CeMbio is a defined, ecologically informed twelve-strain bacterial community representing the natural Caenorhabditis elegans microbiome. The v1.0 community includes Enterobacter hormaechei CEent1, Lelliottia amnigena JUb66, Acinetobacter guillouiae MYb10, Sphingomonas molluscorum JUb134, Stenotrophomonas indicatrix JUb19, Pseudomonas lurida MYb11, Pseudomonas berkeleyensis MSPm1, Comamonas piscis BIGb0172, Pantoea nemavictus BIGb0393, Ochrobactrum vermis MYb71, Sphingobacterium multivorum BIGb0170, and Chryseobacterium scophthalmum JUb44. The resource pairs a genetically tractable host with cultured, genome-sequenced, CGC-distributed commensal isolates that colonize the worm gut as a community, alter nematode developmental timing, and support follow-up behavioral and metabolic studies with the same reference composition.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| CeMbio v1.0 bacterial strain consortium — ontology label: Bacteria | NCBITaxon:2 · TaxonMech · TraitMech |
CROSS_FEEDER
SECONDARY_FERMENTER
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N/A |
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| Caenorhabditis elegans | NCBITaxon:6239 · TaxonMech · TraitMech | N/A | |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Multi-Strain C. elegans Gut Colonization
CeMbio members colonized C. elegans individually and in mixtures, with medium-, time- and strain-dependent abundance. This establishes gut association, not member-to-member colonization facilitation or mediation of host development.
Source Taxon: CeMbio v1.0 bacterial strain consortium
Target Taxon: Caenorhabditis elegans
Biological Processes:
- multi-organism process (GO:0044419 · PathwayMech)
Evidence
-
PMID:32669368 - SUPPORT (IN_VIVO)"all CeMbio strains can establish themselves in the worm gut as community members"
Community Effects on Nematode Development
The complete CeMbio mixture accelerated developmental timing relative to OP50 food in N2 and CB4856 worms. Individual members had heterogeneous effects. Adult-fraction timing is not direct biomass growth or evidence that both host and bacteria benefit.
Source Taxon: CeMbio v1.0 bacterial strain consortium
Target Taxon: Caenorhabditis elegans
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:32669368 - SUPPORT (IN_VIVO)"the CeMbio community as a whole significantly enhanced growth rates for both host strains compared to growth on E. coli OP50"
Strain-Resolved Metabolic Diversity
NICHE_PARTITIONINGCOMPUTATIONAL - gapseq/FBA models and substrate phenotyping distinguish member metabolic capacities. PARTIAL - the authors propose niche differentiation as a contributor to assembly; pathway counts did not explain individual colonization or community competitive fitness. Model agreement after training is not independent validation or measured gut flux.
Source Taxon: CeMbio v1.0 bacterial strain consortium
Biological Processes:
- carbohydrate metabolic process (GO:0005975 · PathwayMech)
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
HYPOTHESIZED - differentiated nutrient-use capacities could favor community assembly. The source proposes this explanation but does not demonstrate that these capacities cause gut colonization patterns.
Evidence
-
PMID:32669368 - PARTIAL (COMPUTATIONAL)"The greatest differences in the predicted metabolic capabilities among the strains is observed in both biosynthesis and degradation of amino acids, carbohydrates, cofactors and vitamins"
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PMID:32669368 - PARTIAL (COMPUTATIONAL)"The carbon source utilization by the whole CeMbio community is highlighted in yellow."
CeMbio Odor Preference and Food-Seeking
Individual-member odor assays favored JUb66, CEent1 and BIGb0393 relative to OP50. Inaccessible bacteria on the lid supplied volatile cues; these were not mixed-community, feeding or colonization assays. The preferred members are not all Enterobacteriaceae.
Source Taxon: CeMbio v1.0 bacterial strain consortium
Target Taxon: Caenorhabditis elegans
Biological Processes:
- chemotaxis (GO:0006935 · PathwayMech)
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:38228683 - SUPPORT (IN_VIVO)"We set out to measure the preference of C. elegans for the odors of the twelve bacterial species that comprise CeMbio."
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Exact-composition publication - CeMbio twelve-strain microbiome resource
Primary CeMbio publication defining the twelve-strain reference community, member selection, colonization assays, strain genomes, diagnostic primers, and metabolic models. |
OTHER | OTHER | PMID:32669368 |
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Exact-composition publication - CeMbio odor preference study
Follow-up publication studying C. elegans odor preference toward the same twelve CeMbio reference strains. |
PHENOTYPE | OTHER | PMID:38228683 |
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CeMbio whole-genome sequencing BioProject
European Nucleotide Archive genome sequencing data for the CeMbio bacterial strains. |
GENOMICS | OTHER | PRJEB37895 |
|
CeMbio 16S amplicon sequencing datasets
Public 16S amplicon sequencing datasets from CeMbio colonization experiments. |
AMPLICON_16S | OTHER | PRJEB37101; PRJEB37154 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which metabolic functions mediate gut assembly, and how do diet quality and volatile responses relate to development?
PMID:32669368 proposes metabolic differentiation; PMID:38228683 assays inaccessible individual-member odors. Neither isolates gut colonization as the mediator of developmental timing. Preserve the broad Bacteria grounding pending separate roster curation and #615 host-system modeling.
Attaches to: ecological_interactions#Multi-Strain C. elegans Gut Colonization, ecological_interactions#Community Effects on Nematode Development, ecological_interactions#Strain-Resolved Metabolic Diversity, ecological_interactions#CeMbio Odor Preference and Food-Seeking
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
CeMbio strain resource at Caenorhabditis Genetics Center
CGC distributes CeMbio strains; the primary paper instructs users to search for CeMbio in strain descriptions. |
OTHER | CeMbio |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| NGM and peptone-free NGM plate environment | NGM or PFM plates seeded with CeMbio bacterial inoculum | N/A |
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| culture medium and temperature | LB at 25-28 C; nematodes at 20 C | N/A |
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Growth Media
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