SlideShare a Scribd company logo
1 of 37
Download to read offline
“Measuring the Human Brain-Gut Microbiome-Immune
System Dynamics: a Big Data Challenge”
Plenary Talk
45th Annual Meeting of the Behavior Genetics Association
San Diego, CA
June 18, 2015
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
1
June 8, 2012 June 14, 2012
Interest in the Human Microbiome
Has Moved Quickly From Frontier Science to Public Awareness
August 18, 2012June, 2012
To Understand the Interaction of Genetics and Human Behavior
We Must Consider the Human Microbiome
Your Microbiome is
Your “Near-Body” Environment
and its Cells
Contain 300x
as Many DNA Genes
As Your Human Cells
Your Body Has 10 Times
As Many Microbe Cells As Human Cells
The Microbiome–Gut–Brain Axis
Provides New Systemic Insights into Shifts in Behavior and Disease
Source: Montiel-Castro, et al.
Frontiers in Integrative Neuroscience 2013
Many New Research Studies are Demonstrating Deep Relationships
Between the Gut Microbiome and Behavioral Disorders
Gut Microbes Regulate Serotonin 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)
How Can One Combine Human Genetic GWAS
With Gut Microbiome Metagenomics and Immune System Dynamics?
An N=1 Case Study of an Autoimmune Disease
I Have Turned My Body into
a Genomic and Biomarker Observatory
One Blood Draw
For MeCalit2 64 Megapixel VROOM
Only One of My Blood Measurements
Was Far Out of Range--Indicating Chronic Inflammation
Normal Range <1 mg/L
27x Upper Limit
Complex Reactive Protein (CRP) is a Blood Biomarker
for Detecting Presence of Inflammation
Episodic Peaks in Inflammation
Followed by Spontaneous Drops
Adding Stool Tests Revealed
Oscillatory Behavior in an Immune Variable Which is Antibacterial
Normal Range
<7.3 µg/mL
124x Upper Limit for Healthy
Lactoferrin is a Protein Shed from Neutrophils -
An Antibacterial that Sequesters Iron
Typical
Lactoferrin Value for
Active Inflammatory
Bowel Disease
(IBD)
I Turned to SNP Analysis and GWAS
to Understand My Human Genomic Predispositions
I Found I Had One of the Earliest Known SNPs
Associated with Crohn’s Disease
From www.23andme.com
SNPs Associated with CD
Polymorphism in
Interleukin-23 Receptor Gene
— 80% Higher Risk
of Pro-inflammatory
Immune Response
rs1004819
NOD2
IRGM
ATG16L1
There May Be a Correlation Between CD SNPs
and Where and When the Disease Manifests
Me-Male
CD Onset
At 60-Years Old
Female
CD Onset
At 20-Years Old
NOD2 (1)
Rs2066844
2.08x Increased Risk
Il-23R
Rs1004819
1.8x Increased Risk
Subject with
Ileal Crohn’s
Subject with
Colonic Crohn’s
Source: Larry Smarr and 23andme
I Also Had an Increased Risk for Ulcerative Colitis,
But a SNP that is Also Associated with Colonic CD
I Have a
33% Increased Risk
for Ulcerative Colitis
HLA-DRA (rs2395185)
I Have the Same Level
of HLA-DRA Increased Risk
as Another Male Who Has Had
Ulcerative Colitis for 20 Years
“Our results suggest that at least for the SNPs investigated
[including HLA-DRA],
colonic CD and UC have common genetic basis.”
-Waterman, et al., IBD 17, 1936-42 (2011)
So IBD May be Stratified by a Personalized Combination
of the 163 Known SNP Loci Associated with IBD
The width of the bar is proportional to the variance explained by that locus
“Host–microbe interactions have shaped the genetic architecture
of inflammatory bowel disease,” Jostins, et al. Nature 491, 119-124 (2012)
Could Changes in the Microbiome Ecology and Genetic Structure
Provide Some of the Missing Variance?
However, the Total Disease Variance Explained Is Only:
• 13.6% for Crohn’s
• 7.5% for Ulcerative Colitis
Why Did I Have an Autoimmune Disease like IBD?
Despite decades of research,
the etiology of Crohn's disease
remains unknown.
Its pathogenesis may involve
a complex interplay between
host genetics,
immune dysfunction,
and microbial or environmental factors.
--The Role of Microbes in Crohn's Disease
Paul B. Eckburg & David A. Relman
Clin Infect Dis. 44:256-262 (2007)
I Have Been Quantifying All Three
The Genetic Distance Between Microbes
Vastly Exceeds That Among All Animals and Plants
You
Are
Here
Source: Carl Woese, et al
Tree of Life Derived from 16S rRNA Sequences
For Deep Analysis of Changes in the Gut Microbiome Ecology
Our Team Compared a Healthy Population with 3 Types of IBD
5 Ileal Crohn’s Patients,
3 Points in Time
2 Ulcerative Colitis Patients,
6 Points in Time
“Healthy” Individuals
Source: Jerry Sheehan, Calit2
Weizhong Li, Sitao Wu, CRBS, UCSD
Total of 27 Billion Reads
Or 2.7 Trillion Bases
Inflammatory Bowel Disease (IBD) Patients
250 Subjects
1 Point in Time
7 Points in Time
Each Sample Has 100-200 Million Illumina Short Reads (100 bases)
Larry Smarr
(Colonic Crohn’s)
From Swedish Twin Study
To Map Out the Dynamics of Autoimmune Microbiome Ecology
Couples Next Generation Genome Sequencers to Big Data Supercomputers
Illumina HiSeq 2000 at JCVI
SDSC Gordon Data Supercomputer
Example: Inflammatory Bowel Disease (IBD)
We used 25 CPU-years
to compute
comparative gut microbiomes
starting from
7 trillion DNA bases
of my samples,
255 healthy,
and 20 IBD controls
Computational NextGen Sequencing Pipeline:
From Sequence to Taxonomy and Function
PI: (Weizhong Li, CRBS, UCSD):
NIH R01HG005978 (2010-2013, $1.1M)
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
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
We Found Major State Shifts in Microbial Ecology Phyla
Between Healthy and Three Forms of IBD
Most
Common
Microbial
Phyla
Average HE
Average
Ulcerative Colitis
Average LS
Colonic Crohn’s Disease
Average
Ileal Crohn’s Disease
Collapse of Bacteroidetes
Explosion of Actinobacteria
Explosion of
Proteobacteria
Hybrid of UC and CD
High Level of Archaea
Dell Analytics Separates The 4 Patient Types in Our Data
Using Our Microbiome Species Data
Source: Thomas Hill, Ph.D.
Executive Director Analytics
Dell | Information Management Group, Dell Software
Healthy
Ulcerative Colitis
Colonic Crohn’s
Ileal Crohn’s
I Built on Dell Analytics to Show Dynamic Evolution of My Microbiome
Toward and Away from Healthy State – Colonic Crohn’s
Healthy
Ileal Crohn’s
Seven Time Samples Over 1.5 Years
Colonic Crohn’s
This Year We Will Extend My Stool Time Series
Collaborating with the UCSD Knight Lab
Larry’s 40 Stool Samples Over 3.5 Years
to Rob’s lab on April 30, 2015
Time Series Reveals Behavior Changes (Depression, Malaise)
Associated with Time Progression of Autoimmune Disease
Immune &
Inflammation
Variables
Weekly
Symptoms
Pharma
Therapies
Stool
Samples
Mood Disorders
2009 20142013201220112010 2015
In a “Healthy” Gut Microbiome:
Large Taxonomy Variation, Low Protein Family Variation
Source: Nature, 486, 207-212 (2012)
Over 200 People
We Computed the Relative Abundance of Microbial Gene Families -
~10,000 KEGG Orthologous Genes, Across Healthy and IBD Subjects
How Large is the Microbiome’s Genetic Change
Between Health and Disease States?
Ratio of One of the Healthy Subjects to the Average KEGG for 35 Healthy:
Test to see How Much Inter-Personal Variation There is Within Healthy
Most KEGGs Are Within 10x
Of Healthy for a Random HE
Ratio of Random HE11529 to Healthy Average for Each Nonzero KEGG
Nonzero KEGGs
We Computed
the Relative
Abundance of
10,000 KEGGs
in 35 Healthy
And 25 IBD
Patients
However, Our Research Shows Large Changes
in Protein Families Between Health and Disease
Most KEGGs Are Within 10x
In Healthy and Ileal Crohn’s Disease
KEGGs Greatly Increased
In the Disease State
KEGGs Greatly Decreased
In the Disease State
Over 7000 KEGGs Which Are Nonzero
in Health and Disease States
Ratio of CD Average to Healthy Average for Each Nonzero KEGG
Note Hi/Low
Symmetry
Note 700 KEGGs
With Ratio >10
Note 1000 KEGGs
With Ratio <0.1
Next Step: Compute Genes and Function
For All ~300 People’s Gut Microbiome
Full Processing to Function:
Genes & Protein Families
(COGs, KEGGs)
Would Require
~1-2 Million
Core-Hours
UC San Diego Will Be Carrying Out
a Major Clinical Study of IBD Using These Techniques
Inflammatory Bowel Disease Biobank
For Healthy and Disease Patients
Drs. William J. Sandborn, John Chang, & Brigid Boland
UCSD School of Medicine, Division of Gastroenterology
Already 185 Enrolled
Announced November 7, 2014!
We Must Move From 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
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]
Human
Microbiome
Project
Missing Microbes
The Coupled Neural, Immune, and Microbiome Systems
Provide a Model Explaining How Nutrition Can Alter Neurodevelopment
Thanks to Our Great Team!
UCSD Metagenomics Team
Weizhong Li
Sitao Wu
Calit2@UCSD
Future Patient Team
Jerry Sheehan
Tom DeFanti
Kevin Patrick
Jurgen Schulze
Andrew Prudhomme
Philip Weber
Fred Raab
Joe Keefe
Ernesto Ramirez
Ayasdi
Devi Ramanan
Pek Lum
JCVI Team
Karen Nelson
Shibu Yooseph
Manolito Torralba
SDSC Team
Michael Norman
Mahidhar Tatineni
Robert Sinkovits
UCSD Health Sciences Team
Rob Knight
William J. Sandborn
Elisabeth Evans
John Chang
Brigid Boland
David Brenner
Dell/R Systems
Brian Kucic
John Thompson

