IAI Accepted Manuscript Posted Online 2 March 2015 Infect. Immun. doi:10.1128/IAI.02943-14 Copyright © 2015, American Society for Microbiology. All Rights Reserved.
1
Escherichia coli EDL933 Requires Gluconeogenic Nutrients to Successfully Colonize the
2
Intestines of Streptomycin-Treated Mice Pre-colonized with E. coli Nissle 1917
3 4
Silvia A. C. Schinner1, Matthew E. Mokszycki1, Jimmy Adediran1, Mary Leatham Jensen1,
5
Tyrrell Conway2, and Paul S. Cohen1*
6 7 8 9 10
Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 028811 Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 730192
11 12 13 14
Running Title: Gluconeogenesis and Intestinal Colonization
15 16
17
Corresponding Author
18
Phone: 401-874-5920
19
Fax:
20
e-mail: [email protected]
401-874-9750
1
21 22
Abstract E. coli MG1655, a K-12 strain, uses glycolytic nutrients exclusively to colonize the
23
streptomycin-treated mouse intestine when it is the only E. coli strain present or when confronted
24
with E. coli EDL933, an O157:H7 strain. In contrast, E. coli EDL933 uses glycolytic nutrients
25
exclusively when it is the only E. coli strain in the intestine, but switches in part to
26
gluconeogenic nutrients to colonize mice pre-colonized with E. coli MG1655 (Miranda et al
27
Infect. Immun. 72:1666-1676, 2004). Recently, Njoroge et al (mBio 3:e00280–12, 2012)
28
reported that E. coli 86-24, an O157:H7 strain, activates expression of virulence genes under
29
gluconeogenic conditions, suggesting that colonization of the intestine with a probiotic E. coli
30
strain that out-competes O157:H7 strains for gluconeogenic nutrients could render them non-
31
pathogenic. Here we report that E. coli Nissle 1917, a probiotic strain, uses both glycolytic and
32
gluconeogenic nutrients to colonize the mouse intestine between 1 and 5 days post-feeding,
33
appears to stop using gluconeogenic nutrients thereafter in a large long-term colonization niche,
34
but continues to use them in a smaller niche to compete with invading E. coli EDL933.
35
Evidence is also presented suggesting that invading E. coli EDL933 uses both glycolytic and
36
gluconeogenic nutrients and requires the ability to perform gluconeogenesis to colonize mice
37
pre-colonized with E. coli Nissle 1917. The data presented here therefore rule out the possibility
38
that E. coli Nissle 1917 can starve the O157:H7 strain E. coli EDL933 for gluconeogenic
39
nutrients despite using them to compete with it in the mouse intestine.
40 41 42 2
43 44
Introduction While much attention has been paid to the role of specific virulence factors in bacterial
45
pathogenesis, until recently little attention has been paid to the roles of specific metabolic
46
pathways in the ability of bacterial pathogens to initiate the pathogenic process. Yet clearly, if a
47
bacterial pathogen is unable to initiate pathogenesis because essential nutrients for its growth are
48
unavailable in the host, it will be unable to establish itself and cause disease. Therefore, it is
49
important to determine whether pathogens require glycolytic nutrients, gluconeogenic nutrients,
50
or both for success in invading and subsequently colonizing the host. Indeed, recent studies
51
suggest that some pathogens use glycolytic nutrients, some use gluconeogenic nutrients and
52
some use both to adapt to diverse host habitats (1-7).
53
We are interested in the nutritional basis of E. coli colonization of the intestine and whether
54
pre-colonization by E. coli commensal strains can be used to prevent invading E. coli intestinal
55
pathogens from colonizing. Commensal E. coli strains colonize the human intestine in the
56
presence of a dense and diverse intestinal microbiota comprised of at least 500 cultivable species
57
and 1013 to 1014 total bacteria (8). Unfortunately, E. coli colonization cannot be studied
58
experimentally in conventional animals due to colonization resistance, which results when all
59
niches are filled by the microbiota (9). Such experiments require an animal model with open
60
niches for E. coli to colonize the intestine in relatively high numbers, but to be authentic the
61
model intestine must also have a dense and diverse anaerobic community that matches as closely
62
as possible the native microbiota of the conventional animal. The streptomycin-treated mouse
63
model is used routinely for this purpose since streptomycin-treated mice fulfill these criteria (10,
64
11). Using this model, we have shown that for E. coli to colonize it must obtain nutrients in the
65
mucus layer, which overlays the epithelium (10, 11), that it resides in the mucus layer as a 3
66
member of mixed biofilms (12, 13), and that each E. coli strain displays a unique nutritional
67
program in the intestine (14).
