proteobacteria

15. I Can Track Changes in My Microbiome Before and After 1 Month Antibiotic & 2 Month Prednisone Therapy Reduced 45x Reduced 90x Therapy Greatly Reduced Two Phyla, But Massive Reduction in Bacteroidetes And Large % Proteobacteria Remain Small Changes With No Therapy I am Trapped in a Local Ecological Equilibrium “Far from Home”

16. Refining the Dance • I Now Know Where I Am • And Where I Need to Get to • Startups Enable Tracking the Dance • Novel Interventions Become Possible Where There is Data There is Hope