More Related Content

What's hot

Human Microbiome - An Evolving Clinical Frontier
Human Microbiome - An Evolving Clinical FrontierHuman Microbiome - An Evolving Clinical Frontier
Human Microbiome - An Evolving Clinical FrontierB. Ravinder Reddy
 
The Human Microbiome in Sports Performance and Health
The Human Microbiome in Sports Performance and HealthThe Human Microbiome in Sports Performance and Health
The Human Microbiome in Sports Performance and Healthctorgan
 
Microbial endocrinology
Microbial endocrinologyMicrobial endocrinology
Microbial endocrinologyKevin B Hugins
 
Dynamics of Your Gut Microbiome in Health and Disease
Dynamics of Your Gut Microbiome in Health and DiseaseDynamics of Your Gut Microbiome in Health and Disease
Dynamics of Your Gut Microbiome in Health and DiseaseLarry Smarr
 
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...Larry Smarr
 
DCSI presentation 2015
DCSI presentation 2015DCSI presentation 2015
DCSI presentation 2015beiko
 
Gut microbiome obesity nafld
Gut microbiome obesity nafldGut microbiome obesity nafld
Gut microbiome obesity nafldjoannayeh
 
We are what we eat - how diet is shaping our health
We are what we eat - how diet is shaping our healthWe are what we eat - how diet is shaping our health
We are what we eat - how diet is shaping our healthNorwich Research Park
 
High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...
High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...
High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...Copenhagenomics
 
2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...
2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...
2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...Daniel Chan
 