68
E. coli strains can utilize both glycolytic and gluconeogenic nutrients for growth in vitro and
69
we reported previously that both E. coli MG1655, a commensal strain, and E. coli EDL933, an
70
O157:H7 pathogenic strain, use glycolytic, but not gluconeogenic nutrients to colonize the
71
streptomycin-treated mouse intestine when each is the only E. coli strain fed to mice (15).
72
However, we also reported that in the presence of E. coli MG1655, E. coli EDL933 switches, at
73
least in part, to gluconeogenesis in order to maintain itself in the intestine, while E. coli MG1655
74
continues to use glycolytic nutrients exclusively (15). These findings are of extreme interest in
75
view of recent reports showing that E. coli 86-24, also an O157:H7 strain, activates expression of
76
virulence genes under gluconeogenic conditions (16, 17), because this suggests the possibility
77
that pre-colonization of the intestine with a probiotic E. coli strain that starves E. coli O157:H7
78
strains of gluconeogenic nutrients might render them non-pathogenic.
79
E. coli Nissle 1917 is a commensal strain that has been used as a probiotic agent to treat
80
gastrointestinal infections in humans since the early 1920’s (18). Several features of E. coli
81
Nissle 1917 have been proposed to be responsible for its probiotic nature including its ability to
82
express two microcins (19), the absence of known protein toxins, its semi-rough
83
lipopolysaccharide and hence its serum sensitivity (20, 21), and the presence of six iron uptake
84
systems (22). More recently, it has been shown that E. coli Nissle 1917 inhibits adherence of E.
85
coli EDL933 to human epithelial cells in vitro and simultaneously inhibits its growth and Shiga
86
toxin 2 (Stx2) production (23). It has also been shown that in the streptomycin-treated mouse
87
intestine, E. coli Nissle 1917 is better than a number of commensal E. coli strains at limiting E.
88
coli EDL933 growth (12,13). In this study, we examine whether E. coli Nissle 1917 uses both
4
89
glycolytic and gluconeogenic nutrients to colonize the streptomycin-treated mouse intestine and
90
whether E. coli EDL933 switches to gluconeogenic nutrients to maintain itself in the intestine in
91
the presence of E. coli Nissle 1917.
92
Materials and Methods
93
Bacterial strains. Bacterial strains used in this study are listed in Table 1. The original E.
94
coli K-12 strain was obtained from a stool sample from a convalescing diphtheria patient in Palo
95
Alto, CA, in 1922 (24). The sequenced E. coli MG1655 strain (CGSC 7740) was derived from
96
the original K-12 strain, having only been cured of the temperate bacteriophage lambda and the F
97
plasmid by means of UV light and acridine orange treatment (24). It has an IS1 element in
98
the flhDC promoter (25). E. coli EDL933 is the prototype strain of EHEC strain O157:H7
99
(26). E. coli Nissle 1917 was originally isolated during World War I from a soldier who escaped
100
a severe outbreak of diarrhea (18). It has a beneficial effect on several types of intestinal
101
disorders, is well tolerated by humans, and has been marketed as a probiotic remedy against
102
intestinal disorders in several European countries since the 1920s (18).
103
Media and growth conditions. LB broth Lennox (Difco Laboratories, Detroit, MI), LB agar
104
Lennox (Difco), and MacConkey agar (Difco) were used for routine cultivation. SOC medium
105
was prepared as described by Datsenko and Wanner (27). For testing carbon and energy source
106
utilization in the Biolog, M9 minimal medium (28) was modified by addition of 120 mM NaCl
107
to more closely approximate the sodium chloride concentration in the intestine (29).
108
Mutant construction. The allelic exchange method described by Datsenko and Wanner (27)
109
was used to construct E. coli Nissle 1917 StrR ΔpckA ΔppsA::cat (Table 1). The method allows
110
the sequential construction of double deletion mutants by use of a removable chloramphenicol
5
111
cassette (27). Primers used to construct the deletion mutants were designed according to the E.
