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BioModels MODEL2204300001 Kefir Community Model

Community ID CommunityMech:000009
Ecological State ENGINEERED
Environment laboratory environment
ENVO:01001405

BioModels record MODEL2204300001 is a genome-scale model from the Blasche et al. kefir study and is described as a model of a microbial species participating in a kefir community.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Lactobacillus kefiranofaciens NCBITaxon:33962
PRIMARY_DEGRADER
DOMINANT
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "L. kefiranofaciens, which is dominant in the grain as well as in the milk fraction"
Lactococcus lactis NCBITaxon:1358
PRIMARY_DEGRADER
N/A
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "bacterial core community consisting of Lactobacillus sp. (mainly L. kefiranofaciens and L. kefiri), Leuconostoc sp. (usually L. mesenteroides), Lactococcus lactis, and Acetobacter sp., which together accounted for > 95% of total abundance"
Leuconostoc mesenteroides NCBITaxon:1245
SECONDARY_FERMENTER
N/A
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "bacterial core community consisting of Lactobacillus sp. (mainly L. kefiranofaciens and L. kefiri), Leuconostoc sp. (usually L. mesenteroides), Lactococcus lactis, and Acetobacter sp., which together accounted for > 95% of total abundance"
Lactobacillus kefiri NCBITaxon:33963
SECONDARY_FERMENTER
N/A
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "bacterial core community consisting of Lactobacillus sp. (mainly L. kefiranofaciens and L. kefiri), Leuconostoc sp. (usually L. mesenteroides), Lactococcus lactis, and Acetobacter sp., which together accounted for > 95% of total abundance"
Acetobacter fabarum NCBITaxon:728467
CROSS_FEEDER
N/A
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "bacterial core community consisting of Lactobacillus sp. (mainly L. kefiranofaciens and L. kefiri), Leuconostoc sp. (usually L. mesenteroides), Lactococcus lactis, and Acetobacter sp., which together accounted for > 95% of total abundance"
Kazachstania exigua NCBITaxon:1380867
CROSS_FEEDER
N/A
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "Kazachstania exigua (and Saccharomyces unisporus) were also promoted by lactate but at lower concentrations"

Ecological Interactions

Ecological interaction network for BioModels MODEL2204300001 Kefir Community Model Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).
Taxon
Cross-feeding
Mutualism
Syntrophy
Competition
Commensalism
Niche partitioning
Colonization facilitation
Strain competition
Predation

L. kefiranofaciens Proteolytic Support for L. mesenteroides

MUTUALISM

Source Taxon: Lactobacillus kefiranofaciens

Target Taxon: Leuconostoc mesenteroides

Metabolites: peptide (CHEBI:16670), amino acid (CHEBI:33709)

Evidence

  • PMID:33398099 - SUPPORT (IN_VITRO)
    "proteolytic activity of L. kefiranofaciens constitutes its beneficial impact on L. mesenteroides"
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "casein peptides as well as free amino acids restore the growth of L. mesenteroides"

L. mesenteroides Lactate Provisioning to L. kefiranofaciens

MUTUALISM

Source Taxon: Leuconostoc mesenteroides

Target Taxon: Lactobacillus kefiranofaciens

Metabolites: L-lactate (CHEBI:422)

Evidence

  • PMID:33398099 - SUPPORT (IN_VITRO)
    "lactate considerably boosted (circa three-fold) the growth of L. kefiranofaciens"
  • PMID:33398099 - PARTIAL (IN_VITRO)
    "early members open the niche for the followers by making available metabolites such as amino acids and lactate"

Acetobacter Lactate Cross-Feeding

CROSS_FEEDING

Source Taxon: Acetobacter fabarum

Metabolites: L-lactate (CHEBI:422)

Evidence

  • PMID:33398099 - SUPPORT (IN_VITRO)
    "The majority of the mutualistic interactions, 8 in total, involved A. fabarum and a lactate-producing partner, supporting its dependency on lactate and late onset during fermentation."
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "Acetobacter sp. benefited from lactate most between 7 and 12 mg/ml"

Kazachstania Lactate-Promoted Growth

CROSS_FEEDING

Source Taxon: Kazachstania exigua

Metabolites: L-lactate (CHEBI:422)

Evidence

  • PMID:33398099 - SUPPORT (IN_VITRO)
    "Kazachstania exigua (and Saccharomyces unisporus) were also promoted by lactate but at lower concentrations"
  • PMID:33398099 - SUPPORT (IN_VITRO)
    "the time-windows of yeast and Acetobacter growth align well with the beneficial or inhibitory range of lactate and acetate concentration"

Associated Datasets

Dataset Type Repository Accession
BioModels model file
SBML file deposited as MODEL2204300001. 		OTHER OTHER kefir_bacterium_1.xml
Primary publication
Publication describing metabolic cooperation and niche partitioning in kefir. 		OTHER OTHER PMID:33398099

External Resources

Name Repository Resource ID
BioModels entry
Metabolic cooperation and spatiotemporal niche partitioning in a kefir community. 		BIOMODELS MODEL2204300001
  • PMID:33398099 - SUPPORT (COMPUTATIONAL)
    "Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community."
  • PMID:41343683 - PARTIAL (COMPUTATIONAL)
    "we report here on our work updating, correcting and generating new SED-ML files for 1055 curated mechanistic models in BioModels..we used a wrapper architecture for interpreting SED-ML, and report verification results across five different ODE-based biosimulation engines"