Microsleepome final powerpoint.ppt
Microsleepome final powerpoint.pptMicrosleepome final powerpoint.ppt
Microsleepome final powerpoint.pptJon Lendrum
 
Slideshare lahti-isme2014
Slideshare lahti-isme2014Slideshare lahti-isme2014
Slideshare lahti-isme2014Leo Lahti
 
2009 hattori metagenomics
2009 hattori metagenomics2009 hattori metagenomics
2009 hattori metagenomicsdrugmetabol
 
Feel Better Already! Microbiome Health
Feel Better Already!  Microbiome HealthFeel Better Already!  Microbiome Health
Feel Better Already! Microbiome HealthMika Davies
 
The Human Microbiome, Supercomputers,and the Advancement of Medicine
The Human Microbiome, Supercomputers,and the Advancement of MedicineThe Human Microbiome, Supercomputers,and the Advancement of Medicine
The Human Microbiome, Supercomputers,and the Advancement of MedicineLarry Smarr
 
Dr. Heather Allen - The Swine Gut Microbiota: Status and Outlook
Dr. Heather Allen - The Swine Gut Microbiota: Status and OutlookDr. Heather Allen - The Swine Gut Microbiota: Status and Outlook
Dr. Heather Allen - The Swine Gut Microbiota: Status and OutlookJohn Blue
 
Your microbiome may be key factor determining your health and longevity
Your microbiome may be key factor determining your health and longevityYour microbiome may be key factor determining your health and longevity
Your microbiome may be key factor determining your health and longevitykirti betai
 
M derrien yakult vf
M derrien yakult vfM derrien yakult vf
M derrien yakult vfneerjayakult
 

What's hot (20)

Human Microbiome - An Evolving Clinical Frontier
Human Microbiome - An Evolving Clinical FrontierHuman Microbiome - An Evolving Clinical Frontier
Human Microbiome - An Evolving Clinical Frontier
 
The Human Microbiome in Sports Performance and Health
The Human Microbiome in Sports Performance and HealthThe Human Microbiome in Sports Performance and Health
The Human Microbiome in Sports Performance and Health
 
Microbial endocrinology
Microbial endocrinologyMicrobial endocrinology
Microbial endocrinology
 
Dynamics of Your Gut Microbiome in Health and Disease
Dynamics of Your Gut Microbiome in Health and DiseaseDynamics of Your Gut Microbiome in Health and Disease
Dynamics of Your Gut Microbiome in Health and Disease
 
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...
 
DCSI presentation 2015
DCSI presentation 2015DCSI presentation 2015
DCSI presentation 2015
 
Gut microbiome obesity nafld
Gut microbiome obesity nafldGut microbiome obesity nafld
Gut microbiome obesity nafld
 
We are what we eat - how diet is shaping our health
We are what we eat - how diet is shaping our healthWe are what we eat - how diet is shaping our health
We are what we eat - how diet is shaping our health
 
High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...
High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...
High-Throughput Sequencing of the Human Microbiome, Rob Knight Research Group...
 
2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...
2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...
2 (2011) the role of gut micriobiota and the mucosal barrier in the pathogene...
 
Microsleepome final powerpoint.ppt
Microsleepome final powerpoint.pptMicrosleepome final powerpoint.ppt
Microsleepome final powerpoint.ppt
 
Slideshare lahti-isme2014
Slideshare lahti-isme2014Slideshare lahti-isme2014
Slideshare lahti-isme2014
 
Poster Final Final Draft
Poster Final Final DraftPoster Final Final Draft
Poster Final Final Draft
 
2009 hattori metagenomics
2009 hattori metagenomics2009 hattori metagenomics
2009 hattori metagenomics
 
Feel Better Already! Microbiome Health
Feel Better Already!  Microbiome HealthFeel Better Already!  Microbiome Health
Feel Better Already! Microbiome Health
 
The Human Microbiome, Supercomputers,and the Advancement of Medicine
The Human Microbiome, Supercomputers,and the Advancement of MedicineThe Human Microbiome, Supercomputers,and the Advancement of Medicine
The Human Microbiome, Supercomputers,and the Advancement of Medicine
 
Dr. Heather Allen - The Swine Gut Microbiota: Status and Outlook
Dr. Heather Allen - The Swine Gut Microbiota: Status and OutlookDr. Heather Allen - The Swine Gut Microbiota: Status and Outlook
Dr. Heather Allen - The Swine Gut Microbiota: Status and Outlook
 
Your microbiome may be key factor determining your health and longevity
Your microbiome may be key factor determining your health and longevityYour microbiome may be key factor determining your health and longevity
Your microbiome may be key factor determining your health and longevity
 
M derrien yakult vf
M derrien yakult vfM derrien yakult vf
M derrien yakult vf
 
My microbiome and me
My microbiome and meMy microbiome and me
My microbiome and me
 

Similar to Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data Challenge

The Human Gut Microbiome: A New Diagnostic for Disease?
The Human Gut Microbiome: A New Diagnostic for Disease?The Human Gut Microbiome: A New Diagnostic for Disease?
The Human Gut Microbiome: A New Diagnostic for Disease?Larry Smarr
 
The Digital Transformation of Healthcare
The Digital Transformation of HealthcareThe Digital Transformation of Healthcare
The Digital Transformation of HealthcareLarry Smarr
 
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism Body
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyUsing Genetic Sequencing to Unravel the Dynamics of Your Superorganism Body
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyLarry Smarr
 
Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...
Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...
Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...Larry Smarr
 
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human Genomics
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsBig Data and Superorganism Genomics: Microbial Metagenomics Meets Human Genomics
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
 
Discovering the Other 90% of our Human Superorganism
Discovering the Other 90% of our Human SuperorganismDiscovering the Other 90% of our Human Superorganism
Discovering the Other 90% of our Human SuperorganismLarry Smarr
 
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Larry Smarr
 
Quantifying Your Superorganism Body Using Big Data Supercomputing
Quantifying Your Superorganism Body Using Big Data SupercomputingQuantifying Your Superorganism Body Using Big Data Supercomputing
Quantifying Your Superorganism Body Using Big Data SupercomputingLarry Smarr
 