112
coli CFT073 genome sequence (30), which is closely related to the E. coli Nissle 1917 genome
113
sequence (31). Deletions of 1327 bp and 2367 bp were made in the pckA gene and the ppsA gene,
114
respectively. The pckA deletion primers used to make E. coli Nissle 1917 StrR ΔpckA::cat
115
(uppercase letters, E. coli Nissle 1917 DNA; lowercase letters, chloramphenicol resistance
116
cassette DNA) were: primer 1, 5-AGACTTTACTATTCAGGCAATACATATTGGC
117
TAAGGAGCAGTGgtgtaggctggagctgcttcg-3; primer 2, 5-GCGGGTATCTTTAATC
118
GAGATACGTTTGCCAGTGCCGTTCCA gcatatgaatatcctccttag-3. The ppsA deletion primers
119
used to make E. coli Nissle 1917 StrR ΔpckA ΔppsA::cat (uppercase letters, E. coli Nissle 1917
120
DNA; lowercase letters, chloramphenicol resistance cassette DNA) were: primer 1, 5-GCGACT
121
AAACGCCGCCGGGGATTTATTT TATTTCTTCAGTgtgtaggctggagctgcttcg-3; primer 2, 5-
122
AATGTGTTTCTCAAAC CGTTCATTTATCACAAAAGGATTGTTCgcatatgaatatcctccttag-3.
123
Gene knockouts were confirmed by PCR and sequencing using the following upstream and
124
downstream primers: ΔpckA forward, 5'-GTTAATTATCGCATCCGGGCA-3'; ΔpckA reverse,
125
5'-GTTGTCGATAAACAG TTTCGCCAG-3'; ΔppsA forward, 5'-CCTGTGTGG
126
TTGCAATGTCCG-3'; ΔppsA reverse, 5'-TTGTTCTTCCCGTGATGCAGAC-3'. DNA
127
sequencing was done at the URI Genomics and Sequencing Center, University of Rhode Island,
128
Kingston, RI, using an Applied Biosystems 3130xl genetic analyzer (Applied Biosystems, Foster
129
City, CA). A BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems) was used for
130
the sequencing reactions.
131
Biolog phenotypic analysis. For confirmation that E. coli Nissle 1917 StrR ΔpckA
132
ΔppsA::cat was able to grow on glycolytic substrates, but unable to grow on gluconeogenic
133
substrates, it and its wild type parent were grown over night in M9 minimal medium containing 6
134
0.4 % glycerol (v/v) and 0.2 M NaCl at 37oC. Cultures were washed twice in M9 minimal
135
medium containing 0.2 M NaCl without any carbon source and were then diluted to an OD600 of
136
0.06 in 5 ml of M9 minimal medium without any carbon source. Each culture was diluted an
137
additional 10-fold and 100 μl/well was added to a microtiter 96-well Biolog GN2 MicroPlate.
138
Plates were incubated at 37 °C for 48 h in the OmniLog system. Tetrazolium violet dye reduction
139
was measured at 15 min intervals and plotted vs. time, resulting in a kinetic curve. E. coli Nissle
140
1917 and E. coli Nissle 1917 ΔpckA ΔppsA each displayed the highest final level of tetrazolium
141
reduction when using either gluconate or glycerol as sole carbon source. Final levels of
142
tetrazolium reduction on all other carbon sources were normalized to that on glycerol.
143
Mouse colonization experiments. The specifics of the streptomycin-treated mouse model used
144
to compare the large intestine-colonizing abilities of E. coli strains in mice have been described
145
previously (12). Briefly, sets of three male CD-1 mice (5 to 8 weeks old) were given drinking
146
water containing streptomycin sulfate (5 g/liter) for 24 h to eliminate resident facultative bacteria
147
(32). Following 18 h of starvation for food and water, the mice were fed 1 ml of 20% (wt/vol)
148
sucrose containing 105 CFU of LB broth Lennox-grown E. coli strains, as described in Results.
149
After ingestion of the bacterial suspension, both the food (Teklad mouse and rat diet; Harlan
150
Laboratories, Madison, WI) and streptomycin-water were returned to the mice, and 1 g of feces
151
was collected after 5 h and 24 h and on odd-numbered days, at the indicated times. Mice were
152
housed individually in cages without bedding and were placed in clean cages at 24-h intervals.
