Fitness for 5 genes in Escherichia coli BW25113

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500 nttfaX and appY are separated by 545 nucleotidesappY and ompT are separated by 249 nucleotidesompT and pauD are separated by 423 nucleotidespauD and envY are separated by 45 nucleotides b0563: tfaX - DLP12 prophage; predicted protein (RefSeq), at 582,176 to 582,358 tfaX b0564: appY - DLP12 prophage; DNA-binding transcriptional activator (NCBI), at 582,904 to 583,653 appY b0565: ompT - DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) (NCBI), at 583,903 to 584,856 ompT b4635: pauD - tRNA-OTHER (RefSeq), at 585,280 to 585,324 pauD b0566: envY - DNA-binding transcriptional activator of porin biosynthesis (NCBI), at 585,370 to 586,131 envY
Group Condition b0563 b0564 b0565 b4635 b0566
tfaX appY ompT pauD envY
M9 Acetate 0.5% aerobic -0.4 -4.8 -0.2 N.D. -0.3
motility outer cut, LB soft agar motility assay -0.2 -3.9 +0.0 N.D. -0.0
M9 Glucose 2% anaerobic -0.2 -3.1 -0.2 N.D. -0.1
nutrient M9 Glucose 0.2%, Thauer's vit mix without biotin with Avidin -0.3 -3.0 -0.2 N.D. -0.0
nutrient M9 Glucose 0.2%, Thauer's vit mix without biotin with Avidin -0.2 -3.2 -0.1 N.D. -0.0
msc 22hr_mediaonly_rep1_highinoculum -0.3 -3.0 +0.0 N.D. -0.3
msc 22hr_mediaonly_rep2_lowinoculum -0.2 -2.8 -0.1 N.D. -0.3
stress Cisplatin 0.1 mg/ml -0.7 -2.3 -0.3 N.D. -0.1
nutrient M9 Glucose 0.2%, Thauer's vit mix without biotin -0.2 -3.1 -0.1 N.D. -0.0
carbon source Casamino-acids -0.1 -3.2 -0.1 N.D. -0.0
carbon source Cytidine 0.41115 mM (C) -0.3 -3.0 -0.1 N.D. +0.0
carbon source D-Glucose -0.2 -3.3 +0.0 N.D. +0.1
carbon source Sodium-DL-Lactate -0.0 -3.2 +0.0 N.D. -0.1
carbon source D-Mannose (C) -0.0 -3.3 +0.0 N.D. +0.1
msc 6hr_MSC_rep1_highinoculum +0.1 -3.1 -0.0 N.D. -0.1
carbon source Casamino-acids -0.0 -3.2 +0.1 N.D. -0.1
motility outer cut, LB soft agar motility assay +0.1 -3.6 -0.0 N.D. +0.4
carbon source D-Glucose +0.1 -3.2 -0.0 N.D. +0.1
predation 6 hr rep2_HD100_10fold_dilution_grewON +0.5 -2.8 +0.1 N.D. -0.7
carbon source carbon source D-Glucose 5mM +1.0 -2.2 -0.0 N.D. -1.6
carbon source carbon source D-Mannose 5mM +0.4 -2.4 -0.2 N.D. -0.4
carbon source carbon source D-Glucose 0.5mM +0.4 -2.6 -0.1 N.D. -0.3
carbon source carbon source D-Mannose 1mM +0.4 -2.4 -0.1 N.D. -0.5
control PBS_cage_2_mouse_2_Cecum_40 hr +0.4 -3.2 +0.2 N.D. +0.4
attachment_assay_attached_sample Time0_Wash=PBS; Attachment_time=2hrs; Attachment_surface=PDMS; Sample_type=attached; Outgrowth=LB +0.4 -2.6 +0.1 N.D. +0.1
phage T7_phage 0.00015625 MOI TC3 +0.9 -2.0 +0.2 N.D. -1.0
phage T7_phage 0.0015625 MOI TC1 +1.0 -0.7 -2.1 N.D. +0.0
phage T7_phage 0.00015625 MOI TC4 +0.9 +2.0 -1.0 N.D. +0.1
stress LB Anaerobic with Nitrofurantoin 0.00003125 mM -0.1 +3.0 -0.2 N.D. -0.2
predation 6 hr rep1_HD100_10fold_dilution_grewON +0.4 +2.2 +0.3 N.D. +0.7
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