Fitness for 5 genes in Bifidobacterium breve UCC2003

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500 ntBBR_RS14020 and BBR_RS20815 are separated by 67 nucleotidesBBR_RS20815 and BBR_RS14025 are separated by 225 nucleotidesBBR_RS14025 and BBR_RS14030 overlap by 1 nucleotidesBBR_RS14030 and BBR_RS14035 overlap by 4 nucleotides BBR_RS14020: BBR_RS14020 - TrkA family potassium uptake protein, at 921,915 to 922,337 _RS14020 BBR_RS20815: BBR_RS20815 - potassium transporter Trk, at 922,405 to 922,824 _RS20815 BBR_RS14025: BBR_RS14025 - NAD kinase, at 923,050 to 924,030 _RS14025 BBR_RS14030: BBR_RS14030 - DNA repair protein RecN, at 924,030 to 925,880 _RS14030 BBR_RS14035: BBR_RS14035 - HAD family phosphatase, at 925,877 to 926,524 _RS14035
Group Condition BBR_RS14020 BBR_RS20815 BBR_RS14025 BBR_RS14030 BBR_RS14035
chicken chicken 2; day 6; diet=StandardDiet; sample=FecalPellet -0.7 +0.3 N.D. -1.6 -1.1
nutrient dropout CDM1 without Glycine +0.3 -1.8 N.D. -0.1 -1.4
chicken chicken 1; day 2; diet=StandardDiet; sample=FecalPellet -0.2 -0.3 N.D. -1.3 -1.0
stress Recovery broth with Moxifloxacin 0.004 mM +0.1 +0.3 N.D. -2.9 -0.0
carbon source reconstituted MRS with Difucosyllactose 7.9 mM -0.4 -3.0 N.D. +0.5 +0.3
chicken chicken 5; day 7; diet=StandardDiet; sample=FecalPellet -0.8 +0.1 N.D. -1.6 -0.2
chicken chicken 2; day 5; diet=StandardDiet; sample=FecalPellet +0.1 -0.7 N.D. -1.3 -0.4
stress Recovery broth with Metronidazole 0.03 mM +0.1 -0.2 N.D. -1.7 -0.1
mouse diet=StandardDiet2; sample=FecalPellet; mouse16; day3 -1.0 +0.4 N.D. -0.9 -0.1
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day4 -0.2 +0.5 N.D. -0.6 -1.0
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day3 +0.4 +0.4 N.D. -1.4 -0.1
stress Recovery broth with Dimetridazole 0.1 mM +0.3 +0.1 N.D. -1.4 +0.3
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse16; day6 +0.2 +0.5 N.D. -1.6 +0.2
stress Recovery broth with Nitrofurantoin 0.05 mM -1.3 +0.0 N.D. -0.3 +0.9
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse17; day5 -0.0 +0.9 N.D. -1.2 -0.2
chicken coculture chicken 2; day 7; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron +0.8 +0.1 N.D. -1.2 -0.2
mouse diet=StandardDiet; sample=FecalPellet; mouse4; day2 -0.2 +0.8 N.D. -1.1 +0.1
chicken coculture chicken 4; day 4; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron +0.0 +1.0 N.D. -1.3 -0.2
chicken chicken 21; day 7; diet=StandardDiet; sample=Cecum +1.0 +0.0 N.D. -1.7 +0.4
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse16; day5 +0.3 +0.6 N.D. -1.1 -0.2
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse18; day6 +0.7 +0.5 N.D. -1.1 -0.3
chicken chicken 21; day 7; diet=StandardDiet; sample=Small_intestine +0.8 +0.1 N.D. -1.5 +0.4
stress timecourse MRS + carbenicillin Time48hr +0.7 -0.9 N.D. -0.1 +0.2
chicken coculture chicken 4; day 3; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron +0.2 +1.1 N.D. -0.8 -0.3
mouse diet=StandardDiet; sample=FecalPellet; mouse3; day5 -0.2 +1.2 N.D. -0.4 -0.4
mouse diet=HighFatHighSugar; sample=FecalPellet; mouse13; day3 -0.2 -1.1 N.D. +0.9 +0.7
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day5 +0.0 +1.2 N.D. -0.8 -0.1
nutrient dropout CDM1 without Phenylalanine +0.3 +1.2 N.D. -0.2 -0.4
supernatant CDM1Gut with 50% spent media from Escherichia fergusonnii TT2 +0.9 -0.5 N.D. +0.1 +0.6
mouse mouse 10; day 1; diet=PolysaccharideDeficient; sample=FecalPellet +0.7 +1.5 N.D. +0.0 +0.1
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