153
Individual fecal pellets were therefore no older than 24 h. Each fecal sample (1 g) was
154
homogenized in 10 ml of 1% Bacto tryptone (Difco), diluted in the same medium, and plated on
155
MacConkey agar plates with appropriate antibiotics. When appropriate, 1 ml of a fecal
156
homogenate (sampled after the large debris had settled) was centrifuged at 12,000 × g,
7
157
resuspended in 100 μl of 1% Bacto tryptone, and plated on a MacConkey agar plate with
158
appropriate antibiotics. This procedure increased the sensitivity of the assay from 102 CFU/gram
159
feces to 10 CFU/gram feces. To distinguish the various E. coli strains in feces, dilutions were
160
plated on lactose MacConkey agar containing streptomycin sulfate (100 μg/ml), streptomycin
161
sulfate (100 μg/ml) and nalidixic acid (50 μg/ml), streptomycin sulfate (100 μg/ml) and
162
chloramphenicol (30 μg/ml), or streptomycin sulfate (100 μg/ml) and rifampin (50 μg/ml).
163
Streptomycin sulfate, chloramphenicol, and nalidixic acid were purchased from Sigma-Aldrich
164
(St. Louis, MO). All plates were incubated for 18 to 24 h at 37°C prior to counting. Each
165
colonization experiment was performed at least twice, with essentially identical results. Pooled
166
data from at least two independent experiments (for a total of six mice) are presented in the
167
figures. All animal protocols were approved by the University Committee on Use and Care of
168
Animals at the University of Rhode Island.
169
Fluorescence in situ hybridization. FISH was performed as described previously (12, 33).
170
Briefly, the cecum of a mouse designated for FISH was cut into 1-2 cm pieces, suspended in
171
Tissue-Tek O.C.T compound (Sakura, Torrance, CA) and snap frozen in 2-methylbutane
172
suspended in liquid nitrogen. Pieces were then stored at -80oC until ready for sectioning. For
173
sectioning, the UltraPro 5000 Cryostat (Vibratome, St. Louis, MO) was used to cut 10μm
174
sections, which were adhered to poly-L-lysine treated slides for visualization. Slides were fixed
175
in 4% paraformaldehyde for 1 hour at room temperature, followed by a wash in phosphate
176
buffered saline for 10 min. Slides were allowed to air dry overnight prior to hybridization.
177
Fluorescent probes (IDT DNA, Coralville, IA) were diluted in hybridization solution (0.1 M
178
Tris-HCl buffer pH 7.2, 0.9 M NaCl, and 0.1% SDS). The E.coli 23S rRNA specific Cy-3
179
probe (5’-/5Cy3/ CAC CGT AGT GCC TCG TCA TCA-3’) (red) and the Eubacteria 23S rRNA
8
180
specific FitC probe (5’-GCT GCC TCC CGT AGG AGT /36-FAM/-3’) (green) were used at
181
concentrations of 5 ηg/µl and 25 ηg/µl, respectively. Subsequently, 10 ul of diluted probes in
182
hybridization solution was pipetted to each slide. Each slide was then covered with a HybriSlip
183
hybridization cover (Life Technologies, Carlsbad, CA) and allowed to incubate in the dark for 2
184
hours at 50oC. The slides were then placed in a wash buffer (0.1 M Tris-HCl buffer pH 7.2, and
185
0.9 M NaCl), and allowed to soak for 20 min at 50oC. Slides were then rinsed with distilled
186
water and air dried overnight. Sections were viewed by confocal microscopy. Prior to viewing,
187
sections on the poly-L-lysine treated slides were treated with Vectashield mounting medium
188
(Vector Laboratories, Burlingame, CA), an antibleaching agent which helps prolong
189
fluorescence for imaging.
190
Statistics. The colonization data of E. coli EDL933 between days 17 and 21 in Fig. 3A were
191
combined, as were those of E. coli EDL933 between days 17 and 21 in Fig. 6A, and the Fig. 3A
192
data and Fig. 6A data were compared by two-tailed Student's t test. Also, the colonization data
193
of E. coli MG1655 between days 17 and 21 in Figs. 2A and B were combined as were those of E.
