Evaluating human gut microbiota and microbe-host
phenotype relationships
Jeremiah Faith
Icahn School of Medicine at Mount Sinai
Immunology Institute
Institute for Genomics and Multiscale Biology
2014 Advances in Inflammatory Bowel Diseases
Orlando, FL
Dec 6, 2014
Associations between our microbes and
intestinal disease
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•
•
•
•
•
•
Crohn’s disease
Ulcerative colitis
Pouchitis
Necrotizing enterocolitis
Coeliac disease
Diarrhea (C. diff)
Colorectal cancer
What must be done
1. Verify causation
2. Identify microbial effector strains
3. Modify effector strains to improve health
Identifying human microbial effector strains
in mice
Germ-free and gnotobiotic mice
• Germ-free: devoid of microbial life
• Gnotobiotic: “known life”, colonized with defined collections of microbes
• Humanized microbiota: gnotobiotic animals harboring a human community
Effector strain identification successes
• B. vulgatus accelerates colitis in gnotobiotic guinea pigs [A.
Onderdonk et.al., 1980s]
• IL10-/- mice; HLA-B27 rats [B. Sartor 1990s-now]
• B. fragilis matures immune system [Mazmanian, et.al., Cell 2005]
• SFB increase Th17 in small intestine [Ivanov, et.al., Cell 2009]
• K. pneumoniae and P. mirabilis elicit colitis in T-bet-/- x Rag2-/[Garrett et. al., Cell Host Microbe 2010]
• Clostridia increase Treg in colonic lamina propria [Atarashi, et.al.,
Science 2011]
• E. coli NC101 modulates colorectal cancer (AOM/IL10) [Arthur, et.al.,
Science 2012]
We are getting better at this.
But can we be more exhaustive
A systematic pipeline for identifying
human effector strains in mice
Screening “humanized” mice
Diverse donors
Gnotobiotic mice
%FoxP3+ among
CD4+ Tcells
Humanized with the
microbiota of a unique donor
Which bacteria are
causing this?!?
Faith, et.al., Sci Transl Med 2014
High-throughput anaerobic bacterial isolation
Anaerobic isolation
Donor
Protein extraction
Goodman, et.al., PNAS 2011
Faith, et.al., Science 2013
Identification
(MALDI-TOF)
Each well contains a unique
bacterial strain
Large scale bacterial isolation
Each well contains a unique
bacterial strain
(17 total microbes)
Donor
Fractionate community
Gnotobiotic mice
Community size
Adiposity
Serine
% Tregs
Phenotype screen
Phenotype response
Which bacteria are
causing this?!?
%FoxP3+ among
CD4+ T cells
%FoxP3+ among
CD4+ Tcells
Identifying effector strains
Faith, et.al, Sci Transl Med 2014
Next steps for understanding
host/microbe interactions in IBD
Diverse donors
Gnotobiotic mice
Humanized with the
microbiota of a unique donor
UC, Crohn’s, Pouchitis, PSC
DSS, IL10, T-cell transfer
Next steps
• Contributions of host/genotype?
• Diversity of effector strains
• Effector strains consistent across mouse colitis models?
Identifying human microbial effector strains
in humans!
Identifying effector strains
Hypothesis: members of human gut microbiota
modulate complex disease risk
Microbial inheritance in complex disease
1.
The “strain” is the key unit of measure
a.
b.
c.
acquired during the first three years of life.
stable inhabitants for decades.
decades to manifest clinical symptoms
Microbial inheritance in complex disease
1.
The “strain” is the key unit of measure
a.
b.
c.
acquired during the first three years of life.
stable inhabitants for decades.
decades to manifest clinical symptoms
Microbiome’s Future: optimal colonization at birth
H. pylori
cagA-
cagA+
Microbial inheritance in complex disease
1.
The “strain” is the key unit of measure
a.
b.
c.
acquired during the first three years of life.
stable inhabitants for decades.
decades to manifest clinical symptoms
Disease
Agent
Time to manifest clinical symptoms
Leprosy
Mycobacterium leprae
10-30 years; (13% of household contacts are
carriers; Araujo et.al., mem Inst Oswaldo Cruz 2012)
Whipple’s disease
Tropheryma whipplei
~10 years (many asymptomatic carriers)
Peptic ulcer
Helicobacter pylori
~10 years (few infected progress)
Gastric cancer
Helicobacter pylori
>50 years (few infected progress)
Hypothesized:
Crohn’s disease
Rheumatoid arthritis
Multiple sclerosis
Evidence of microbial role:
MZ < 40% concordant
GWAS loci involved in immune regulation, microbial recognition/defense
Antibiotics somewhat effective
Germ-free models have no or significantly less pathology than colonized
Treatment: slow the progressive pathology (like Pre-1982 peptic ulcer)
Microbial inheritance in complex disease:
a simple model
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•
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P(transmissioni) is the probability of transmission of strain i
P(accessi) is the probability of access to strain i
P(resistancei) is the resistance of the host to the colonization by strain i
Microbial inheritance in complex disease:
consequences
High
•
Family members share microbes!
Majority of family members share strains
Faith, et.al., Science 2013
Microbial diseases can “look” genetic
Microbial inheritance in complex disease:
consequences
High
•
•
*p<10-5; **p<10-14; ***p<10-41
Turnbaugh et al, Nature 2009
Schloss et al, Microbiome 2014
Low
Family members share microbes!
Sibling microbiotas should be more similar than
parents
Microbial inheritance in complex disease:
consequences
High
•
•
1.
2.
Low
Family members share microbes!
Sibling microbiotas should be more similar than
parents
• Increase in disease risk in siblings, especially
sequential
Gastric Cancer risk 2x higher in sibships of 7 individuals compared to 1-3 [Blaser et.al., PLoS Med 2007]
Crohn’s disease risk higher in consecutive births relative to non-consecutive births [Hugot et.al., Eur J
Hum Genet 2003]
Microbial inheritance in complex disease:
consequences
Low
•
•
•
•
Family members share microbes!
Sibling microbiotas should be more similar than
parents
• Increase in disease risk in siblings, especially
sequential
Very hard for cohabiting adults to pass microbes
• Disease takes years to manifest
• P(resistance) is HIGH
Unrelated individuals do not!
Microbial inheritance in complex disease
1.
gene is the key unit of measure
The “strain”
a.
b.
c.
acquired during the first three years of life.
stable inhabitants for decades.
decades to manifest clinical symptoms
We can use methods similar to human genetics!
Microbial inheritance in complex disease:
using the rules to identify effector strains
We can use methods similar to human genetics!
Case-control association: difficulty unrelated individuals do not share microbial strains
Crohn’s
No Crohn’s
Microbial inheritance in complex disease:
using the rules to identify effector strains
We can use methods similar to human genetics!
Familial association: difficulty powering study
Microbial inheritance in complex disease:
moving forwards
Need methods to microbe-type at the strain-level
Thanks to
Jeffrey Gordon, Philip Ahern, Andrew Goodman, Jean-Frederic Colombel
Faith laboratory
IBD Collaborators
Eduardo Contijoch
Sean Llewellyn
Ilaria Mogno
Cinkia Fermin
Zhihua Li
Ruby Ng
Eddie Vazquez
Jose Clemente
Sergio Lira
Miriam Merad
Judy Cho
Inga Peter
Ari Grinspan
Funding
NIH GM108505
SUCCESS
Immunology Institute
Institute for Genomics and Multiscale Biology
Icahn School of Medicine at
Mount Sinai