Fitness for 5 genes in Bifidobacterium breve UCC2003

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500 ntBBR_RS16560 and BBR_RS16565 are separated by 42 nucleotidesBBR_RS16565 and BBR_RS16570 are separated by 122 nucleotidesBBR_RS16570 and BBR_RS16575 are separated by 132 nucleotidesBBR_RS16575 and BBR_RS16580 overlap by 4 nucleotides BBR_RS16560: BBR_RS16560 - hypothetical protein, at 1,482,594 to 1,483,343 _RS16560 BBR_RS16565: BBR_RS16565 - tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA, at 1,483,386 to 1,484,369 _RS16565 BBR_RS16570: BBR_RS16570 - tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB, at 1,484,492 to 1,485,943 _RS16570 BBR_RS16575: BBR_RS16575 - (p)ppGpp synthetase, at 1,486,076 to 1,486,816 _RS16575 BBR_RS16580: BBR_RS16580 - EamA/RhaT family transporter, at 1,486,813 to 1,487,760 _RS16580
Group Condition BBR_RS16560 BBR_RS16565 BBR_RS16570 BBR_RS16575 BBR_RS16580
chicken chicken 2; day 5; diet=StandardDiet; sample=FecalPellet -0.1 N.D. -2.8 +0.1 +0.1
chicken chicken 5; day 7; diet=StandardDiet; sample=FecalPellet +0.3 N.D. -1.5 -1.5 +0.3
chicken coculture chicken 2; day 7; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron +0.0 N.D. -1.7 -1.2 +0.4
chicken coculture chicken 4; day 4; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron +0.3 N.D. -2.9 +0.5 -0.1
chicken chicken 5; day 6; diet=StandardDiet; sample=FecalPellet +0.4 N.D. -1.3 -1.6 +0.4
chicken coculture chicken 4; day 3; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron +0.1 N.D. -2.4 +0.3 -0.1
nutrient dropout CDM1 without Biotin +0.6 N.D. -0.1 -2.1 -0.3
mouse preculture cage3; mouse3; day5; diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs +0.9 N.D. -1.1 -0.5 -1.2
mouse diet=HighFatHighSugar; sample=FecalPellet; mouse14; day3 -0.9 N.D. -1.5 +0.3 +0.7
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse18; day6 +0.8 N.D. -1.3 -0.9 +0.8
supernatant CDM1Gut with 50% spent media from Escherichia fergusonnii TT2 +1.1 N.D. +0.2 -0.5 -1.0
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse16; day3 +0.6 N.D. -0.9 -0.6 +1.0
mouse diet=StandardDiet; sample=FecalPellet; mouse5; day3 +0.4 N.D. -0.1 -1.2 +1.1
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse17; day5 +0.7 N.D. -1.1 -0.4 +1.1
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse18; day3 +0.8 N.D. -0.6 -0.8 +0.9
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day4 +0.8 N.D. +0.3 -1.5 +0.7
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse16; day4 +0.7 N.D. -0.7 -0.6 +1.0
mouse diet=StandardDiet2; sample=FecalPellet; mouse17; day4 +0.9 N.D. -0.5 -1.0 +1.1
nutrient dropout CDM1 without Glycine +0.7 N.D. +0.5 -1.4 +0.7
mouse diet=StandardDiet; sample=FecalPellet; mouse5; day6 +1.1 N.D. +0.5 -1.8 +0.9
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse16; day5 +0.9 N.D. -0.9 -0.3 +1.0
mouse diet=StandardDiet; sample=FecalPellet; mouse2; day5 +0.9 N.D. +0.6 -1.5 +0.7
mouse diet=StandardDiet; sample=FecalPellet; mouse5; day4 +0.6 N.D. +0.2 -1.1 +1.2
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse18; day5 +0.9 N.D. -0.9 -0.0 +1.1
mouse diet=StandardDiet; sample=FecalPellet; mouse4; day4 +1.2 N.D. -0.1 -0.9 +1.0
mouse diet=StandardDiet; sample=FecalPellet; mouse4; day5 +1.2 N.D. -0.1 -1.0 +1.0
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse17; day6 +1.1 N.D. -0.4 -1.1 +1.6
mouse diet=StandardDiet; sample=FecalPellet; mouse3; day5 +1.2 N.D. +0.1 -1.2 +1.3
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day5 +1.1 N.D. +0.4 -1.0 +1.1
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse16; day6 +1.0 N.D. -1.1 +0.4 +1.4
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