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step Further
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step FurtherIndividual, Consumer-Driven Care of the Future: Taking Wellness One Step Further
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step FurtherLarry Smarr
 
From Me To We: Discovering the Trillions of Microorganisms That are a Part of Us
From Me To We: Discovering the Trillions of Microorganisms That are a Part of UsFrom Me To We: Discovering the Trillions of Microorganisms That are a Part of Us
From Me To We: Discovering the Trillions of Microorganisms That are a Part of UsLarry Smarr
 
From N=1 to N=100: What I Have Learned from Quantifying My Superorganism Body
From N=1 to N=100: What I Have Learned from Quantifying My Superorganism BodyFrom N=1 to N=100: What I Have Learned from Quantifying My Superorganism Body
From N=1 to N=100: What I Have Learned from Quantifying My Superorganism BodyLarry Smarr
 
The Systems Biology Dynamics of the Human Immune System and Gut Microbiome
The Systems Biology Dynamics of the Human Immune System and Gut MicrobiomeThe Systems Biology Dynamics of the Human Immune System and Gut Microbiome
The Systems Biology Dynamics of the Human Immune System and Gut MicrobiomeLarry Smarr
 
Capturing the Interactive Dynamics of the Human Host/Microbiome System
Capturing the Interactive Dynamics of the Human Host/Microbiome SystemCapturing the Interactive Dynamics of the Human Host/Microbiome System
Capturing the Interactive Dynamics of the Human Host/Microbiome SystemLarry Smarr
 
Using Supercomputers and Data Science to Reveal Your Inner Microbiome
Using Supercomputers and Data Science to Reveal Your Inner MicrobiomeUsing Supercomputers and Data Science to Reveal Your Inner Microbiome
Using Supercomputers and Data Science to Reveal Your Inner MicrobiomeLarry Smarr
 
Digitally Revealing the Dynamics of Your Superorganism Body
Digitally Revealing the Dynamics of Your Superorganism BodyDigitally Revealing the Dynamics of Your Superorganism Body
Digitally Revealing the Dynamics of Your Superorganism BodyLarry Smarr
 
Assay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and BiomesAssay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
 
Assay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and BiomesAssay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
 
Finding the Patterns in the Big Data From Human Microbiome Ecology
Finding the Patterns in the Big Data From Human Microbiome EcologyFinding the Patterns in the Big Data From Human Microbiome Ecology
Finding the Patterns in the Big Data From Human Microbiome EcologyLarry Smarr
 
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Larry Smarr
 
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion Microbes
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion MicrobesKnow Thyself: Quantifying Your Human Body and Its One Hundred Trillion Microbes
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion MicrobesLarry Smarr
 

Similar to Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data Challenge (20)

The Human Gut Microbiome: A New Diagnostic for Disease?
The Human Gut Microbiome: A New Diagnostic for Disease?The Human Gut Microbiome: A New Diagnostic for Disease?
The Human Gut Microbiome: A New Diagnostic for Disease?
 
The Digital Transformation of Healthcare
The Digital Transformation of HealthcareThe Digital Transformation of Healthcare
The Digital Transformation of Healthcare
 
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism Body
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyUsing Genetic Sequencing to Unravel the Dynamics of Your Superorganism Body
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism Body
 
Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...
Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...
Using Supercomputing & Advanced Analytic Software to Discover Radical Changes...
 
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human Genomics
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsBig Data and Superorganism Genomics: Microbial Metagenomics Meets Human Genomics
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human Genomics
 
Discovering the Other 90% of our Human Superorganism
Discovering the Other 90% of our Human SuperorganismDiscovering the Other 90% of our Human Superorganism
Discovering the Other 90% of our Human Superorganism
 
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...
 
Quantifying Your Superorganism Body Using Big Data Supercomputing
Quantifying Your Superorganism Body Using Big Data SupercomputingQuantifying Your Superorganism Body Using Big Data Supercomputing
Quantifying Your Superorganism Body Using Big Data Supercomputing
 
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step Further
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step FurtherIndividual, Consumer-Driven Care of the Future: Taking Wellness One Step Further
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step Further
 
From Me To We: Discovering the Trillions of Microorganisms That are a Part of Us
From Me To We: Discovering the Trillions of Microorganisms That are a Part of UsFrom Me To We: Discovering the Trillions of Microorganisms That are a Part of Us
From Me To We: Discovering the Trillions of Microorganisms That are a Part of Us
 
From N=1 to N=100: What I Have Learned from Quantifying My Superorganism Body
From N=1 to N=100: What I Have Learned from Quantifying My Superorganism BodyFrom N=1 to N=100: What I Have Learned from Quantifying My Superorganism Body
From N=1 to N=100: What I Have Learned from Quantifying My Superorganism Body
 
The Systems Biology Dynamics of the Human Immune System and Gut Microbiome
The Systems Biology Dynamics of the Human Immune System and Gut MicrobiomeThe Systems Biology Dynamics of the Human Immune System and Gut Microbiome
The Systems Biology Dynamics of the Human Immune System and Gut Microbiome
 
Capturing the Interactive Dynamics of the Human Host/Microbiome System
Capturing the Interactive Dynamics of the Human Host/Microbiome SystemCapturing the Interactive Dynamics of the Human Host/Microbiome System
Capturing the Interactive Dynamics of the Human Host/Microbiome System
 
Using Supercomputers and Data Science to Reveal Your Inner Microbiome
Using Supercomputers and Data Science to Reveal Your Inner MicrobiomeUsing Supercomputers and Data Science to Reveal Your Inner Microbiome
Using Supercomputers and Data Science to Reveal Your Inner Microbiome
 
Digitally Revealing the Dynamics of Your Superorganism Body
Digitally Revealing the Dynamics of Your Superorganism BodyDigitally Revealing the Dynamics of Your Superorganism Body
Digitally Revealing the Dynamics of Your Superorganism Body
 
Assay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and BiomesAssay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and Biomes
 
Assay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and BiomesAssay Lab Within Your Body: Biometrics and Biomes
Assay Lab Within Your Body: Biometrics and Biomes
 
Finding the Patterns in the Big Data From Human Microbiome Ecology
Finding the Patterns in the Big Data From Human Microbiome EcologyFinding the Patterns in the Big Data From Human Microbiome Ecology
Finding the Patterns in the Big Data From Human Microbiome Ecology
 
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...
 
