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Clostridium phytofermentans-E. coli Cellobiose Biofilm Consortium

Community ID CommunityMech:000196
Ecological State ENGINEERED
Environment laboratory cellobiose biofilm consortium
ENVO:01001405

A rationally designed two-member artificial consortium composed of Clostridium phytofermentans ISDg, currently represented in NCBI Taxonomy as Lachnoclostridium phytofermentans ISDg, and Escherichia coli K-12 MG1655. The community was built to improve conversion of cellulose-derived sugars into ethanol, biomass, and other bioproduct-relevant outputs through division of labor between a cellulolytic obligate anaerobe and a facultative anaerobe. It is DOE-relevant because it models consolidated lignocellulosic bioprocessing, cellobiose conversion, biofilm oxygen partitioning, and cross-feeding mechanisms that can improve cellulosic fuel and chemical production.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Clostridium phytofermentans ISDg NCBITaxon:357809
PRIMARY_DEGRADER
COMMON
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "primary resource specialist was Clostridium phytofermentans"
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "C. phytofermentans ISDg (ATCC 700394)"
Escherichia coli K-12 MG1655 NCBITaxon:511145
SECONDARY_FERMENTER CROSS_FEEDER
COMMON
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "secondary-resource specialist was Escherichia coli"
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "E. coli K-12 MG1655 were used for all experiments"

Ecological Interactions

Ecological interaction network for Clostridium phytofermentans-E. coli Cellobiose Biofilm Consortium 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

Cellobiose Hydrolysis And Glucose Scavenging Feedback

CROSS_FEEDING

Source Taxon: Clostridium phytofermentans ISDg

Target Taxon: Escherichia coli K-12 MG1655

Metabolites: cellobiose (CHEBI:17057), glucose (CHEBI:17234)

Biological Processes:

Evidence

  • PMID:33268782 - SUPPORT (IN_VITRO)
    "E. coli consumed inhibitory byproducts from cellobiose catabolism"
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "released cellobiase enzyme which hydrolyzed cellobiose into glucose extracellularly"

Reciprocal Necromass Catabolism

CROSS_FEEDING

Source Taxon: Clostridium phytofermentans ISDg

Target Taxon: Escherichia coli K-12 MG1655

Metabolites: peptide (CHEBI:16670)

Biological Processes:

Evidence

  • PMID:33268782 - SUPPORT (IN_VITRO)
    "E. coli necromass enhanced C. phytofermentans growth"
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "C. phytofermentans necromass aided E. coli growth"

Biofilm Oxygen Partitioning

COLONIZATION_FACILITATION

Source Taxon: Escherichia coli K-12 MG1655

Target Taxon: Clostridium phytofermentans ISDg

Metabolites: oxygen (CHEBI:15379)

Biological Processes:

Evidence

  • PMID:33268782 - SUPPORT (IN_VITRO)
    "E. coli consuming O2, creating an anoxic environment for C. phytofermentans"
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "C. phytofermentans resided primarily in the anoxic bottom of the biofilm"

Associated Datasets

Dataset Type Repository Accession
Lachnoclostridium phytofermentans ISDg genome BioProject
NCBI BioProject for the complete genome of the C. phytofermentans ISDg member. 		GENOME NCBI_BIOPROJECT PRJNA16184
Escherichia coli K-12 MG1655 reference genome
Reference genome assembly for the E. coli K-12 MG1655 member. 		GENOME OTHER GCA_000005845.2

External Resources

Name Repository Resource ID
Primary publication - artificial cellobiose biofilm consortium
PubMed record for the primary publication reporting the C. phytofermentans and E. coli artificial consortium. 		OTHER PMID:33268782
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "Artificial consortium demonstrates emergent properties"
Full-text article - npj Biofilms and Microbiomes
Open-access full text containing methods, medium recipe, biofilm assays, and mechanistic interpretation for the exact two-member consortium. 		OTHER doi:10.1038/s41522-020-00170-8
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "C. phytofermentans, and E. coli binary consortia with necromass catabolism"

Environmental Factors

Factor Value Unit
Modified GS-2 medium mGS-2 N/A
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "All reported planktonic and biofilm growth were performed in modified GS-2 media"
Temperature 37 C
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "150 revolutions per minute and 37"
Anoxic and oxic biofilm regimes anoxic, oxic, and anoxic-to-oxic switch N/A
  • PMID:33268782 - SUPPORT (IN_VITRO)
    "an anoxic to oxic switch (AOS)"

Growth Media

Modified GS-2 cellobiose-glycerol medium

pH 6.9
Temperature 37 C
Atmosphere ANAEROBIC

Composition

Component Concentration Unit CHEBI
cellobiose 5 g/L CHEBI:17057
glycerol 2.3 g/L CHEBI:17754
yeast extract 1 g/L N/A
urea 2.1 g/L CHEBI:16199
sodium citrate 3.0 g/L CHEBI:30769
MOPS 10 g/L N/A
trace metal solution 10 mL/L N/A

Preparation notes: The published medium recipe also included phosphate buffer salts, magnesium chloride, calcium chloride, ferrous sulfate, resazurin, and a trace metal solution. Biofilms were transferred to fresh medium plates every 2 days.

Evidence

PMID:33268782

"cellobiose and 10"

PMID:33268782

"Initial OD600 of each strain was 0.01 OD600 for C. phytofermentans and 0.001 for E. coli"