Animal models for Microbiome Research:

The Role of Host Genetics

Jake Lusis
Departments of Microbiology, Medicine and
Human Genetics
University of California, Los Angeles
jlusis@mednet.ucla.edu

Outlineoftalk
Estimatingtheimportanceofhostgeneticsingut
microbiotacomposition
Usinghostgeneticvariationtostudyhostgutmicrobiome
interactions.

Why do we differ in our gut microbiota?

Gutmicrobiotain200men5070yearsofagefromKuopio,Finland

Why do we differ in our gut microbiota?

Gutmicrobiotain200men5070yearsofagefromKuopio,Finland

1.Maternalseeding
2.Diet
3.Genetics
4.Age
5.Antibiotics
6.Disease

TheHybridMouseDiversityPanel(HMDP)
About100commerciallyavailable,
highlydiverseinbredstrainsofmice
Sequencedordenselygenotyped
Sufficientlypoweredforhigh
resolutionassociationmapping
Usefulforgenebyenvironment
studies

Bennett et al. 2010

Gutmicrobiotain200men5070yearsofagefromKuopio,Finland

HybridMouseDiversityPanel:113mousestrains(males)

Membersofaninbredstraintendtosharemicrobiomecomposition

Strains
(Diet)

BUB
(Chow)

BXA14
(Chow)

BXD15
(HF)

NON
SEA SWR
MA
(HF) (chow) (chow) (HF)

Heritability: Thefractionofvarianceofatraitthatis
explainedbygenetics.

Heritability: Thefractionofvarianceofatraitthatis
explainedbygenetics.
r

Phenotype similarity

Phenotype similarity

Genetic similarity
Xby descent)
(identity

Genetic similarity

Correlation coefficient r

Phenotype similarity

Phenotype similarity

Heritability: Thefractionofvarianceofatraitthatis
explainedbygenetics.

Genetic similarity
(identity by descent)

Heritability h2

Genetic similarity
(identity by descent)

TheinbredstrainsoftheHMDParerelatedtoone
another,havingbeenderivedfromapoolofpetmice
about100yearsago.

Genealogy of
inbred strains

Heritabilityofgutmicrobiotabasedonmousediversitypanel
Phyla

Avg.Frequency(%)

Heritability(%)

Actinobacteria

0.49

60

Bacteroidetes

43

62

Firmicutes

48

67

Proteobacteria

0.43

32

Tenericutes

0.73

40

Verrucomicrobia

7.3

56

Heritabilityestimatedusingmicrobiotacompositionandgenotypesof110
inbredstrainsofmice,employingalinearmixedmodelassumingadditive
geneticeffects.

Org et al. Genome Res (2015)

(2016)

Hostdependentregulationofgutmicrobiota

Hooper and Macpherson Nat Rev Immunol, 2010

Sex hormones:
One way the host controls gut microbiota
Gonadectomy (GDX) experiments in strain C57BL/6J

Org et al.Gut Microbes (2016)

Genebydietinteractionsofgutmicrobiota
Chow

HighFat/
HighSucrose

HighFat/
Cholesterol

HMDPstrainsin
sameorderinall
plots

Outlineoftalk
Estimatingtheimportanceofhostgeneticsingut
microbiotacomposition
Usinghostgeneticvariationtostudyhostgutmicrobe
interactions.

Genomewideassociationstudy:
Locicontrollinggutmicrobiotainmice
Lrrk2

Nr2f2

Tle4

Lrrc19

Org et al. Genome Res (2015)

Nat Genetics Oct 2016

60

0
BxH20/KccJ
AXB19b/PgnJ
BXD68/RwwJ
CXB12/HiAJ
C3H/HeJ
BXD50/RwwJ
CXB13/HiAJ
CXB6/ByJ
SWR/J
BXD87/RwwJ
CxB3/ByJ
BXD55/RwwJ
BxA4/PgnJ
BXD45/RwwJ
AXB19/PgnJ
BXD49/RwwJ
BXA24/PgnJ
BxD1/TyJ
BXD84/RwwJ
BXD86/RwwJ
BxD12/TyJ
BxD38/TyJ
CXB11/HiAJ
BXD48/RwwJ
BXD13/TyJ
BXD75/RwwJ
BxA16/PgnJ
AxB19a/PgnJ
BUB/BnJ
MA/MyJ
BXD56/RwwJ
DBA/2J
BXD85/RwwJ
BxD5/TyJ
CxB7/ByJ
AxB6/PgnJ
BXD61/RwwJ
BxD19/TyJ
C57BLKS/J
BXH19/TyJ
BXD73/RwwJ
BXH8/TyJ
SM/J
BXD20/TyJ
NOD/ShiLtJ
CXB4/ByJ
BTBR T<+> tf/J
BXD40/TyJ
RIIIS/J
C57BL/6J
BXD64/RwwJ
BXD62/RwwJ
BxA11/PgnJ
BXD79/RwwJ
LP/J
BXD27/TyJ
BXH6/TyJ
BALB/cJ
BxA7/PgnJ
BXD71/RwwJ
BXD14/TyJ
BXD21/TyJ
BXA14/PgnJ
A/J
BXD43/RwwJ
BXD74/RwwJ
FVB/NJ
BxH22/KccJ
AxB15/PgnJ
NON/SHiLtJ
BXD66/RwwJ
SEA/GnJ
AxB4/PgnJ
BXD70/RwwJ
CBA/J
BXD51/RwwJ
BXD6/TyJ
BXD32/TyJ
AXB10/PgnJ
PL/J
NZW/LacJ
BxH9/TyJ
BxA8/PgnJ
BXD24/TyJ-Cep290<rd16>/J
BXD69/RwwJ
BxD31/TyJ
BXA2/PgnJ
BXD34/TyJ
BXD44/RwwJ
BXD9/TyJ
BXA1/PgnJ
BXD60/RwwJ
KK/HlJ

