“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
Interest in the Human Microbiome
Has Moved Quickly From Frontier Science to Public Awareness
June 8, 2012
June 14, 2012
June, 2012
August 18, 2012
To Understand the Interaction of Genetics and Human Behavior
We Must Consider the Human Microbiome
Your Body Has 10 Times
As Many Microbe Cells As Human Cells
Your Microbiome is
Your “Near-Body” Environment
and its Cells
Contain 300x
as Many DNA Genes
As Your 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
Calit2 64 Megapixel VROOM
One Blood Draw
For Me
Only One of My Blood Measurements
Was Far Out of Range--Indicating Chronic Inflammation
27x Upper Limit
Episodic Peaks in Inflammation
Followed by Spontaneous Drops
Normal Range <1 mg/L
Complex Reactive Protein (CRP) is a Blood Biomarker
for Detecting Presence of Inflammation
Adding Stool Tests Revealed
Oscillatory Behavior in an Immune Variable Which is Antibacterial
Typical
Lactoferrin Value for
Active Inflammatory
Bowel Disease
(IBD)
124x Upper Limit for Healthy
Normal Range
<7.3 µg/mL
Lactoferrin is a Protein Shed from Neutrophils An Antibacterial that Sequesters Iron
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
ATG16L1
IRGM
NOD2
Polymorphism in
Interleukin-23 Receptor Gene
— 80% Higher Risk
of Pro-inflammatory
Immune Response
rs1004819
SNPs Associated with CD
There May Be a Correlation Between CD SNPs
and Where and When the Disease Manifests
NOD2 (1)
Rs2066844
2.08x Increased Risk
Subject with
Ileal Crohn’s
Female
CD Onset
At 20-Years Old
Il-23R
Rs1004819
1.8x Increased Risk
Subject with
Colonic Crohn’s
Me-Male
CD Onset
At 60-Years Old
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
Could Changes in the Microbiome Ecology and Genetic Structure
Provide Some of the Missing Variance?
The width of the bar is proportional to the variance explained by that locus
However, the Total Disease Variance Explained Is Only:
• 13.6% for Crohn’s
• 7.5% for Ulcerative Colitis
“Host–microbe interactions have shaped the genetic architecture
of inflammatory bowel disease,” Jostins, et al. Nature 491, 119-124 (2012)
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
I Have Been Quantifying All Three
Paul B. Eckburg & David A. Relman
Clin Infect Dis. 44:256-262 (2007)
The Genetic Distance Between Microbes
Vastly Exceeds That Among All Animals and Plants
You
Are
Here
Tree of Life Derived from 16S rRNA Sequences
Source: Carl Woese, et al
For Deep Analysis of Changes in the Gut Microbiome Ecology
Our Team Compared a Healthy Population with 3 Types of IBD
Each Sample Has 100-200 Million Illumina Short Reads (100 bases)
“Healthy” Individuals
Inflammatory Bowel Disease (IBD) Patients
250 Subjects
1 Point in Time
2 Ulcerative Colitis Patients,
6 Points in Time
Larry Smarr
(Colonic Crohn’s)
7 Points in Time
5 Ileal Crohn’s Patients,
3 Points in Time
Total of 27 Billion Reads
Or 2.7 Trillion Bases
Source: Jerry Sheehan, Calit2
Weizhong Li, Sitao Wu, CRBS, UCSD
From Swedish Twin Study
To Map Out the Dynamics of Autoimmune Microbiome Ecology
Couples Next Generation Genome Sequencers to Big Data Supercomputers
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
Illumina HiSeq 2000 at JCVI
SDSC Gordon Data Supercomputer
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
Phylum
Chordata
Phylum
Cnidaria
Phylum
Echinodermata
Phylum
Annelida
Phylum
Mollusca
Phylum
Arthropoda
All images from WikiMedia Commons.
Photos are public domain or by Dan Hershman, Michael Linnenbach, Manuae, B_cool
We Found Major State Shifts in Microbial Ecology Phyla
Between Healthy and Three Forms of IBD
Average HE
Most
Common
Microbial
Phyla
Average
Ulcerative Colitis
Average LS
Colonic Crohn’s Disease
Average
Ileal Crohn’s Disease
Explosion of
Proteobacteria
Hybrid of UC and CD
High Level of Archaea
Collapse of Bacteroidetes
Explosion of Actinobacteria
Dell Analytics Separates The 4 Patient Types in Our Data
Using Our Microbiome Species Data
Ulcerative Colitis
Colonic Crohn’s
Healthy
Ileal Crohn’s
Source: Thomas Hill, Ph.D.
Executive Director Analytics
Dell | Information Management Group, Dell Software
I Built on Dell Analytics to Show Dynamic Evolution of My Microbiome
Toward and Away from Healthy State – Colonic Crohn’s
Seven Time Samples Over 1.5 Years
Healthy
Colonic Crohn’s
Ileal 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
2009
2010
2011
2012
2013
2014
2015
Weekly
Symptoms
Mood Disorders
Pharma
Therapies
Stool
Samples
In a “Healthy” Gut Microbiome:
Large Taxonomy Variation, Low Protein Family Variation
Over 200 People
Source: Nature, 486, 207-212 (2012)
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
Ratio of Random HE11529 to Healthy Average for Each Nonzero KEGG
We Computed
the Relative
Abundance of
10,000 KEGGs
in 35 Healthy
And 25 IBD
Patients
Most KEGGs Are Within 10x
Of Healthy for a Random HE
Nonzero KEGGs
However, Our Research Shows Large Changes
in Protein Families Between Health and Disease
Ratio of CD Average to Healthy Average for Each Nonzero KEGG
KEGGs Greatly Increased
In the Disease State
Note Hi/Low
Symmetry
Note 700 KEGGs
With Ratio >10
Most KEGGs Are Within 10x
In Healthy and Ileal Crohn’s Disease
Note 1000 KEGGs
With Ratio <0.1
KEGGs Greatly Decreased
In the Disease State
Over 7000 KEGGs Which Are Nonzero
in Health and Disease States
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
Announced November 7, 2014!
Inflammatory Bowel Disease Biobank
For Healthy and Disease Patients
Already 185 Enrolled
Drs. William J. Sandborn, John Chang, & Brigid Boland
UCSD School of Medicine, Division of Gastroenterology
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
[Amerindians in
Venezuela/Columbia]
[Africa]
Missing Microbes
Human
Microbiome
Project
“The microbiome of uncontacted Amerindians,” J. C. Clemente, et al. Science Advances 1, e1500183 (2015).
The Coupled Neural, Immune, and Microbiome Systems
Provide a Model Explaining How Nutrition Can Alter Neurodevelopment
Thanks to Our Great Team!
UCSD Metagenomics Team
JCVI Team
Weizhong Li
Sitao Wu
Karen Nelson
Shibu Yooseph
Manolito Torralba
Calit2@UCSD
Future Patient Team
SDSC Team
Jerry Sheehan
Tom DeFanti
Kevin Patrick
Jurgen Schulze
Andrew Prudhomme
Philip Weber
Fred Raab
Joe Keefe
Ernesto Ramirez
Dell/R Systems
Ayasdi
Devi Ramanan
Pek Lum
Michael Norman
Mahidhar Tatineni
Robert Sinkovits
Brian Kucic
John Thompson
UCSD Health Sciences Team
Rob Knight
William J. Sandborn
Elisabeth Evans
John Chang
Brigid Boland
David Brenner