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Culture Documents
Angela E Douglas
bacteria
culturable
resynthesize
the association
(gnotobiotic flies)
1. Composition of microbiota
2. Axenic flies and gnotobiotic flies
3. Genetic & genomic resources
of Drosophila
4. Implications for animal welfare,
translatability, and challenges
Drosophila &
gut microbiota
Low diversity:
15-80 OTUs per fly
Acetobacteraceae
(Acetobacter, Gluconobacter)
axenic
Drosophila
bacteria
culturable
resynthesize
the association
(gnotobiotic flies)
Lactobacillales
(Lactobacillus, Vagococcus, Leuconostoc)
-proteobacteria
(Stenotrophomonas, Erwinia, Providencia)
79 lines of D. melanogaster
reared under uniform conditions
12-85 OTUs
Chaston et al. 2015
50
40
30
20
10
ct
iv
or
po ans
m
A. or
tro um
L. pic
al
pl
an is
ta
ru
m
L.
br
ev
is
O
th
er
fru
resynthesize
the association
(gnotobiotic flies)
% 16S reads
bacteria
culturable
L.
axenic
Drosophila
Ourstandardizedmicrobiota
A.
Drosophila &
gut microbiota
Drosophila &
gut microbiota
axenic
Drosophila
bacteria
culturable
resynthesize
the association
(gnotobiotic flies)
4,000 conventional
& 4,000 axenic flies
0.8
0.6
1.0
proportion pupated
Proportion surviving
to pupa
0.8
0.6
0.4
0.2
0.4
B vitamins
0.2
animal
0.0
no
ne
th a
ia ll
m
r
i
ni bo ine
co fl
a
pa tinic vin
nt a
ot ci
h d
py ena
rid te
ox
in
e
fo bio
lic tin
ac
id
0.4
150
p<0.001
125
100
75
p<0.001
50
25
0
15
10
p<0.005
hyperglycemia and
hyperlipidemia
in axenic flies
p<0.001
0
male
female
conventional flies
axenic flies
Drosophila line
Drosophila line
Correlation coefficient
Bacterial taxon
Acetobacteraceae
n.s.
Komagataeibacter
Lactobacillus OTU7
n.s.
50
10
er
1000
c
800
120
c
c
-1
-1
g triglyceride mg protein
(mean + s.e.)
bacterial species
O
th
L.
br
ev
is
uc
tiv
or
an
s
A.
po
m
or
um
A.
tro
pic
ali
s
L.
pla
nta
ru
m
600
b
400
200
a,b
a
co
nv
en
tio
5- na
s
l
A. pec
po ies
m
A. oru
tro m
pi
ca
l
L
. b is
L.
fru re
ct vis
i
L. vor
pl an
an s
ta
ru
m
ax
en
ic
100
80
a
a
60
40
20
0
co
nv
en
tio
5- na
s
l
A. pec
po ies
m
A. oru
tro m
pi
ca
l
L
. b is
L.
fru re
ct vis
i
L. vor
pl an
an s
ta
ru
m
ax
en
ic
20
g glucose mg protein
(mean + s.e.)
30
L.
fr
% 16S reads
40
bacteria
culturable
resynthesize
the association
(gnotobiotic flies)
1. Composition of microbiota
2. Axenic flies and gnotobiotic flies
3. Genetic & genomic resources
of Drosophila
4. Translatability and challenges
of the Drosophila system
ProximalpH7
pH4
Acetobacter
parent 1
RNAi
parent 2
1.0e+5
8.0e+4
6.0e+4
4.0e+4
gut region
distal
transition
neutral
0.0
acidic
2.0e+4
proximal
Acetobacter abundance
(mean + s.e.)
1.4e+5
325
300
g TAG
-1
mg dry wt
250
90
80
70
60
50
16
Response index
275
g glucose
-1
mg dry wt
g protein
-1
mg dry wt
14
12
10
-4
Drosophila line
AX GN
Averaged across all DGRP tested
AX= axenic; GN=gnotobiotic
1. Host genotype is a
major determinant of
elevated
in axenic microbiotadependent traits
flies
2. Apply GWAS to
identify genetic
determinants of
variation in
microbiotadependent traits
3. Validate candidate
genes by quantifying
phenotype of
mutants
Dobson et al., 2015
100
rugose
75
n.s.
50
25
0
50
bg
rg
bg
rg
Dscam3
n.s.
40
30
20
10
0
bg
dscam
gnotobiotic
flies
bg
dscam
axenic
flies
11.2
11.0
11.0
10.8
10.6
10.4
p=0.004
10.2
11.4
11.6
11.8
12.0
12.2
12.4
12.6
10.8
10.6
10.4
10.2
p>0.05
10.0
11.6
11.7
11.8
11.9
12.0
12.1
12.2
0.20
0.15
0.10
0.05
0.00
GN
AX
not differentially co-expressed
AX
GN
differentially co-expressed
transcriptional modules
Gain of function in microbiome-dependent transcriptional modules
Dobson et al. 2016
0.20
0.15
0.10
0.05
0.00
GN
AX
not differentially co-expressed
AX
GN
differentially co-expressed
Drosophila:
a superb model system
for microbiome science
Association is amenable to manipulation
Genetic and genomic tools
Large and complex experimental designs
1. Inconstant microbiota, with community composition
shaped by a mix of deterministic and stochastic factors
2. Nutritional benefit of microbiota that both provides
nutrients and competes for nutrients
3. Drosophila genetic determinants of microbiotadependent effects on energy storage are conserved
across animal kingdom to humans
4. Penetrance of deleterious mutations can be
increased by perturbation of the microbiota
5. Microbiota-dependent co-expression may promote
healthy phenotype
Drosophila:
Implications for welfare
of laboratory animals
https://upload.wikimedia.org/wikipedia/
commons/f/f2/Lab_mouse_mg_3263.jpg
Drosophila:
For enhanced quality
of microbiome science
Translatability
Drosophila to fast-track understanding of
fundamental principles of animal-microbial
associations
Mammalian models and human data to verify
relevance to humans
Challenges
Strengthen the framework and infrastructure for
integrating model systems with biomedical and
clinical science
Acknowledgements
Karen Adair
Alyssa Bost
Eduardo Bueno
John Chaston
Adam Dobson
Leanne Donahue
Sara Hermann
Jia Hsin Huang
Yuan Luo
John McMullen
Emma Ridley
Adam Wong
Cornell University
Andy Clark
Brian Lazzaro
Memorial Sloan Kettering
Cancer Center
Justin Cross
University of Glasgow, UK
Julian Dow
Gayle Overend