evaluating human gut microbiota and microbe-host phenotype relationships jeremiah faith icahn school...
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Evaluating human gut microbiota and microbe-host phenotype relationships
Jeremiah FaithIcahn 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
• Crohn’s disease • Ulcerative colitis• Pouchitis • Necrotizing enterocolitis • Coeliac disease • Diarrhea (C. diff)• Colorectal cancer
What must be done1. Verify causation2. Identify microbial effector strains3. Modify effector strains to improve health
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
Screening “humanized” mice
Which bacteria are causing this?!?
Faith, et.al., Sci Transl Med 2014
Diverse donors
Gnotobiotic miceHumanized with the
microbiota of a unique donor
%Fo
xP3+
am
ong
CD4+
Tce
lls
Donor1
Donor2
Donor3
Donor4
Donor5
Germ-fr
ee
High-throughput anaerobic bacterial isolation
Anaerobic isolation Protein extraction Identification(MALDI-TOF)
Each well contains a unique bacterial strain
Donor Goodman, et.al., PNAS 2011Faith, et.al., Science 2013
Large scale bacterial isolation
Each well contains a unique bacterial strain
(17 total microbes) Donor
Fractionate community
Gnotobiotic mice
Phenotype screen
Phenotype response
Community size
% T
regs
Serin
e
Adip
osity
Identifying effector strains%
FoxP
3+ a
mon
g CD
4+ T
cel
ls
Which bacteria are causing this?!?
%Fo
xP3+
am
ong
CD4+
Tce
lls
Donor1
Donor2
Donor3
Donor4
Donor5
Germ-fr
ee
Faith, et.al, Sci Transl Med 2014
Next steps for understanding host/microbe interactions in IBD
Diverse donors
Gnotobiotic miceHumanized 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 effector strains
Hypothesis: members of human gut microbiota modulate complex disease risk
Microbial inheritance in complex disease1. The “strain” is the key unit of measure
a. acquired during the first three years of life.b. stable inhabitants for decades.c. decades to manifest clinical symptoms
Microbial inheritance in complex disease
Microbiome’s Future: optimal colonization at birth
H. pylori
cagA- cagA+
1. The “strain” is the key unit of measurea. acquired during the first three years of life.b. stable inhabitants for decades.c. decades to manifest clinical symptoms
Microbial inheritance in complex disease
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)
1. The “strain” is the key unit of measurea. acquired during the first three years of life.b. stable inhabitants for decades.c. decades to manifest clinical symptoms
Evidence of microbial role:MZ < 40% concordantGWAS loci involved in immune regulation, microbial recognition/defenseAntibiotics somewhat effectiveGerm-free models have no or significantly less pathology than colonized
Hypothesized:Crohn’s diseaseRheumatoid arthritisMultiple sclerosis
Treatment: slow the progressive pathology (like Pre-1982 peptic ulcer)
Microbial inheritance in complex disease: a simple model
• 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
• Family members share microbes!
High
Microbial diseases can “look” genetic
Majority of family members share strains
Faith, et.al., Science 2013
Microbial inheritance in complex disease: consequences
• Family members share microbes!• Sibling microbiotas should be more similar than
parents
Turnbaugh et al, Nature 2009
*p<10-5; **p<10-14; ***p<10-41
Schloss et al, Microbiome 2014
LowHigh
Microbial inheritance in complex disease: consequences
• Family members share microbes!• Sibling microbiotas should be more similar than
parents• Increase in disease risk in siblings, especially
sequential
1. Gastric Cancer risk 2x higher in sibships of 7 individuals compared to 1-3 [Blaser et.al., PLoS Med 2007] 2. Crohn’s disease risk higher in consecutive births relative to non-consecutive births [Hugot et.al., Eur J
Hum Genet 2003]
LowHigh
Microbial inheritance in complex disease: consequences
• 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!
Low
Microbial inheritance in complex disease1. The “strain” is the key unit of measure
a. acquired during the first three years of life.b. stable inhabitants for decades.c. decades to manifest clinical symptoms
We can use methods similar to human genetics!
gene
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
Faith laboratory
Eduardo ContijochSean LlewellynIlaria Mogno Cinkia FerminZhihua LiRuby NgEddie Vazquez
Immunology InstituteInstitute for Genomics and Multiscale BiologyIcahn School of Medicine atMount Sinai
Jeffrey Gordon, Philip Ahern, Andrew Goodman, Jean-Frederic Colombel
IBD Collaborators
Jose ClementeSergio LiraMiriam MeradJudy ChoInga PeterAri Grinspan
Funding
NIH GM108505SUCCESS