194
coli Nissle 1917 between days 17 and 21 in Figs.3A and B and the data for the two strains were
195
compared by two-tailed Student's t test. P values of
1
Escherichia coli EDL933 Requires Gluconeogenic Nutrients to Successfully Colonize the
2
Intestines of Streptomycin-Treated Mice Pre-colonized with E. coli Nissle 1917
3 4
Silvia A. C. Schinner1, Matthew E. Mokszycki1, Jimmy Adediran1, Mary Leatham Jensen1,
5
Tyrrell Conway2, and Paul S. Cohen1*
6 7 8 9 10
Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 028811 Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 730192
11 12 13 14
Running Title: Gluconeogenesis and Intestinal Colonization
15 16
17
Corresponding Author
18
Phone: 401-874-5920
19
Fax:
20
e-mail: [email protected]
401-874-9750
1
21 22
Abstract E. coli MG1655, a K-12 strain, uses glycolytic nutrients exclusively to colonize the
23
streptomycin-treated mouse intestine when it is the only E. coli strain present or when confronted
24
with E. coli EDL933, an O157:H7 strain. In contrast, E. coli EDL933 uses glycolytic nutrients
25
exclusively when it is the only E. coli strain in the intestine, but switches in part to
26
gluconeogenic nutrients to colonize mice pre-colonized with E. coli MG1655 (Miranda et al
27
Infect. Immun. 72:1666-1676, 2004). Recently, Njoroge et al (mBio 3:e00280–12, 2012)
28
reported that E. coli 86-24, an O157:H7 strain, activates expression of virulence genes under
29
gluconeogenic conditions, suggesting that colonization of the intestine with a probiotic E. coli
30
strain that out-competes O157:H7 strains for gluconeogenic nutrients could render them non-
31
pathogenic. Here we report that E. coli Nissle 1917, a probiotic strain, uses both glycolytic and
32
gluconeogenic nutrients to colonize the mouse intestine between 1 and 5 days post-feeding,
33
appears to stop using gluconeogenic nutrients thereafter in a large long-term colonization niche,
34
but continues to use them in a smaller niche to compete with invading E. coli EDL933.
35
Evidence is also presented suggesting that invading E. coli EDL933 uses both glycolytic and
36
gluconeogenic nutrients and requires the ability to perform gluconeogenesis to colonize mice
37
pre-colonized with E. coli Nissle 1917. The data presented here therefore rule out the possibility
38
that E. coli Nissle 1917 can starve the O157:H7 strain E. coli EDL933 for gluconeogenic
39
nutrients despite using them to compete with it in the mouse intestine.
40 41 42 2
43 44
Introduction While much attention has been paid to the role of specific virulence factors in bacterial
45
pathogenesis, until recently little attention has been paid to the roles of specific metabolic
46
pathways in the ability of bacterial pathogens to initiate the pathogenic process. Yet clearly, if a
47
bacterial pathogen is unable to initiate pathogenesis because essential nutrients for its growth are
48
unavailable in the host, it will be unable to establish itself and cause disease. Therefore, it is
49
important to determine whether pathogens require glycolytic nutrients, gluconeogenic nutrients,
50
or both for success in invading and subsequently colonizing the host. Indeed, recent studies
51
suggest that some pathogens use glycolytic nutrients, some use gluconeogenic nutrients and
52
some use both to adapt to diverse host habitats (1-7).
53
We are interested in the nutritional basis of E. coli colonization of the intestine and whether
54
pre-colonization by E. coli commensal strains can be used to prevent invading E. coli intestinal
55
pathogens from colonizing. Commensal E. coli strains colonize the human intestine in the
56
presence of a dense and diverse intestinal microbiota comprised of at least 500 cultivable species
57
and 1013 to 1014 total bacteria (8). Unfortunately, E. coli colonization cannot be studied
58
experimentally in conventional animals due to colonization resistance, which results when all
59
niches are filled by the microbiota (9). Such experiments require an animal model with open
60
niches for E. coli to colonize the intestine in relatively high numbers, but to be authentic the
61
model intestine must also have a dense and diverse anaerobic community that matches as closely
62
as possible the native microbiota of the conventional animal. The streptomycin-treated mouse
63
model is used routinely for this purpose since streptomycin-treated mice fulfill these criteria (10,
64
11). Using this model, we have shown that for E. coli to colonize it must obtain nutrients in the
65
mucus layer, which overlays the epithelium (10, 11), that it resides in the mucus layer as a 3
66
member of mixed biofilms (12, 13), and that each E. coli strain displays a unique nutritional
67
program in the intestine (14).
