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Fitness for 5 genes in
Escherichia coli BW25113
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500 nt
folM and ydgC overlap by 4 nucleotides
ydgC and rstA are separated by 128 nucleotides
rstA and rstB are separated by 3 nucleotides
rstB and tus are separated by 75 nucleotides
b1606: folM - short chain dehydrogenase (NCBI), at 1,679,000 to 1,679,722
folM
b1607: ydgC - conserved inner membrane protein associated with alginate biosynthesis (NCBI), at 1,679,719 to 1,680,054
ydgC
b1608: rstA - DNA-binding response regulator in two-component regulatory system with RstB (RefSeq), at 1,680,183 to 1,680,902
rstA
b1609: rstB - sensory histidine kinase in two-component regulatory system with RstA (NCBI), at 1,680,906 to 1,682,207
rstB
b1610: tus - DNA replication terminus site-binding protein (NCBI), at 1,682,283 to 1,683,212
tus
Group
Condition
b1606
b1607
b1608
b1609
b1610
folM
ydgC
rstA
rstB
tus
predation
6 hr rep1_HD100_10fold_dilution_grewON
+0.6
-4.2
+0.7
-1.8
-0.0
phage
T7_phage 0.00015625 MOI TC4
-0.5
-3.7
+0.8
-0.5
-0.9
phage
T7_phage 0.0015625 MOI TC2
+0.3
-2.7
-2.1
+0.4
-0.5
carbon source
carbon source D-Mannose 5mM
+0.9
-4.7
+0.4
-1.0
+0.1
phage
TP4
-0.1
-4.5
-0.1
+0.4
+0.0
stress
LB Anaerobic with Amoxicillin 0.0000078125 mM
-0.4
-2.5
-0.1
-0.7
-0.4
stress
LB Anaerobic with Doxycycline hyclate 0.00000078125 mM
-0.2
-3.3
+0.1
-0.4
-0.0
control
PBS_cage_2_mouse_1_Cecum_40 hr
-0.2
-1.4
-0.9
-0.4
-0.6
stress
LB Anaerobic with Benzethonium chloride 0.00003125 mM
-0.1
-1.0
-0.7
-1.1
-0.7
stress
Ciprofloxacin Hydrochloride 0.0003 mM
-0.2
-2.9
+0.2
-0.9
+0.2
control
PBS_cage_1_mouse_1_Cecum_40 hr
-0.3
-1.7
-1.1
-0.2
-0.2
phage
N4_phage 0.00009375 MOI TC5
-0.1
-2.1
-0.2
-0.9
-0.2
stress
LB Anaerobic with Nitrofurantoin 0.00003125 mM
+0.2
-1.9
-0.6
+0.6
-1.1
stress
LB Anaerobic with Chlorhexidine diacetate salt 0.000000625 mM
-0.0
-2.5
-0.3
+0.2
-0.2
stress
LB Aerobic with Chlorhexidine diacetate salt 0.000000625 mM
+0.4
-2.7
+0.4
-0.7
-0.2
phage
RB68
-0.2
-1.7
+0.1
+0.4
-1.2
stress
LB Aerobic with Chlorhexidine diacetate salt 0.000000625 mM
-0.4
-1.9
-1.1
+0.9
+0.2
stress
LB Anaerobic with Trimethoprim 0.0000003125 mM
+0.8
-1.7
-0.4
-0.4
+0.1
stress
LB Anaerobic with Ciprofloxacin Hydrochloride 0.0000000390625 mM
+0.2
-1.5
+0.4
-0.8
+0.7
phage
T7_phage 0.00015625 MOI TC3
+0.1
+1.2
-1.1
-0.5
-0.5
stress
LB Aerobic with Nitrofurantoin 0.00003125 mM
+0.3
-1.6
+0.3
+0.9
+0.2
stress
Trimethoprim 0.005 mM
+1.5
-0.7
+1.2
-1.0
+0.2
phage
N4_phage 0.009375 MOI TC2
-0.3
+1.1
-0.9
+1.0
+0.2
plasmid transformation
mariner vector transformation; liquid outgrowth assay
+0.2
+1.6
+0.4
-1.2
+0.2
stress
M9 with Methotrexate 1.98 mM 24 hr
+2.9
+0.0
-0.3
-0.9
-0.2
phage
N4_phage 0.09375 MOI TC1
+0.1
+2.1
-0.4
+0.4
-0.5
supernatant
Fungal_growth_media_mCAFEs_v1_noCarbon with Supernatant; Trichoderma virens G41 grown in Fungal_growth_media_mCAFEs_v1, filtered and pH-adjusted 0.1x; and D-Glucose 99.9 mM
+0.2
+0.5
+1.4
+1.1
-0.1
supernatant
Fungal_growth_media_mCAFEs_v1_noCarbon with Supernatant; Trichoderma virens G41 grown in Fungal_growth_media_mCAFEs_v1, filtered and pH-adjusted 0.1x; and D-Glucose 99.9 mM
+0.1
+1.2
+1.2
+1.0
+0.1
phage
N4_phage 0.0009375 MOI TC3
+0.6
+2.6
+0.6
+0.4
-0.0
carbon source
carbon source D-Glucose 0.25mM
+0.3
+2.6
-0.0
+1.1
+0.3
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