CeMbio Caenorhabditis elegans Microbiome

Community ID CommunityMech:000159

Ecological State ENGINEERED

Environment Caenorhabditis elegans intestine
UBERON:0000160

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	NCBITaxon:2	CROSS_FEEDER SECONDARY_FERMENTER	N/A
PMID:32669368 - SUPPORT (IN_VITRO) "CEent1 Enterobacter hormaechei C. elegans N2 from mesocosm" PMID:32669368 - SUPPORT (IN_VITRO) "Based on the above analyses, we selected 12 isolates to constitute the CeMbio resource."
Caenorhabditis elegans	NCBITaxon:6239		N/A
PMID:32669368 - SUPPORT (IN_VITRO) "C. elegans adult is consistently colonized by at least 1,000 and usually more than 10,000 bacteria"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Multi-Strain C. elegans Gut Colonization

COLONIZATION_FACILITATION

Source Taxon: CeMbio v1.0 bacterial strain consortium

Target Taxon: Caenorhabditis elegans

Biological Processes:

multi-organism process (GO:0051704)
biological process involved in interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32669368 - SUPPORT (IN_VITRO)

"all CeMbio strains can establish themselves in the worm gut as community members"

Community Effects on Nematode Development

MUTUALISM

Source Taxon: CeMbio v1.0 bacterial strain consortium

Target Taxon: Caenorhabditis elegans

Biological Processes:

growth (GO:0040007)
biological process involved in interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32669368 - SUPPORT (IN_VITRO)

"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_PARTITIONING

Source Taxon: CeMbio v1.0 bacterial strain consortium

Biological Processes:

carbohydrate metabolic process (GO:0005975)
biological process involved in interspecies interaction between organisms (GO:0044419)

Evidence

PMID:32669368 - SUPPORT (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"
PMID:32669368 - SUPPORT (COMPUTATIONAL)

"The carbon source utilization by the whole CeMbio community is highlighted in yellow."

CeMbio Odor Preference and Food-Seeking

COLONIZATION_FACILITATION

Source Taxon: CeMbio v1.0 bacterial strain consortium

Target Taxon: Caenorhabditis elegans

Biological Processes:

chemotaxis (GO:0006935)
biological process involved in interspecies interaction between organisms (GO:0044419)

Evidence

PMID:38228683 - SUPPORT (IN_VITRO)

"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
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
CeMbio whole-genome sequencing BioProject European Nucleotide Archive genome sequencing data for the CeMbio bacterial strains.	GENOME	OTHER	PRJEB37895
CeMbio 16S amplicon sequencing datasets Public 16S amplicon sequencing datasets from CeMbio colonization experiments.	AMPLICON_16S	OTHER	PRJEB37101; PRJEB37154

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
PMID:32669368 - SUPPORT (OTHER) "all isolates are available from the Caenorhabditis Genetics Center (CGC, http://cgc.umn.edu; search for ‘CeMbio’ in strain descriptions)"

Environmental Factors

Factor	Value	Unit
NGM and peptone-free NGM plate environment	NGM or PFM plates seeded with CeMbio bacterial inoculum	N/A
PMID:32669368 - SUPPORT (IN_VITRO) "Synchronized C. elegans L1 animals were raised at 20° on 6 cm plates containing either NGM or peptone-free NGM (PFM)"
culture medium and temperature	LB at 25-28 C; nematodes at 20 C	N/A
PMID:32669368 - SUPPORT (IN_VITRO) "All CeMbio strains grow in Luria broth medium (LB; 10 g/l tryptone, 5 g/l yeast extract, 5 g/l NaCl"

Growth Media

Luria broth for CeMbio strain propagation

Temperature 25-28 C

Atmosphere AEROBIC

Preparation notes: CeMbio strains are cryopreserved in glycerol/LB and can be grown in LB or on LB agar before mixing into inocula for C. elegans plate assays.

Evidence

PMID:32669368

"All CeMbio strains grow in Luria broth medium (LB; 10 g/l tryptone, 5 g/l yeast extract, 5 g/l NaCl"

Nematode growth medium seeded with CeMbio

Temperature 20 C

Atmosphere AEROBIC

Preparation notes: Synchronized C. elegans L1 larvae were raised on NGM or peptone-free NGM seeded with CeMbio bacterial inoculum.

Evidence

PMID:32669368

"Around 50 synchronized C. elegans stage 1 larvae (L1) were raised at 20° on NGM"