Fitness for 5 genes in Bifidobacterium breve UCC2003

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500 ntBBR_RS20420 and BBR_RS20425 overlap by 4 nucleotidesBBR_RS20425 and BBR_RS20430 are separated by 45 nucleotidesBBR_RS20430 and BBR_RS20435 are separated by 128 nucleotidesBBR_RS20435 and BBR_RS20440 are separated by 86 nucleotides BBR_RS20420: BBR_RS20420 - 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))- dimethyltransferase RsmA, at 2,404,171 to 2,405,100 _RS20420 BBR_RS20425: BBR_RS20425 - 4-diphosphocytidyl-2C-methyl-D-erythritol kinase, at 2,405,097 to 2,406,044 _RS20425 BBR_RS20430: BBR_RS20430 - hypothetical protein, at 2,406,090 to 2,406,719 _RS20430 BBR_RS20435: BBR_RS20435 - CCA tRNA nucleotidyltransferase, at 2,406,848 to 2,408,266 _RS20435 BBR_RS20440: BBR_RS20440 - NUDIX hydrolase, at 2,408,353 to 2,409,324 _RS20440
Group Condition BBR_RS20420 BBR_RS20425 BBR_RS20430 BBR_RS20435 BBR_RS20440
chicken chicken 1; day 2; diet=StandardDiet; sample=FecalPellet -3.1 N.D. -3.4 -3.3 -4.8
mouse coculture cage1; mouse2; day5; diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482 -2.3 N.D. -1.7 -3.5 -5.1
chicken chicken 2; day 5; diet=StandardDiet; sample=FecalPellet -3.5 N.D. -2.4 -2.9 -3.8
chicken chicken 10; day 5; diet=StandardDiet; sample=FecalPellet -3.0 N.D. -2.6 -2.9 -3.9
chicken coculture chicken 4; day 3; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron -3.5 N.D. -2.5 -3.4 -3.1
mouse coculture cage1; mouse2; day4; diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482 -2.6 N.D. -1.9 -3.4 -4.5
chicken chicken 5; day 6; diet=StandardDiet; sample=FecalPellet -2.9 N.D. -2.7 -3.0 -3.7
mouse coculture cage1; mouse1; day5; diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482 -3.0 N.D. -1.2 -3.2 -5.0
chicken chicken 10; day 4; diet=StandardDiet; sample=FecalPellet -2.6 N.D. -3.0 -3.1 -3.7
mouse diet=StandardDiet2; sample=FecalPellet; mouse18; day4 -4.0 N.D. -0.0 -3.8 -4.3
chicken chicken 9; day 2; diet=StandardDiet; sample=FecalPellet -2.9 N.D. -3.3 -3.2 -2.8
mouse preculture cage3; mouse1; day5; diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs -2.6 N.D. -1.2 -3.1 -4.7
chicken chicken 3; day 2; diet=StandardDiet; sample=FecalPellet -3.1 N.D. -3.1 -3.1 -2.2
chicken coculture chicken 4; day 4; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron -3.4 N.D. -2.3 -3.3 -2.5
mouse coculture cage1; mouse1; day3; diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482 -2.5 N.D. -2.2 -3.6 -3.2
chicken chicken 3; day 3; diet=StandardDiet; sample=FecalPellet -2.1 N.D. -3.2 -3.2 -2.9
mouse diet=StandardDiet2; sample=FecalPellet; mouse18; day3 -2.9 N.D. -0.3 -3.8 -4.4
chicken chicken 5; day 7; diet=StandardDiet; sample=FecalPellet -2.6 N.D. -2.3 -2.7 -3.5
mouse coculture cage1; mouse2; day3; diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482 -2.0 N.D. -2.4 -3.7 -2.6
mouse diet=StandardDiet2; sample=FecalPellet; mouse16; day3 -2.9 N.D. -0.4 -3.7 -3.7
chicken coculture chicken 2; day 7; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron -2.8 N.D. -1.8 -2.9 -3.0
mouse diet=StandardDiet; sample=FecalPellet; mouse1; day2 -2.8 N.D. -0.5 -3.9 -3.2
mouse diet=StandardDiet2; sample=FecalPellet; mouse17; day4 -3.4 N.D. +0.1 -3.3 -3.6
mouse diet=StandardDiet; sample=FecalPellet; treatment=Methotrexate; mouse18; day5 -3.0 N.D. +0.8 -2.7 -3.9
nutrient dropout CDM1 without Serine -2.4 N.D. -5.3 +2.0 -1.5
nutrient dropout control CDM1 -2.1 N.D. -5.3 +1.6 -1.4
nutrient dropout CDM1 without Pyridoxamine -2.2 N.D. -4.8 +2.1 -1.9
nutrient dropout CDM1 without Adenine -3.6 N.D. -5.0 +2.9 -0.6
nutrient dropout CDM1 without Asparagine -2.2 N.D. -4.4 +2.4 -1.5
nutrient dropout CDM1 with Glycine Leucine Cysteine Methionine Glutamate as the only aminos -2.9 N.D. -5.1 +3.6 -0.6
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