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion Microbes
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion MicrobesKnow Thyself: Quantifying Your Human Body and Its One Hundred Trillion Microbes
Know Thyself: Quantifying Your Human Body and Its One Hundred Trillion Microbes
 

More from Larry Smarr

My Remembrances of Mike Norman Over The Last 45 Years
My Remembrances of Mike Norman Over The Last 45 YearsMy Remembrances of Mike Norman Over The Last 45 Years
My Remembrances of Mike Norman Over The Last 45 YearsLarry Smarr
 
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019Larry Smarr
 
Panel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving InstitutionsPanel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
 
Global Network Advancement Group - Next Generation Network-Integrated Systems
Global Network Advancement Group - Next Generation Network-Integrated SystemsGlobal Network Advancement Group - Next Generation Network-Integrated Systems
Global Network Advancement Group - Next Generation Network-Integrated SystemsLarry Smarr
 
Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...
 Wireless FasterData and Distributed Open Compute Opportunities and (some) Us... Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...
Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...Larry Smarr
 
Panel Discussion: Engaging underrepresented technologists, researchers, and e...
Panel Discussion: Engaging underrepresented technologists, researchers, and e...Panel Discussion: Engaging underrepresented technologists, researchers, and e...
Panel Discussion: Engaging underrepresented technologists, researchers, and e...Larry Smarr
 
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon Moon
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon MoonThe Asia Pacific and Korea Research Platforms: An Overview Jeonghoon Moon
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon MoonLarry Smarr
 
Panel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving InstitutionsPanel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
 
Panel: The Global Research Platform: An Overview
Panel: The Global Research Platform: An OverviewPanel: The Global Research Platform: An Overview
Panel: The Global Research Platform: An OverviewLarry Smarr
 
Panel: Future Wireless Extensions of Regional Optical Networks
Panel: Future Wireless Extensions of Regional Optical NetworksPanel: Future Wireless Extensions of Regional Optical Networks
Panel: Future Wireless Extensions of Regional Optical NetworksLarry Smarr
 
Global Research Platform Workshops - Maxine Brown
Global Research Platform Workshops - Maxine BrownGlobal Research Platform Workshops - Maxine Brown
Global Research Platform Workshops - Maxine BrownLarry Smarr
 
Built around answering questions
Built around answering questionsBuilt around answering questions
Built around answering questionsLarry Smarr
 
Panel: NRP Science Impacts​
Panel: NRP Science Impacts​Panel: NRP Science Impacts​
Panel: NRP Science Impacts​Larry Smarr
 
Democratizing Science through Cyberinfrastructure - Manish Parashar
Democratizing Science through Cyberinfrastructure - Manish ParasharDemocratizing Science through Cyberinfrastructure - Manish Parashar
Democratizing Science through Cyberinfrastructure - Manish ParasharLarry Smarr
 
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;Larry Smarr
 
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...Larry Smarr
 
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
 
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
 
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
 
Frank Würthwein - NRP and the Path forward
Frank Würthwein - NRP and the Path forwardFrank Würthwein - NRP and the Path forward
Frank Würthwein - NRP and the Path forwardLarry Smarr
 

More from Larry Smarr (20)

My Remembrances of Mike Norman Over The Last 45 Years
My Remembrances of Mike Norman Over The Last 45 YearsMy Remembrances of Mike Norman Over The Last 45 Years
My Remembrances of Mike Norman Over The Last 45 Years
 
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019
 
Panel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving InstitutionsPanel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving Institutions
 
Global Network Advancement Group - Next Generation Network-Integrated Systems
Global Network Advancement Group - Next Generation Network-Integrated SystemsGlobal Network Advancement Group - Next Generation Network-Integrated Systems
Global Network Advancement Group - Next Generation Network-Integrated Systems
 
Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...
 Wireless FasterData and Distributed Open Compute Opportunities and (some) Us... Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...
Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...
 
Panel Discussion: Engaging underrepresented technologists, researchers, and e...
Panel Discussion: Engaging underrepresented technologists, researchers, and e...Panel Discussion: Engaging underrepresented technologists, researchers, and e...
Panel Discussion: Engaging underrepresented technologists, researchers, and e...
 
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon Moon
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon MoonThe Asia Pacific and Korea Research Platforms: An Overview Jeonghoon Moon
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon Moon
 
Panel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving InstitutionsPanel: Reaching More Minority Serving Institutions
Panel: Reaching More Minority Serving Institutions
 
Panel: The Global Research Platform: An Overview
Panel: The Global Research Platform: An OverviewPanel: The Global Research Platform: An Overview
Panel: The Global Research Platform: An Overview
 
Panel: Future Wireless Extensions of Regional Optical Networks
Panel: Future Wireless Extensions of Regional Optical NetworksPanel: Future Wireless Extensions of Regional Optical Networks
Panel: Future Wireless Extensions of Regional Optical Networks
 
Global Research Platform Workshops - Maxine Brown
Global Research Platform Workshops - Maxine BrownGlobal Research Platform Workshops - Maxine Brown
Global Research Platform Workshops - Maxine Brown
 
Built around answering questions
Built around answering questionsBuilt around answering questions
Built around answering questions
 
Panel: NRP Science Impacts​
Panel: NRP Science Impacts​Panel: NRP Science Impacts​
Panel: NRP Science Impacts​
 
Democratizing Science through Cyberinfrastructure - Manish Parashar
Democratizing Science through Cyberinfrastructure - Manish ParasharDemocratizing Science through Cyberinfrastructure - Manish Parashar
Democratizing Science through Cyberinfrastructure - Manish Parashar
 
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;
 
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...
 
