Modeling our microbial selves:

insights from the zebrafish intestine

Karen Guillemin
META Center for Systems Biology
University of Oregon

Each of us is a unique interacting system of

host and microbial cells

Gnotobiotic zebrafish: a model vertebrate

for studying host-microbe systems

1. Large populations in defined environments

2. Optically transparent
3. Accessible early development

Gnotobiotic zebrafish: challenges

1. Rearing adult germ-free zebrafish

Nutritional requirements poorly understood

Challenges of maintaining water quality

2. Standardization of conventionalized zebrafish

No defined inoculum such as a Shaedlers flora

Pathogen screening (for SPF) is not standard

A host-microbe system of scalable complexity

conventionally
reared

mono-associated

germ-free

A host-microbe system of scalable complexity

conventionally
reared

mono-associated

germ-free

1. Gnotobiotic zebrafish:
large populations in defined environments

Does microbiota dispersal modulate the

effects of the innate immune system?
Immune competent

Immune deficient

WT

myd88Adam Burns

Experimental manipulation of inter-host

dispersal
Immune competent
WT

Immune deficient
myd88-

Cohoused

Solitary

No inter-host
dispersal

Segregated

Mixed

Inter-host dispersal
only within genotypes

Inter-host
dispersal between
genotypes

Burns et al., in preparation

Strong effect of host genotype for solitary

individuals
PerMANOVA Results

WT
myd88-

PseudoF
Solitary:
Genotype

Mixed:
Genotype

R2

P-value

34.108 0.577 < 0.001

2.790 0.054

0.001

Weak effect of host genotype for mixedcohoused individuals

PerMANOVA Results

WT
myd88-

PseudoF
Solitary:
Genotype

Mixed:
Genotype

R2

P-value

34.108 0.577 < 0.001

2.790 0.054

0.001

Cohousing homogenizes genotypes,

regardless of whether genotypes are mixed
PerMANOVA Results

WT
myd88-

Pseudo
-F
Solitary:
Genotype

R2

P-value

34.108 0.577 < 0.001

Segregated:
Genotype

3.391 0.151

0.010

Mixed:
Genotype

2.790 0.054

0.001

Cohoused associated taxa are predicted to be enriched

for gene pathways likely involved in dispersal

Co-housing homogenizes microbiomes and

selects for transmissible members

A host-microbe system of scalable complexity

conventionally
reared

mono-associated

germ-free

2. Gnotobiotic zebrafish:
optically transparent

Aeromonas growth over 14 hrs

in a larval zebrafish gut

Jemielita et al. mBio 2014

Host Gut Motility Promotes Competitive Exclusion

within a Model Intestinal Microbiota

Travis Wiles

Matthew Jemielita

Vibrio and Aeromonas inhabit the gut differently

Aeromonas mono-association

Clusters, little motility

50 microns
Anterior

Posterior
Vibrio mono-association

No clusters, highly motile

50 microns

Vibrio can displace Aeromonas

Wiles, Jemielita et al., PLoS Bio 2016

Modeling from both imaging and

microbiology
time series data

plating
data

(detailed dynamics)

(good statistics)

validate

model:
logistic growth +
Poisson collapses

Reducing gut motility (in ret mutant lacking ENS)

alters bacterial competition

Reducing gut motility (in ret mutant lacking ENS)

alters bacterial competition

Reducing gut motility (in ret mutant lacking ENS)

alters bacterial competition

host environment (peristalsis) contributes to bacterial competition

A host-microbe system of scalable complexity

conventionally
reared

mono-associated

germ-free

3. Gnotobiotic zebrafish:
Accessible early development

insulin:gfp

Zebrafish pancreas and microbiota development

Jennifer Hampton Hill

0 days post fertilization (dpf)

2 dpf

3 dpf

4 dpf

gut tube
patent
mouth open, initiation of
intestinal colonization

larvae hatch from

sterile chorion

5 dpf

robust intestinal
microbiota

6 dpf

Zebrafish pancreas and microbiota development

cell population expansion

3 dpf: fully functional
pancreas, with newly
differentiated cells

0 days post fertilization (dpf)

2 dpf

3 dpf

4 dpf

gut tube
patent
mouth open, initiation of
intestinal colonization

larvae hatch from

sterile chorion

5 dpf

robust intestinal
microbiota

6 dpf

Microbiota promote pancreatic beta cell mass

conventional

germ-free

beta cells (insulin::gfp)

Hampton Hill et al. eLIFE, 2016

Microbiota promote pancreatic beta cell mass

Monoassociation with specific microbiota

members restores beta cell expansion

Aeromonas secretes a protein that

promotes beta cell expansion

Identification of Beta cell Expansion Factor (BefA)

mass spec analysis
163 proteins
genomes +/- beta cell expansion
1 predicted protein (10165)

A specific bacterial protein promotes beta cell expansion

BefA homologues in human-associated bacteria

BefA homologues in human-associated bacteria

BefA homologues from human-associated

bacteria induce beta cell expansion

Human beta cells proliferate early in life,

concurrently with microbiota establishment

Gregg et al. J Clin Endocrinol Metab 2012

Gnotobiotic zebrafish

1. Large populations in defined environments

microbiota transmission
2. Optically transparent
microbiota dynamics
3. Accessible early development
microbiota activities

META Center for Systems Biology

Guillemin lab
Allison Banse
Matthew Barber
Maria Banuelo
Brendan Bohannan
Adam Burns
William Cresko
Kristi Hamilton
Judith Eisen
Jennifer Hampton
Jessica Green
Diane Hernandez
Eric Johnson
Melissa Hinman
David Levin
Tiffani Jones
Raghuveer Parthasarathy
Ellie Melancon
Matthew Jemielita
Arden Perkins
Annie Powell
Cathy Robinson
Patrick Phillips
Annah Rolig
John Postlethwait
Michelle Sconce
Tristan Ursell
Sophie Sichel
Rose Sockol
Collaborators
Keaton Stagaman
Eric Franzosa
Emily Goers Sweeney
Curtis Huttenhower
Elena Wall
Funding
Travis Wiles
NIH/NIDDK/NCI/NIGMS
META Center P50 GM098911