title: Caenorhabditis elegansas a Model for Microbiome Research.
abstract: The nematodeCaenorhabditis elegansis used as a central model system across biological disciplines. Surprisingly, almost all research with this worm is performed in the absence of its native microbiome, possibly affecting generality of the obtained results. In fact, theC. elegansmicrobiome had been unknown until recently. This review brings together results from the first three studies onC. elegansmicrobiomes, all published in 2016. Meta-analysis of the data demonstrates a considerable conservation in the composition of the microbial communities, despite the distinct geographical sample origins, study approaches, labs involved and perturbations during worm processing. TheC. elegansmicrobiome is enriched and in some cases selective for distinct phylotypes compared to corresponding substrate samples (e.g., rotting fruits, decomposing plant matter, and compost soil). The dominant bacterial groups include severalGammaproteobacteria(Enterobacteriaceae, Pseudomonaceae, andXanthomonodaceae) andBacteroidetes (Sphingobacteriaceae, Weeksellaceae, Flavobacteriaceae). They are consistently joined by several rare putative keystone taxa likeAcetobacteriaceae. The bacteria are able to enhance growth of nematode populations, as well as resistance to biotic and abiotic stressors, including high/low temperatures, osmotic stress, and pathogenic bacteria and fungi. The associated microbes thus appear to display a variety of effects beneficial for the worm. The characteristics of these effects, their relevance forC. elegansfitness, the presence of specific co-adaptations between microbiome members and the worm, and the molecular underpinnings of microbiome-host interactions represent promising areas of future research, for which the advantages ofC. elegansas an experimental system should prove of particular value.
authors.affiliation: Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine Houston, TX, USA.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA.
authors.forename: Maureen
authors.initials: M
authors.lastname: Berg
authors.affiliation: Zoological Institute, Christian-Albrechts University Kiel Kiel, Germany.
authors.forename: Katja
authors.initials: K
authors.lastname: Dierking
authors.affiliation: Centre National de la Recherche Scientifique, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, ENS, PSL Research University Paris, France.
authors.forename: Marie-Anne
authors.initials: MA
authors.lastname: Félix
authors.affiliation: Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Shapira
authors.affiliation: Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine Houston, TX, USA.
authors.forename: Buck S
authors.initials: BS
authors.lastname: Samuel
authors.affiliation: Zoological Institute, Christian-Albrechts University Kiel Kiel, Germany.
authors.forename: Hinrich
authors.initials: H
authors.lastname: Schulenburg
keywords: Caenorhabditis elegans; Enterobacter; Gluconobacter; Ochrobactrum; Pseudomonas; meta-analysis; microbiome; microbiota