Fitness for 5 genes in Escherichia coli BW25113

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500 ntydfR and b1556 are separated by 4 nucleotidesb1556 and cspB are separated by 753 nucleotidescspB and cspF are separated by 300 nucleotidescspF and b1559 are separated by 421 nucleotides b1555: ydfR - Qin prophage; predicted protein (NCBI), at 1,638,078 to 1,638,389 ydfR b1556: b1556 - orf, hypothetical protein (VIMSS), at 1,638,394 to 1,638,609 b1556 b1557: cspB - Qin prophage; cold shock protein (NCBI), at 1,639,363 to 1,639,578 cspB b1558: cspF - Qin prophage; cold shock protein (NCBI), at 1,639,879 to 1,640,091 cspF b1559: b1559 - orf, hypothetical protein (VIMSS), at 1,640,513 to 1,641,265 b1559
Group Condition b1555 b1556 b1557 b1558 b1559
ydfR b1556 cspB cspF b1559
plasmid transformation mariner vector transformation; liquid outgrowth assay N.D. -1.3 -2.7 -1.1 +0.1
phage N4_phage 0.00009375 MOI TC4 N.D. -1.7 -3.3 +0.6 -0.1
control NoBALOControl N.D. -0.8 -2.6 -0.9 -0.1
gfp_control GFP_control N.D. -0.0 -2.7 -1.2 +0.0
plasmid transformation mariner vector transformation; liquid outgrowth assay N.D. -0.9 -1.9 -0.7 -0.2
TN_18CS_warm37C_5dbl_rep1 N.D. -1.3 -0.9 -0.8 -0.1
stress LB Anaerobic with Mecillinam 0.0000078125 mM N.D. -0.9 -2.1 +0.2 +0.3
control PBS_cage_2_mouse_1_Cecum_40 hr N.D. +0.5 -2.4 -1.0 +0.8
phage Phage_N4_cage_3_mouse_4_Cecum_40 hr N.D. -1.6 +0.9 -1.3 -0.1
carbon source carbon source D-Glucose 0.25mM N.D. -1.8 -1.2 +0.8 +0.2
plasmid transformation vcDART vector transformation; liquid outgrowth assay N.D. +0.0 -1.3 -1.3 +0.4
phage R2_N4_T2_phage10 N.D. -1.7 +0.6 -0.4 -0.3
stress Ciprofloxacin Hydrochloride 0.0003 mM N.D. +0.7 -1.1 +0.6 -1.7
stress LB Anaerobic with Nitrofurantoin 0.00003125 mM N.D. -1.9 -1.7 +2.3 -0.1
attachment_assay_attached_sample Time0_Wash=PBS; Attachment_time=2hrs; Attachment_surface=PDMS; Sample_type=attached; Outgrowth=None N.D. -2.2 +0.3 +0.4 +0.3
phage Ste41 N.D. +2.0 -2.5 +0.4 -0.9
plasmid transformation vcDART vector transformation; liquid outgrowth assay N.D. -0.5 -0.8 -0.4 +1.0
phage T7_phage 0.0015625 MOI TC2 N.D. +1.2 -2.4 +0.8 +0.1
phage Ste41 N.D. +1.0 -0.9 +0.3 -0.5
phage T7_phage 0.00015625 MOI TC3 N.D. -1.8 +1.1 +0.8 +1.2
micoeukaryotes Tetrahymena sp., Mixed culture-1 N.D. -0.9 +0.2 +1.8 +0.3
stress benzenesulfonyl fluoride N.D. -1.3 +2.5 +0.4 -0.1
carbon source carbon source D-Mannose 5mM N.D. +1.5 -1.1 +1.0 +0.2
stress Trimethoprim 0.005 mM N.D. +1.6 +0.2 +1.3 -0.9
phage TP4 N.D. -0.1 +1.0 +1.3 +0.3
balo Mixed culture, Halobacteriovorax-1 N.D. +1.0 +1.2 +0.5 -0.1
stress LB Aerobic with Zinc Pyrithione 0.0000025 mM N.D. +0.8 +0.9 +0.7 +0.3
stress LB Anaerobic with Ciprofloxacin Hydrochloride 0.0000000390625 mM N.D. +1.1 +1.3 +0.7 -0.3
stress LB Aerobic with Irgasan 0.0000003125 mM N.D. +0.6 +1.3 +1.0 +0.1
stress LB Anaerobic with Cefoxitin 0.000003125 mM N.D. +1.0 +1.3 +0.8 +0.0
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