Experiment set19S44 for Bifidobacterium breve UCC2003

cage3; mouse2; day5; diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs

Group: mouse preculture
Media: + diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs
Culturing: Bifido_ML2
By: Anthony Shiver on 4/3/2024

Specific Phenotypes

For 6 genes in this experiment

For mouse preculture diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs in Bifidobacterium breve UCC2003

For mouse preculture diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs across organisms

SEED Subsystems

Subsystem	#Specific
Biotin biosynthesis	1
Sialic Acid Metabolism	1
Thiamin biosynthesis	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Thiamine metabolism
• Nucleotide sugars metabolism
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Fatty acid metabolism
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Aminosugars metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydroxymethylpyrimidine salvage	2	2	2
long-chain fatty acid activation	1	1	1
thiamine diphosphate salvage II	5	4	3
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
trehalose degradation I (low osmolarity)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
trehalose degradation II (cytosolic)	2	1	1
thiamine diphosphate salvage IV (yeast)	7	6	3
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	5	3
trehalose degradation IV	3	3	1
GDP-α-D-glucose biosynthesis	3	2	1
thiamine diphosphate salvage V	3	2	1
trehalose degradation V	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
sucrose degradation III (sucrose invertase)	4	4	1
phytol degradation	4	3	1
N-acetylneuraminate and N-acetylmannosamine degradation I	4	2	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
glucose and glucose-1-phosphate degradation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	2	1
octane oxidation	5	2	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	4	1
stearate biosynthesis II (bacteria and plants)	6	4	1
glycogen degradation II	6	4	1
stearate biosynthesis IV	6	3	1
6-gingerol analog biosynthesis (engineered)	6	1	1
stearate biosynthesis I (animals)	6	1	1
fatty acid salvage	6	1	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	4	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
chitin biosynthesis	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
superpathway of thiamine diphosphate biosynthesis I	10	6	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	29	4
glycolysis III (from glucose)	11	10	1
superpathway of thiamine diphosphate biosynthesis II	11	7	1
homolactic fermentation	12	11	1
Bifidobacterium shunt	15	15	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
palmitate biosynthesis II (type II fatty acid synthase)	31	22	2
cutin biosynthesis	16	1	1
heterolactic fermentation	18	16	1
superpathway of N-acetylneuraminate degradation	22	17	1
superpathway of fatty acids biosynthesis (E. coli)	53	35	2
palmitate biosynthesis III	29	14	1
oleate β-oxidation	35	1	1