68
E. coli strains can utilize both glycolytic and gluconeogenic nutrients for growth in vitro and
69
we reported previously that both E. coli MG1655, a commensal strain, and E. coli EDL933, an
70
O157:H7 pathogenic strain, use glycolytic, but not gluconeogenic nutrients to colonize the
71
streptomycin-treated mouse intestine when each is the only E. coli strain fed to mice (15).
72
However, we also reported that in the presence of E. coli MG1655, E. coli EDL933 switches, at
73
least in part, to gluconeogenesis in order to maintain itself in the intestine, while E. coli MG1655
74
continues to use glycolytic nutrients exclusively (15). These findings are of extreme interest in
75
view of recent reports showing that E. coli 86-24, also an O157:H7 strain, activates expression of
76
virulence genes under gluconeogenic conditions (16, 17), because this suggests the possibility
77
that pre-colonization of the intestine with a probiotic E. coli strain that starves E. coli O157:H7
78
strains of gluconeogenic nutrients might render them non-pathogenic.
79
E. coli Nissle 1917 is a commensal strain that has been used as a probiotic agent to treat
80
gastrointestinal infections in humans since the early 1920’s (18). Several features of E. coli
81
Nissle 1917 have been proposed to be responsible for its probiotic nature including its ability to
82
express two microcins (19), the absence of known protein toxins, its semi-rough
83
lipopolysaccharide and hence its serum sensitivity (20, 21), and the presence of six iron uptake
84
systems (22). More recently, it has been shown that E. coli Nissle 1917 inhibits adherence of E.
85
coli EDL933 to human epithelial cells in vitro and simultaneously inhibits its growth and Shiga
86
toxin 2 (Stx2) production (23). It has also been shown that in the streptomycin-treated mouse
87
intestine, E. coli Nissle 1917 is better than a number of commensal E. coli strains at limiting E.
88
coli EDL933 growth (12,13). In this study, we examine whether E. coli Nissle 1917 uses both
4
89
glycolytic and gluconeogenic nutrients to colonize the streptomycin-treated mouse intestine and
90
whether E. coli EDL933 switches to gluconeogenic nutrients to maintain itself in the intestine in
91
the presence of E. coli Nissle 1917.
92
Materials and Methods
93
Bacterial strains. Bacterial strains used in this study are listed in Table 1. The original E.
94
coli K-12 strain was obtained from a stool sample from a convalescing diphtheria patient in Palo
95
Alto, CA, in 1922 (24). The sequenced E. coli MG1655 strain (CGSC 7740) was derived from
96
the original K-12 strain, having only been cured of the temperate bacteriophage lambda and the F
97
plasmid by means of UV light and acridine orange treatment (24). It has an IS1 element in
98
the flhDC promoter (25). E. coli EDL933 is the prototype strain of EHEC strain O157:H7
99
(26). E. coli Nissle 1917 was originally isolated during World War I from a soldier who escaped
100
a severe outbreak of diarrhea (18). It has a beneficial effect on several types of intestinal
101
disorders, is well tolerated by humans, and has been marketed as a probiotic remedy against
102
intestinal disorders in several European countries since the 1920s (18).
103
Media and growth conditions. LB broth Lennox (Difco Laboratories, Detroit, MI), LB agar
104
Lennox (Difco), and MacConkey agar (Difco) were used for routine cultivation. SOC medium
105
was prepared as described by Datsenko and Wanner (27). For testing carbon and energy source
106
utilization in the Biolog, M9 minimal medium (28) was modified by addition of 120 mM NaCl
107
to more closely approximate the sodium chloride concentration in the intestine (29).
108
Mutant construction. The allelic exchange method described by Datsenko and Wanner (27)
109
was used to construct E. coli Nissle 1917 StrR ΔpckA ΔppsA::cat (Table 1). The method allows
110
the sequential construction of double deletion mutants by use of a removable chloramphenicol
5
111
cassette (27). Primers used to construct the deletion mutants were designed according to the E.