Body Fat Percentage

Trait-microbe associations: Fat gain in response to hi fat diet

Female
Chow diet
High fat/High Sucrose diet

50

40

30

20

10

6-8 mice /strain

6-8 mice/strain

Parks et al. Cell Metab (2013)

Microbiotaassociationswithmetabolictraitsinmice

Taxa

Trait

P value

Akkermansia
muciniphila

Insulin
HOMA-IR
Body Fat % - 8 wks
Triglycerides
Food Intake
Insulin
HOMA-IR
Glucose
Body Fat % - 8 wks
Insulin
HOMA-IR
Body Fat % - 8 wks

4.57E-06
1.51E-04
9.02E-04
8.49E-03
1.45E-04
8.16E-05
2.20E-02
4.27E-03
1.12E-06

Oscillospira spp.
Ruminococcus
gnavus

Roseburia spp.

4.68E-06
4.09E-04
1.04E-06

Akkermansia mucinophila gavagereducesfatgain

Obesity prone AXB19 mice were fed a high fat diet and treated
with either live or heat-killed Akkermansia mucinophila for 5
weeks
Body fat increase (g)

Heat-killed Akk

5
4

killed_Akk

Females

Akk

3
2
1
0

beforediet
diet 2.5
wks
a er 4 wks
er HF/
Start
2.5
wks
4 awks
HS
HF/HS
Akk m.

AXB19 males

Akk
Body fat increase (g)

AXB19 females

8
7
6
5
4
3
2
1
0

Heat-killed Akk

Akk

before diet
diet 2.5
wkswks
a er 4 wks
er HF/
Start
2.5
4 awks
HF/HS
HS
Akk m.

Akk
killed_Akk
Males

Akkermansia mucinophila affectsatherosclerosistraits

Plasma lipids

Body fat

80

100

20
0
H
FA
kk

50

H
F

10

40

H
F

20

H
F
-A
kk

TC mg/dl

150

60

TG mg/dl

30

H
F

200

H
F
-A
kk

Body Fat %

40

Glucose metabolism

***

***
20

1000

H
F
-A
kk

0
H
F

0
H
F
-A
kk

2000

40

H
F
-A
kk

100

3000

H
F

200

60

HOMA-IR

300

Insulin pg/ml

4000

H
F

Glucose mg/dl

400

Org et al. Genome Res (2015)

Nature Med. Oct 2016

Summary
In a controlled environment host genetics contributes
importantly to gut microbiota.
The relationship between host genetics, diet and the gut
microbiome is complex.
Host genetics can be used as a tool to study host-microbiota
interactions.

Welfare:
Oversight
Training
Respect

Challenges to work with mice:

Financial: Costs of purchase and maintenance of mice have
steadily increased.
Regulatory: Increased demands on laboratory to meet
regulatory requirements with no added support (unfunded
mandates).
Scientific: Sharing mice is increasingly difficult and expensive;
technology is rapidly changing (e.g. CRISPR).

Challenge: Embrace diversity as an opportunity to help unravel

the incredible complexity on host-microbe interactions

Challenge: Embrace diversity as an opportunity to help unravel

the incredible complexity on host-microbe interactions

SystemsGenetics:Apopulationbasedapproach
Disease

Thanks to:

Elin Org

Margarete Mehrabian
Brian Parks
Jennifer Lang
Simon Hui
Brian Bennett
Stanley Hazen (Cleve. Clinic)
Rob Gunsalus (UCLA)
Eleazar Eskin (UCLA)
Markku Laakso (Finland)
Rob Knight (UCSD)
Federico Rey (Wisconsin)

Mappinggenesforgutmicrobiotataxa:Akk.mucinophila
rs33129247

Igf1r
68

Nr2f2
69

70

Positiononchr7(Mb)

71

Mappinggenesforgutmicrobiotataxa:Akk.mucinophila
rs33129247

Igf1r
68

Nr2f2
69

70

71

Positiononchr7(Mb)

Org et al. Genome Res (2015)

Experimentinprogress
I. Establishment

II. Mixing

(3 wks)

(8 wks)

III. Recovery

10
C57BL/6J

C57BL/6J

(13 wks)

20
C57BL/6J

C57BL/6J-MIX

MIX

BTBRT+tf/J-MIX

BTBRT+tf/J

BTBRT+tf/J

BTBRT+tf/J

(28 wks)

Challenges to work with mice

1. Financial: Costs of purchase and maintenance of
mice have steadily increased.
2. Regulatory: Increased demands on laboratory to
meet regulatory requirements with no added support
(unfunded mandates).
3. Scientific: Sharing mice is increasingly difficult and
expensive; technology is rapidly changing (e.g.
CRISPR).

Animal welfare

OfficeofAnimalResearchOversight
WorkswiththeUCLAIACUC
ARC(ChancellorsAnimalResearchCommittee

Assurecompliancewith:
AAALACaccreditation(since1976)
PublicHealthServicePolicies
OfficeofLaboratoryAnimalWelfare(OLAW)
USDepartmentofAgriculture
AnimalWelfareAct