Engineered Gut Amino Acid Cross-Feeding Consortium

Community ID CommunityMech:000151

Ecological State ENGINEERED

Environment gnotobiotic mouse gut environment
ENVO:0001998

A four-species engineered mammalian-gut consortium in which Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, and Bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. The design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Escherichia coli	NCBITaxon:562	CROSS_FEEDER	N/A
PMID:31409662 - SUPPORT (IN_VITRO) "Yellow, E. coli"
Salmonella enterica serovar Typhimurium	NCBITaxon:90371	CROSS_FEEDER	N/A
PMID:31409662 - SUPPORT (IN_VITRO) "purple, S. Typhimurium"
Bacteroides thetaiotaomicron	NCBITaxon:818	PRIMARY_DEGRADER CROSS_FEEDER	N/A
PMID:31409662 - SUPPORT (IN_VITRO) "green, B. thetaiotaomicron"
Bacteroides fragilis	NCBITaxon:817	PRIMARY_DEGRADER CROSS_FEEDER	N/A
PMID:31409662 - SUPPORT (IN_VITRO) "blue, B. fragilis"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Engineered Amino Acid Cross-Feeding

CROSS_FEEDING

Metabolites: amino acid (CHEBI:33709)

Biological Processes:

cellular amino acid biosynthetic process (GO:0008652)
amino acid transport (GO:0006865)

Evidence

doi:10.1128/mSystems.00352-19 - SUPPORT (IN_VITRO)

"Each strain is auxotrophic for three amino acids and overproduces one"
doi:10.1128/mSystems.00352-19 - SUPPORT (IN_VITRO)

"Cross-feeding capabilities of each strain were assessed"

Beneficial Interaction Shift

MUTUALISM

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

doi:10.1128/mSystems.00352-19 - SUPPORT (IN_VITRO)

"genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions"

Cross-Feeding Increased Population Evenness

CROSS_FEEDING

Metabolites: amino acid (CHEBI:33709)

Evidence

PMID:31409662 - SUPPORT (IN_VITRO)

"Engineered cross-feeding increased population evenness"
PMID:31409662 - SUPPORT (IN_VIVO)

"low-protein diet showed significantly greater population evenness"

Associated Datasets

Dataset	Type	Repository	Accession
Engineered gut amino acid cross-feeding publication Publication reporting engineered amino acid overproduction, auxotrophy rescue, in vitro consortium dynamics, and gnotobiotic mouse composition measurements.	PHENOTYPE	OTHER	PMID:31409662

Environmental Factors

Factor	Value	Unit
anaerobic modified M9 medium	Modified M9 minimal medium with starch and glucose carbon sources	N/A
doi:10.1128/mSystems.00352-19 - SUPPORT (IN_VITRO) "M9 minimal medium"
low-protein gnotobiotic mouse diet	3% protein low-protein chow	N/A
doi:10.1128/mSystems.00352-19 - SUPPORT (IN_VIVO) "low-protein (3%) chow"

Growth Media

modified M9 amino acid cross-feeding medium

Temperature 37 C

Atmosphere ANAEROBIC

Preparation notes: Modified M9 minimal medium with glucose and starch carbon sources; cross-fed amino acids were omitted or supplemented depending on the assay.

Evidence

doi:10.1128/mSystems.00352-19

"without supplementation of any of the cross-fed amino acids"