112
coli CFT073 genome sequence (30), which is closely related to the E. coli Nissle 1917 genome
113
sequence (31). Deletions of 1327 bp and 2367 bp were made in the pckA gene and the ppsA gene,
114
respectively. The pckA deletion primers used to make E. coli Nissle 1917 StrR ΔpckA::cat
115
(uppercase letters, E. coli Nissle 1917 DNA; lowercase letters, chloramphenicol resistance
116
cassette DNA) were: primer 1, 5-AGACTTTACTATTCAGGCAATACATATTGGC
117
TAAGGAGCAGTGgtgtaggctggagctgcttcg-3; primer 2, 5-GCGGGTATCTTTAATC
118
GAGATACGTTTGCCAGTGCCGTTCCA gcatatgaatatcctccttag-3. The ppsA deletion primers
119
used to make E. coli Nissle 1917 StrR ΔpckA ΔppsA::cat (uppercase letters, E. coli Nissle 1917
120
DNA; lowercase letters, chloramphenicol resistance cassette DNA) were: primer 1, 5-GCGACT
121
AAACGCCGCCGGGGATTTATTT TATTTCTTCAGTgtgtaggctggagctgcttcg-3; primer 2, 5-
122
AATGTGTTTCTCAAAC CGTTCATTTATCACAAAAGGATTGTTCgcatatgaatatcctccttag-3.
123
Gene knockouts were confirmed by PCR and sequencing using the following upstream and
124
downstream primers: ΔpckA forward, 5'-GTTAATTATCGCATCCGGGCA-3'; ΔpckA reverse,
125
5'-GTTGTCGATAAACAG TTTCGCCAG-3'; ΔppsA forward, 5'-CCTGTGTGG
126
TTGCAATGTCCG-3'; ΔppsA reverse, 5'-TTGTTCTTCCCGTGATGCAGAC-3'. DNA
127
sequencing was done at the URI Genomics and Sequencing Center, University of Rhode Island,
128
Kingston, RI, using an Applied Biosystems 3130xl genetic analyzer (Applied Biosystems, Foster
129
City, CA). A BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems) was used for
130
the sequencing reactions.
131
Biolog phenotypic analysis. For confirmation that E. coli Nissle 1917 StrR ΔpckA
132
ΔppsA::cat was able to grow on glycolytic substrates, but unable to grow on gluconeogenic
133
substrates, it and its wild type parent were grown over night in M9 minimal medium containing 6
134
0.4 % glycerol (v/v) and 0.2 M NaCl at 37oC. Cultures were washed twice in M9 minimal
135
medium containing 0.2 M NaCl without any carbon source and were then diluted to an OD600 of
136
0.06 in 5 ml of M9 minimal medium without any carbon source. Each culture was diluted an
137
additional 10-fold and 100 μl/well was added to a microtiter 96-well Biolog GN2 MicroPlate.
138
Plates were incubated at 37 °C for 48 h in the OmniLog system. Tetrazolium violet dye reduction
139
was measured at 15 min intervals and plotted vs. time, resulting in a kinetic curve. E. coli Nissle
140
1917 and E. coli Nissle 1917 ΔpckA ΔppsA each displayed the highest final level of tetrazolium
141
reduction when using either gluconate or glycerol as sole carbon source. Final levels of
142
tetrazolium reduction on all other carbon sources were normalized to that on glycerol.
143
Mouse colonization experiments. The specifics of the streptomycin-treated mouse model used
144
to compare the large intestine-colonizing abilities of E. coli strains in mice have been described
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previously (12). Briefly, sets of three male CD-1 mice (5 to 8 weeks old) were given drinking
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water containing streptomycin sulfate (5 g/liter) for 24 h to eliminate resident facultative bacteria
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(32). Following 18 h of starvation for food and water, the mice were fed 1 ml of 20% (wt/vol)
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sucrose containing 105 CFU of LB broth Lennox-grown E. coli strains, as described in Results.
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After ingestion of the bacterial suspension, both the food (Teklad mouse and rat diet; Harlan
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Laboratories, Madison, WI) and streptomycin-water were returned to the mice, and 1 g of feces
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was collected after 5 h and 24 h and on odd-numbered days, at the indicated times. Mice were
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housed individually in cages without bedding and were placed in clean cages at 24-h intervals.
