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

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Presentation on theme: "An MRI Showed My Sigmoid Colon Wall Was Thickened and Inflamed."— Presentation transcript:

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 Among My 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 Normal Range <1 mg/L Normal 27x Upper Limit CRP Indicates Chronic Episodic Inflammation

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

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

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

8 Exploring the Dance Inside Your Superorganism Between 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 Visualizing the Genomic Dance of the Microbes Sequencing by JCVI or Human Microbiome Program Required 25 CPU-Years on SDSC Gordon Supercomputer Calit2 VROOM-FuturePatient Expedition

10 Almost All Abundant Species (1%) in Healthy Subjects Are 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 Ecology In LS vs. Average Healthy 152x 765x 148x 849x 483x 220x 201x 522x 169x Number Above LS Blue Bar is Multiple of LS Abundance Compared to Average Healthy Abundance Per Species Source: Sequencing JCVI; Analysis Weizhong Li, UCSD, HMP, NIH LS December 28, 2011 Stool Sample

12 When We Think About 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

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

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

15 I Can Track Changes in My Microbiome Before and After 1 Month Antibiotic & 2 Month Prednisone Therapy Therapy Greatly Reduced Two Phyla, But Massive Reduction in Bacteroidetes And Large % Proteobacteria Remain Reduced 45x Reduced 90x 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

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