Caenorhabditis elegans responses to bacteria from its natural habitats

Abstract

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.Caenorhabditis elegans | host-microbe interactions | ecology B iological organisms constantly live in contact with other organisms in a complex web of ecological interactions, which include prey-predator, host-parasite, competitive, or positive symbiotic relationships. Bacteria are now considered key players in multiple aspects of the biology of multicellular organisms (1-3). The richness and importance of these interactions were so far neglected because laboratory biology had succeeded in simplifying and standardizing the environment of the model organisms, providing in most cases a single microbe as a food source, and not necessarily even a naturally encountered one. The many aspects of organismal biology that were shaped by evolution in natural environments are thus undetectable in the artificial laboratory environment and can only be revealed in the presence of other interacting species. Examples include feeding behavior, metabolism of diverse natural food sources, interactions with natural pathogens that have shaped the organism's immune system, behavioral traits, and regulation of development and reproduction. At the genomic level, many individual genes may not be required in a standard laboratory environment but their role may be revealed by using more diverse and relevant environments (4, 5).The nematode Caenorhabditis elegans is a typical example of a model organism that has been disconnected from its natural ecology: although the species has been studied intensively in the laboratory for half a century, its habitat and natural ecology-what it naturally feeds on, its natural predators and pathogens,

In vitro and in vivo defensive effect of probiotic LAB against Pseudomonas aeruginosa using Caenorhabditis elegans model

“…The pathogenicity of P. aeruginosa against C. elegans has been reported elsewhere, slow killing of C. elegans by PA14 involves the colonization and proliferation of pathogen in the host gut. The widespread problems associated with PA14 is principally due to the production of a series of virulence factors including protease, elastase, pyocyanin, and alginate [1,16] and was confirmed in this study; the life span of worms fed with newly isolated LAB strains from fermented soy bean paste were significantly different from the life spans of those grown on E. coli OP50 (Figure 1(c)).…”

“…Caenorhabditis elegans are free-living nematodes that reside in the soil and rotten fruits, where they feed on bacteria [1,2]. When used for in vitro studies, they are normally cultured on a lawn of Escherichia coli ( E. coli OP50 ) on which they feed, leading to the presence of bacterial cells in pharynx and the intestine, which frequently appears distended; it has been widely applied as an experimental system for biological studies due to its transparency, short reproductive cycle, ease of cultivation, and suitability for genetic analysis [2].…”

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“…In the last few years, different studies have focused on the characterization of wild bacterial food sources and their impact on C. elegans metabolism [36][37][38]. For example, the Gram-positive bacterium B. subtilis has been used as an alternative worm diet in a number of studies.…”

A peek into the microbiome of two free-living aquatic nematodes Anticoma & Daptonema

“…The third is the marine nematodes with chemoautotrophic or methanotrophic bacteria, which are studied for their unique associations enabling them to take advantage of the different metabolic pathways available to their symbionts [8,9,10] . The remaining, relatively limited studied, focus on plant parasitic and free-living nematodes and their associated bacteria [11,12,13,14] . Of these the most recent additions are the exploration of the microbiome of free-living nematode Litoditis marina complex by Derycke et al [15] and the most comprehensive look at the microbiome of the model species -Caenorhabditis elegans (Maupas) [12,13,14] .…”

“…The remaining, relatively limited studied, focus on plant parasitic and free-living nematodes and their associated bacteria [11,12,13,14] . Of these the most recent additions are the exploration of the microbiome of free-living nematode Litoditis marina complex by Derycke et al [15] and the most comprehensive look at the microbiome of the model species -Caenorhabditis elegans (Maupas) [12,13,14] . The extensive data accrued on C. elegans has opened unprecedented opportunities to explore the role of associated microbiome on nematode fitness using genetic tools.…”