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Individual fecal pellets were therefore no older than 24 h. Each fecal sample (1 g) was
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homogenized in 10 ml of 1% Bacto tryptone (Difco), diluted in the same medium, and plated on
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MacConkey agar plates with appropriate antibiotics. When appropriate, 1 ml of a fecal
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homogenate (sampled after the large debris had settled) was centrifuged at 12,000 × g,
7
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resuspended in 100 μl of 1% Bacto tryptone, and plated on a MacConkey agar plate with
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appropriate antibiotics. This procedure increased the sensitivity of the assay from 102 CFU/gram
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feces to 10 CFU/gram feces. To distinguish the various E. coli strains in feces, dilutions were
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plated on lactose MacConkey agar containing streptomycin sulfate (100 μg/ml), streptomycin
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sulfate (100 μg/ml) and nalidixic acid (50 μg/ml), streptomycin sulfate (100 μg/ml) and
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chloramphenicol (30 μg/ml), or streptomycin sulfate (100 μg/ml) and rifampin (50 μg/ml).
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Streptomycin sulfate, chloramphenicol, and nalidixic acid were purchased from Sigma-Aldrich
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(St. Louis, MO). All plates were incubated for 18 to 24 h at 37°C prior to counting. Each
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colonization experiment was performed at least twice, with essentially identical results. Pooled
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data from at least two independent experiments (for a total of six mice) are presented in the
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figures. All animal protocols were approved by the University Committee on Use and Care of
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Animals at the University of Rhode Island.
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Fluorescence in situ hybridization. FISH was performed as described previously (12, 33).
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Briefly, the cecum of a mouse designated for FISH was cut into 1-2 cm pieces, suspended in
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Tissue-Tek O.C.T compound (Sakura, Torrance, CA) and snap frozen in 2-methylbutane
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suspended in liquid nitrogen. Pieces were then stored at -80oC until ready for sectioning. For
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sectioning, the UltraPro 5000 Cryostat (Vibratome, St. Louis, MO) was used to cut 10μm
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sections, which were adhered to poly-L-lysine treated slides for visualization. Slides were fixed
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in 4% paraformaldehyde for 1 hour at room temperature, followed by a wash in phosphate
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buffered saline for 10 min. Slides were allowed to air dry overnight prior to hybridization.
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Fluorescent probes (IDT DNA, Coralville, IA) were diluted in hybridization solution (0.1 M
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Tris-HCl buffer pH 7.2, 0.9 M NaCl, and 0.1% SDS). The E.coli 23S rRNA specific Cy-3
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probe (5’-/5Cy3/ CAC CGT AGT GCC TCG TCA TCA-3’) (red) and the Eubacteria 23S rRNA
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specific FitC probe (5’-GCT GCC TCC CGT AGG AGT /36-FAM/-3’) (green) were used at
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concentrations of 5 ηg/µl and 25 ηg/µl, respectively. Subsequently, 10 ul of diluted probes in
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hybridization solution was pipetted to each slide. Each slide was then covered with a HybriSlip
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hybridization cover (Life Technologies, Carlsbad, CA) and allowed to incubate in the dark for 2
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hours at 50oC. The slides were then placed in a wash buffer (0.1 M Tris-HCl buffer pH 7.2, and
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0.9 M NaCl), and allowed to soak for 20 min at 50oC. Slides were then rinsed with distilled
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water and air dried overnight. Sections were viewed by confocal microscopy. Prior to viewing,
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sections on the poly-L-lysine treated slides were treated with Vectashield mounting medium
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(Vector Laboratories, Burlingame, CA), an antibleaching agent which helps prolong
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fluorescence for imaging.
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Statistics. The colonization data of E. coli EDL933 between days 17 and 21 in Fig. 3A were
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combined, as were those of E. coli EDL933 between days 17 and 21 in Fig. 6A, and the Fig. 3A
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data and Fig. 6A data were compared by two-tailed Student's t test. Also, the colonization data
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of E. coli MG1655 between days 17 and 21 in Figs. 2A and B were combined as were those of E.
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coli Nissle 1917 between days 17 and 21 in Figs.3A and B and the data for the two strains were
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compared by two-tailed Student's t test. P values of
