Fitness for 5 genes in Bifidobacterium breve UCC2003

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500 ntBBR_RS14115 and BBR_RS14120 overlap by 4 nucleotidesBBR_RS14120 and BBR_RS14125 are separated by 150 nucleotidesBBR_RS14125 and BBR_RS14130 are separated by 90 nucleotidesBBR_RS14130 and BBR_RS14135 overlap by 4 nucleotides BBR_RS14115: BBR_RS14115 - transcription-repair coupling factor, at 941,761 to 945,351 _RS14115 BBR_RS14120: BBR_RS14120 - aldo/keto reductase, at 945,348 to 946,259 _RS14120 BBR_RS14125: BBR_RS14125 - phosphopyruvate hydratase, at 946,410 to 947,708 _RS14125 BBR_RS14130: BBR_RS14130 - septum formation initiator family protein, at 947,799 to 948,383 _RS14130 BBR_RS14135: BBR_RS14135 - DUF501 domain-containing protein, at 948,380 to 948,946 _RS14135
Group Condition BBR_RS14115 BBR_RS14120 BBR_RS14125 BBR_RS14130 BBR_RS14135
chicken chicken 2; day 5; diet=StandardDiet; sample=FecalPellet -0.9 -0.2 N.D. -4.0 N.D.
mouse diet=StandardDiet2; sample=FecalPellet; mouse16; day3 +0.2 -0.2 N.D. -4.5 N.D.
chicken coculture chicken 4; day 3; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron +0.2 -0.5 N.D. -4.2 N.D.
mouse preculture cage3; mouse3; day3; diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs +0.1 -0.0 N.D. -4.6 N.D.
chicken coculture chicken 4; day 4; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron -0.0 -0.2 N.D. -4.2 N.D.
mouse diet=StandardDiet; sample=FecalPellet; mouse2; day2 +0.1 -0.1 N.D. -4.5 N.D.
mouse preculture cage3; mouse3; day5; diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs -0.0 -0.0 N.D. -4.3 N.D.
mouse diet=StandardDiet2; sample=FecalPellet; mouse18; day3 +0.0 +0.3 N.D. -4.6 N.D.
chicken chicken 2; day 6; diet=StandardDiet; sample=FecalPellet -0.8 -0.1 N.D. -3.3 N.D.
chicken chicken 21; day 7; diet=StandardDiet; sample=Cecum -0.3 -0.4 N.D. -3.5 N.D.
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day2 +0.0 +0.5 N.D. -4.7 N.D.
chicken chicken 3; day 3; diet=StandardDiet; sample=FecalPellet +0.1 +0.1 N.D. -4.4 N.D.
mouse diet=StandardDiet; sample=FecalPellet; mouse4; day2 -0.0 -0.1 N.D. -3.9 N.D.
stress Recovery broth with Ciprofloxacin 0.1 mM -0.2 +0.0 N.D. -3.7 N.D.
stress Recovery broth with Azlocillin 3e-05 mM -0.2 +0.0 N.D. -3.5 N.D.
stress Recovery broth with Tiamulin 2e-04 mM +0.1 +0.0 N.D. -3.7 N.D.
mouse preculture cage3; mouse3; day4; diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs -0.0 -0.3 N.D. -3.2 N.D.
mouse diet=HighFatHighSugar; sample=FecalPellet; mouse12; day2 +0.2 +0.3 N.D. -3.7 N.D.
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse18; day5 -0.1 -0.1 N.D. -3.0 N.D.
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse17; day5 -0.5 +0.1 N.D. -2.7 N.D.
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse16; day3 -0.1 +0.2 N.D. -3.1 N.D.
mouse diet=HighFatHighSugar; sample=FecalPellet; mouse14; day3 +0.1 -0.2 N.D. -2.8 N.D.
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day1 +0.3 +0.3 N.D. -3.5 N.D.
chicken chicken 5; day 6; diet=StandardDiet; sample=FecalPellet -0.3 +0.3 N.D. -2.9 N.D.
carbon source reconstituted MRS with Difucosyllactose 7.9 mM +0.4 +0.2 N.D. -3.3 N.D.
stress Recovery broth with Streptomycin 0.3 mM -0.3 +0.3 N.D. -2.6 N.D.
mouse diet=StandardDiet; sample=FecalPellet; mouse2; day1 +0.1 +0.2 N.D. -2.9 N.D.
mouse diet=StandardDiet; sample=FecalPellet; mouse5; day4 +0.2 +0.4 N.D. -3.0 N.D.
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day3 +0.3 +0.3 N.D. -2.9 N.D.
nutrient dropout CDM1 without Phenylalanine +1.1 -0.6 N.D. -2.3 N.D.
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