Caenorhabditis elegans- microbe interactions are defined as any interaction that encompasses the association with microbes that temporarily or permanently live in or on the nematode C. elegans. The microbes can engage in a commensal, mutualistic or pathogenic interaction with the host. These include bacterial, viral, unicellular eukaryotic, and fungal interactions. In nature C. elegans harbours a diverse set of microbes. In contrast, C. elegans strains that are cultivated in laboratories for research purposes have lost the natural associated microbial communities and are commonly maintained on a single bacterial strain, Escherichia coli OP50. However, E. coli OP50 does not allow for reverse genetic screens because RNAi libraries have only been generated in strain HT115. This limits the ability to study bacterial effects on host phenotypes. The host microbe interactions of C. elegans are closely studied because of their orthologs in humans. Therefore, the better we understand the host interactions of C. elegans the better we can understand the host interactions within the human body.
Natural ecology
C. elegans is a well-established model organism in different research fields, yet its ecology however is only poorly understood. They have a short development cycle only lasting three days with a total life span of about two weeks.C. elegans were previously considered a soil-living nematode, but in the last 10 years it was shown that natural habitats of C. elegans are microbe-rich, such as compost heaps, rotten plant material, and rotten fruits. Most of the studies on C. elegans are based on the N2 strain, which has adapted to laboratory conditions. Only in the last few years the natural ecology of C. elegans has been studied in more detail and one current research focus is its interaction with microbes. As C. elegans feeds on bacteria (microbivory), the intestine of worms isolated from the wild is usually filled with a large number of bacteria. In contrast to the very high diversity of bacteria in the natural habitat of C. elegans, the lab strains are only fed with one bacterial strain, the Escherichia coli derivate OP50 . OP50 was not co-isolated with C. elegans from nature, but was rather used because of its high convenience for laboratory maintenance. Bleaching is a common method in the laboratory to clean C. elegans of contaminations and to synchronize a population of worms. During bleaching the worms are treated with 5N NaOH and household bleach, leading to the death of all worms and survival of only the nematode eggs. The larvae hatching from these eggs lack any microbes, as none of the currently known C. elegans-associated microbes can be transferred vertically. Since most laboratory strains are kept under these gnotobiotic conditions, nothing is known about the composition of the C. elegans microbiota. The ecology of C. elegans can only be fully understood in the light of the multiple interactions with the microorganisms, which it encounters in the wild. The effect of microbes on C. elegans can vary from beneficial to lethal.
Beneficial microbes
In its natural habitat C. elegans is constantly confronted with a variety of bacteria that could have both negative and positive effects on its fitness. To date, most research on C. elegans-microbe interactions focused on interactions with pathogens. Only recently, some studies addressed the role of commensal and mutualistic bacteria on C. elegans fitness. In these studies, C. elegans was exposed to various soil bacteria, either isolated in a different context or from C. elegans lab strains transferred to soil. These bacteria can affect C. elegans either directly through specific metabolites, or they can cause a change in the environmental conditions and thus induce a physiological response in the host. Beneficial bacteria can have a positive effect on the lifespan, generate certain pathogen resistances, or influence the development of C. elegans.