Caenorhabditis elegans responses to bacteria from its natural habitats.
Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114;
Buck S
0000-0002-4347-3997
BS
Samuel
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114;
Holli
H
Rowedder
CNRS, INSERM, Institute of Biology Valrose, University of Nice Sophia Antipolis, Parc Valrose, 06108 Nice, France;
Christian
C
Braendle
Institute of Biology of the Ecole Normale Supérieure, CNRS UMR8197, Ecole Normale Supérieure, INSERM U1024, 75005 Paris, France ruvkun@molbio.mgh.harvard.edu felix@biologie.ens.fr.
Marie-Anne
MA
Félix
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; ruvkun@molbio.mgh.harvard.edu felix@biologie.ens.fr.
Gary
G
Ruvkun
D000818:Animals; D017173:Caenorhabditis elegans / Q000382:microbiology* / Q000502:physiology; D027845:Malus / Q000382:microbiology; D059013:Microbial Consortia
Caenorhabditis elegans; ecology; host–microbe interactions