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
 
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
 
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...
 
Frank Würthwein - NRP and the Path forward
Frank Würthwein - NRP and the Path forwardFrank Würthwein - NRP and the Path forward
Frank Würthwein - NRP and the Path forward
 

Recently uploaded

CI, CD -Tools to integrate without manual intervention
CI, CD -Tools to integrate without manual interventionCI, CD -Tools to integrate without manual intervention
CI, CD -Tools to integrate without manual interventionajayrajaganeshkayala
 
YourView Panel Book.pptx YourView Panel Book.
YourView Panel Book.pptx YourView Panel Book.YourView Panel Book.pptx YourView Panel Book.
YourView Panel Book.pptx YourView Panel Book.JasonViviers2
 
AI for Sustainable Development Goals (SDGs)
AI for Sustainable Development Goals (SDGs)AI for Sustainable Development Goals (SDGs)
AI for Sustainable Development Goals (SDGs)Data & Analytics Magazin
 
SFBA Splunk Usergroup meeting March 13, 2024
SFBA Splunk Usergroup meeting March 13, 2024SFBA Splunk Usergroup meeting March 13, 2024
SFBA Splunk Usergroup meeting March 13, 2024Becky Burwell
 
5 Ds to Define Data Archiving Best Practices
5 Ds to Define Data Archiving Best Practices5 Ds to Define Data Archiving Best Practices
5 Ds to Define Data Archiving Best PracticesDataArchiva
 
Master's Thesis - Data Science - Presentation
Master's Thesis - Data Science - PresentationMaster's Thesis - Data Science - Presentation
Master's Thesis - Data Science - PresentationGiorgio Carbone
 
ChistaDATA Real-Time DATA Analytics Infrastructure
ChistaDATA Real-Time DATA Analytics InfrastructureChistaDATA Real-Time DATA Analytics Infrastructure
ChistaDATA Real-Time DATA Analytics Infrastructuresonikadigital1
 
Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024
Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024
Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024Guido X Jansen
 
Virtuosoft SmartSync Product Introduction
Virtuosoft SmartSync Product IntroductionVirtuosoft SmartSync Product Introduction
Virtuosoft SmartSync Product Introductionsanjaymuralee1
 
TINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptx
TINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptxTINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptx
TINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptxDwiAyuSitiHartinah
 
Elements of language learning - an analysis of how different elements of lang...
Elements of language learning - an analysis of how different elements of lang...Elements of language learning - an analysis of how different elements of lang...
Elements of language learning - an analysis of how different elements of lang...PrithaVashisht1
 
MEASURES OF DISPERSION I BSc Botany .ppt
MEASURES OF DISPERSION I BSc Botany .pptMEASURES OF DISPERSION I BSc Botany .ppt
MEASURES OF DISPERSION I BSc Botany .pptaigil2
 
Cash Is Still King: ATM market research '2023
Cash Is Still King: ATM market research '2023Cash Is Still King: ATM market research '2023
Cash Is Still King: ATM market research '2023Vladislav Solodkiy
 
How is Real-Time Analytics Different from Traditional OLAP?
How is Real-Time Analytics Different from Traditional OLAP?How is Real-Time Analytics Different from Traditional OLAP?
How is Real-Time Analytics Different from Traditional OLAP?sonikadigital1
 
Strategic CX: A Deep Dive into Voice of the Customer Insights for Clarity
Strategic CX: A Deep Dive into Voice of the Customer Insights for ClarityStrategic CX: A Deep Dive into Voice of the Customer Insights for Clarity
Strategic CX: A Deep Dive into Voice of the Customer Insights for ClarityAggregage
 
The Universal GTM - how we design GTM and dataLayer
The Universal GTM - how we design GTM and dataLayerThe Universal GTM - how we design GTM and dataLayer
The Universal GTM - how we design GTM and dataLayerPavel Šabatka
 
Mapping the pubmed data under different suptopics using NLP.pptx
Mapping the pubmed data under different suptopics using NLP.pptxMapping the pubmed data under different suptopics using NLP.pptx
Mapping the pubmed data under different suptopics using NLP.pptxVenkatasubramani13
 

Recently uploaded (17)

CI, CD -Tools to integrate without manual intervention
CI, CD -Tools to integrate without manual interventionCI, CD -Tools to integrate without manual intervention
CI, CD -Tools to integrate without manual intervention
 
YourView Panel Book.pptx YourView Panel Book.
YourView Panel Book.pptx YourView Panel Book.YourView Panel Book.pptx YourView Panel Book.
YourView Panel Book.pptx YourView Panel Book.
 
AI for Sustainable Development Goals (SDGs)
AI for Sustainable Development Goals (SDGs)AI for Sustainable Development Goals (SDGs)
AI for Sustainable Development Goals (SDGs)
 
SFBA Splunk Usergroup meeting March 13, 2024
SFBA Splunk Usergroup meeting March 13, 2024SFBA Splunk Usergroup meeting March 13, 2024
SFBA Splunk Usergroup meeting March 13, 2024
 
5 Ds to Define Data Archiving Best Practices
5 Ds to Define Data Archiving Best Practices5 Ds to Define Data Archiving Best Practices
5 Ds to Define Data Archiving Best Practices
 
Master's Thesis - Data Science - Presentation
Master's Thesis - Data Science - PresentationMaster's Thesis - Data Science - Presentation
Master's Thesis - Data Science - Presentation
 
ChistaDATA Real-Time DATA Analytics Infrastructure
ChistaDATA Real-Time DATA Analytics InfrastructureChistaDATA Real-Time DATA Analytics Infrastructure
ChistaDATA Real-Time DATA Analytics Infrastructure
 
Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024
Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024
Persuasive E-commerce, Our Biased Brain @ Bikkeldag 2024
 
Virtuosoft SmartSync Product Introduction
Virtuosoft SmartSync Product IntroductionVirtuosoft SmartSync Product Introduction
Virtuosoft SmartSync Product Introduction
 
TINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptx
TINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptxTINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptx
TINJUAN PEMROSESAN TRANSAKSI DAN ERP.pptx
 
Elements of language learning - an analysis of how different elements of lang...
Elements of language learning - an analysis of how different elements of lang...Elements of language learning - an analysis of how different elements of lang...
Elements of language learning - an analysis of how different elements of lang...
 
