CeMbio - The Caenorhabditis elegans Microbiome Resource.

G3 : Genes - Genomes - Genetics
Philipp DirksenBuck S. Samuel

Abstract

The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network mo...Continue Reading

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Citations

Feb 23, 2021·Journal of Toxicology and Environmental Health. Part B, Critical Reviews·Jessica H HartmanJoel N Meyer
Mar 3, 2021·Lab Animal·Cassandra BackesFilipe Cabreiro
Mar 19, 2021·Microbiology and Molecular Biology Reviews : MMBR·Leah J Radeke, Michael A Herman
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May 19, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Wei Shen, Hong Ren
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Aug 21, 2021·Environmental Microbiology·Barbara PeesCarola Petersen
Nov 2, 2021·Frontiers in Cellular and Infection Microbiology·Manish GroverMichalis Barkoulas

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Datasets Mentioned

BETA
PRJEB37895
PRJNA624308
PRJEB37101
PRJEB37035

Methods Mentioned

BETA
Fluorescence
PCR
amplicon sequencing

Software Mentioned

ModelFinder
Taxonkit
lima
QUAST
R packages ape
GToTree
DECIPHER
omics
illumina
DESeq2

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