MEASURES OF DISPERSION I BSc Botany .ppt
MEASURES OF DISPERSION I BSc Botany .pptMEASURES OF DISPERSION I BSc Botany .ppt
MEASURES OF DISPERSION I BSc Botany .ppt
 
Cash Is Still King: ATM market research '2023
Cash Is Still King: ATM market research '2023Cash Is Still King: ATM market research '2023
Cash Is Still King: ATM market research '2023
 
How is Real-Time Analytics Different from Traditional OLAP?
How is Real-Time Analytics Different from Traditional OLAP?How is Real-Time Analytics Different from Traditional OLAP?
How is Real-Time Analytics Different from Traditional OLAP?
 
Strategic CX: A Deep Dive into Voice of the Customer Insights for Clarity
Strategic CX: A Deep Dive into Voice of the Customer Insights for ClarityStrategic CX: A Deep Dive into Voice of the Customer Insights for Clarity
Strategic CX: A Deep Dive into Voice of the Customer Insights for Clarity
 
The Universal GTM - how we design GTM and dataLayer
The Universal GTM - how we design GTM and dataLayerThe Universal GTM - how we design GTM and dataLayer
The Universal GTM - how we design GTM and dataLayer
 
Mapping the pubmed data under different suptopics using NLP.pptx
Mapping the pubmed data under different suptopics using NLP.pptxMapping the pubmed data under different suptopics using NLP.pptx
Mapping the pubmed data under different suptopics using NLP.pptx
 

Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data Challenge

  • 1. “Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data Challenge” Plenary Talk 45th Annual Meeting of the Behavior Genetics Association San Diego, CA June 18, 2015 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 1
  • 2. June 8, 2012 June 14, 2012 Interest in the Human Microbiome Has Moved Quickly From Frontier Science to Public Awareness August 18, 2012June, 2012
  • 3. To Understand the Interaction of Genetics and Human Behavior We Must Consider the Human Microbiome Your Microbiome is Your “Near-Body” Environment and its Cells Contain 300x as Many DNA Genes As Your Human Cells Your Body Has 10 Times As Many Microbe Cells As Human Cells
  • 4. The Microbiome–Gut–Brain Axis Provides New Systemic Insights into Shifts in Behavior and Disease Source: Montiel-Castro, et al. Frontiers in Integrative Neuroscience 2013
  • 5. Many New Research Studies are Demonstrating Deep Relationships Between the Gut Microbiome and Behavioral Disorders
  • 6. Gut Microbes Regulate Serotonin 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)
  • 7. How Can One Combine Human Genetic GWAS With Gut Microbiome Metagenomics and Immune System Dynamics? An N=1 Case Study of an Autoimmune Disease
  • 8. I Have Turned My Body into a Genomic and Biomarker Observatory One Blood Draw For MeCalit2 64 Megapixel VROOM
  • 9. Only One of My Blood Measurements Was Far Out of Range--Indicating Chronic Inflammation Normal Range <1 mg/L 27x Upper Limit Complex Reactive Protein (CRP) is a Blood Biomarker for Detecting Presence of Inflammation Episodic Peaks in Inflammation Followed by Spontaneous Drops
  • 10. Adding Stool Tests Revealed Oscillatory Behavior in an Immune Variable Which is Antibacterial Normal Range <7.3 µg/mL 124x Upper Limit for Healthy Lactoferrin is a Protein Shed from Neutrophils - An Antibacterial that Sequesters Iron Typical Lactoferrin Value for Active Inflammatory Bowel Disease (IBD)
  • 11. I Turned to SNP Analysis and GWAS to Understand My Human Genomic Predispositions
  • 12. I Found I Had One of the Earliest Known SNPs Associated with Crohn’s Disease From www.23andme.com SNPs Associated with CD Polymorphism in Interleukin-23 Receptor Gene — 80% Higher Risk of Pro-inflammatory Immune Response rs1004819 NOD2 IRGM ATG16L1
  • 13. There May Be a Correlation Between CD SNPs and Where and When the Disease Manifests Me-Male CD Onset At 60-Years Old Female CD Onset At 20-Years Old NOD2 (1) Rs2066844 2.08x Increased Risk Il-23R Rs1004819 1.8x Increased Risk Subject with Ileal Crohn’s Subject with Colonic Crohn’s Source: Larry Smarr and 23andme
  • 14. I Also Had an Increased Risk for Ulcerative Colitis, But a SNP that is Also Associated with Colonic CD I Have a 33% Increased Risk for Ulcerative Colitis HLA-DRA (rs2395185) I Have the Same Level of HLA-DRA Increased Risk as Another Male Who Has Had Ulcerative Colitis for 20 Years “Our results suggest that at least for the SNPs investigated [including HLA-DRA], colonic CD and UC have common genetic basis.” -Waterman, et al., IBD 17, 1936-42 (2011)
  • 15. So IBD May be Stratified by a Personalized Combination of the 163 Known SNP Loci Associated with IBD The width of the bar is proportional to the variance explained by that locus “Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease,” Jostins, et al. Nature 491, 119-124 (2012) Could Changes in the Microbiome Ecology and Genetic Structure Provide Some of the Missing Variance? However, the Total Disease Variance Explained Is Only: • 13.6% for Crohn’s • 7.5% for Ulcerative Colitis
  • 16. Why Did I Have an Autoimmune Disease like IBD? Despite decades of research, the etiology of Crohn's disease remains unknown. Its pathogenesis may involve a complex interplay between host genetics, immune dysfunction, and microbial or environmental factors. --The Role of Microbes in Crohn's Disease Paul B. Eckburg & David A. Relman Clin Infect Dis. 44:256-262 (2007) I Have Been Quantifying All Three
  • 17. The Genetic Distance Between Microbes Vastly Exceeds That Among All Animals and Plants You Are Here Source: Carl Woese, et al Tree of Life Derived from 16S rRNA Sequences
  • 18. For Deep Analysis of Changes in the Gut Microbiome Ecology Our Team Compared a Healthy Population with 3 Types of IBD 5 Ileal Crohn’s Patients, 3 Points in Time 2 Ulcerative Colitis Patients, 6 Points in Time “Healthy” Individuals Source: Jerry Sheehan, Calit2 Weizhong Li, Sitao Wu, CRBS, UCSD Total of 27 Billion Reads Or 2.7 Trillion Bases Inflammatory Bowel Disease (IBD) Patients 250 Subjects 1 Point in Time 7 Points in Time Each Sample Has 100-200 Million Illumina Short Reads (100 bases) Larry Smarr (Colonic Crohn’s) From Swedish Twin Study
  • 19. To Map Out the Dynamics of Autoimmune Microbiome Ecology Couples Next Generation Genome Sequencers to Big Data Supercomputers Illumina HiSeq 2000 at JCVI SDSC Gordon Data Supercomputer Example: Inflammatory Bowel Disease (IBD) We used 25 CPU-years to compute comparative gut microbiomes starting from 7 trillion DNA bases of my samples, 255 healthy, and 20 IBD controls
  • 20. Computational NextGen Sequencing Pipeline: From Sequence to Taxonomy and Function PI: (Weizhong Li, CRBS, UCSD): NIH R01HG005978 (2010-2013, $1.1M)
  • 21. 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
  • 22. 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
  • 23. We Found Major State Shifts in Microbial Ecology Phyla Between Healthy and Three Forms of IBD Most Common Microbial Phyla Average HE Average Ulcerative Colitis Average LS Colonic Crohn’s Disease Average Ileal Crohn’s Disease Collapse of Bacteroidetes Explosion of Actinobacteria Explosion of Proteobacteria Hybrid of UC and CD High Level of Archaea
  • 24. Dell Analytics Separates The 4 Patient Types in Our Data Using Our Microbiome Species Data Source: Thomas Hill, Ph.D. Executive Director Analytics Dell | Information Management Group, Dell Software Healthy Ulcerative Colitis Colonic Crohn’s Ileal Crohn’s
  • 25. I Built on Dell Analytics to Show Dynamic Evolution of My Microbiome Toward and Away from Healthy State – Colonic Crohn’s Healthy Ileal Crohn’s Seven Time Samples Over 1.5 Years Colonic Crohn’s
  • 26. This Year We Will Extend My Stool Time Series Collaborating with the UCSD Knight Lab Larry’s 40 Stool Samples Over 3.5 Years to Rob’s lab on April 30, 2015
  • 27. Time Series Reveals Behavior Changes (Depression, Malaise) Associated with Time Progression of Autoimmune Disease Immune & Inflammation Variables Weekly Symptoms Pharma Therapies Stool Samples Mood Disorders 2009 20142013201220112010 2015
  • 28. In a “Healthy” Gut Microbiome: Large Taxonomy Variation, Low Protein Family Variation Source: Nature, 486, 207-212 (2012) Over 200 People
  • 29. We Computed the Relative Abundance of Microbial Gene Families - ~10,000 KEGG Orthologous Genes, Across Healthy and IBD Subjects How Large is the Microbiome’s Genetic Change Between Health and Disease States?
  • 30. Ratio of One of the Healthy Subjects to the Average KEGG for 35 Healthy: Test to see How Much Inter-Personal Variation There is Within Healthy Most KEGGs Are Within 10x Of Healthy for a Random HE Ratio of Random HE11529 to Healthy Average for Each Nonzero KEGG Nonzero KEGGs We Computed the Relative Abundance of 10,000 KEGGs in 35 Healthy And 25 IBD Patients
  • 31. However, Our Research Shows Large Changes in Protein Families Between Health and Disease Most KEGGs Are Within 10x In Healthy and Ileal Crohn’s Disease KEGGs Greatly Increased In the Disease State KEGGs Greatly Decreased In the Disease State Over 7000 KEGGs Which Are Nonzero in Health and Disease States Ratio of CD Average to Healthy Average for Each Nonzero KEGG Note Hi/Low Symmetry Note 700 KEGGs With Ratio >10 Note 1000 KEGGs With Ratio <0.1
  • 32. Next Step: Compute Genes and Function For All ~300 People’s Gut Microbiome Full Processing to Function: Genes & Protein Families (COGs, KEGGs) Would Require ~1-2 Million Core-Hours
  • 33. UC San Diego Will Be Carrying Out a Major Clinical Study of IBD Using These Techniques Inflammatory Bowel Disease Biobank For Healthy and Disease Patients Drs. William J. Sandborn, John Chang, & Brigid Boland UCSD School of Medicine, Division of Gastroenterology Already 185 Enrolled Announced November 7, 2014!
  • 34. We Must Move From 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
  • 35. 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] Human Microbiome Project Missing Microbes
  • 36. The Coupled Neural, Immune, and Microbiome Systems Provide a Model Explaining How Nutrition Can Alter Neurodevelopment
  • 37. Thanks to Our Great Team! UCSD Metagenomics Team Weizhong Li Sitao Wu Calit2@UCSD Future Patient Team Jerry Sheehan Tom DeFanti Kevin Patrick Jurgen Schulze Andrew Prudhomme Philip Weber Fred Raab Joe Keefe Ernesto Ramirez Ayasdi Devi Ramanan Pek Lum JCVI Team Karen Nelson Shibu Yooseph Manolito Torralba SDSC Team Michael Norman Mahidhar Tatineni Robert Sinkovits UCSD Health Sciences Team Rob Knight William J. Sandborn Elisabeth Evans John Chang Brigid Boland David Brenner Dell/R Systems Brian Kucic John Thompson