We acknowledge financial support from the German Science Foundation (projects A1.1 and A1.2 of the Collaborative Research Center 1182 on the Origin and Function of Metaorganisms). We thank the members of the Schulenburg lab for their advice and support.

1. Preparation of buffers and media
<ol>
	<li>Prepare S-buffer by adding 5.85 g of NaCl, 1.123 g of K2HPO4, 5.926 g of KH2PO4, and 1 L of deionized H2O to a flask and autoclave for 20 min at 121 &#176;C.</li>
	<li>Prepare a viscous medium by adding S-buffer containing 1.2% (w/v) hydroxymethylcellulose (the substance causing viscosity of the medium), 5 mg/mL cholesterol, 1 mM MgSO4, 1 mM CaCl2, and 0.1% (v/v) acetone. Autoclave and stir the viscous medium until it is completely homogeneous. 
	NOTE: This can take multiple hours. Also, S-buffer can be directly prepared and added to the viscous medium without prior sterilization.</li>
	<li>Prepare M9-buffer by adding 3 g of KH2PO4, 6 g of NA2HPO4&#183;2 H2O, 5 g of NaCl, and 1 L of deionized H2O to a 1 L flask. Autoclave the solution, and after cooling, add 1 mL of 1 M MgSO4 (123.24&#160;g of MgSO4&#183;7H2O in 500 mL of deionized H2O, filter sterilized).</li>
	<li>Prepare 10% (v/v) Triton X-100 stock solution by mixing 5 mL of Triton X-100 with 45 mL of M9-buffer. Filter-sterilize the solution using a 0.2 &#181;m filter.</li>
	<li>Prepare M9-buffer with Triton X-100 (M9-T) by adding 2.5 mL of the 10% (v/v) Triton X-100 stock solution to 1 L of M9-buffer after autoclaving to obtain 0.025% (v/v) M9-T.</li>
	<li>Prepare 30% (v/v) glycerol in S-buffer by mixing 15 mL of sterile 100% glycerol and 35 mL of sterile S-buffer in a 50 mL tube.</li>
</ol>
2. Preparation of environmental samples (Figure 1)
<ol>
	<li>Collect environmental samples like compost or rotten fruits and place each sample in an individual plastic bag, tube, or other clean container. 
	NOTE: In order to attract nematodes, apples can be placed on compost several weeks prior to the sampling.</li>
	<li>Spread pieces of the environmental sample evenly in an empty, sterile, 9 cm Petri dish. 
	NOTE: Samples with higher levels of decay are more likely to contain C. elegans. Optionally, a Petri dish filled with peptone-free agar medium (PFM) can be used to increase contrast.</li>
	<li>Cover the sample carefully with approximately 20 mL of sterile viscous medium. 
	NOTE: Nematodes float to the surface within 1-2 h. The viscous medium slows down the movement of the worms and makes it easier to sample them. Sterile M9-buffer can be used as an alternative, however, worm movement will be faster.</li>
</ol>
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/64249/64249fig01.jpg" /> 
Figure 1: Isolation of nematodes from substrates. Substrate samples are placed in empty Petri dishes and covered with viscous medium to flush out nematodes. Nematodes are transferred to M9-T and repeatedly washed to remove bacteria from the outside. Individual nematodes can be used for DNA isolation, isolation of associated bacteria, or placed on agar plates to culture worm populations. Figure created with BioRender.com. <a href="https://www.jove.com/files/ftp_upload/64249/64249fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
3. Isolation of Caenorhabditis nematodes (Figure 1)
<ol>
	<li>Search for Caenorhabditis nematodes using a dissecting microscope, following the guidelines presented in the WormBook chapter on the isolation of C. elegans and related nematodes by Barri&#232;re and F&#233;lix27. 
	NOTE: Caenorhabditis hermaphrodites/females have a gut of light brown color (under transmitted illumination). Moreover, the gut cells have large cell nuclei, which are visible as white dots. By contrast, other nematode species often have a dark brown gut and may show anteroposterior asymmetry in pigment intensity and usually no visible nuclei. The vulva of adult Caenorhabditis hermaphrodites/females is found in the middle of the animal. This vulva localization is not always shown by other nematode taxa. Caenorhabditis nematodes possess two pharyngeal bulbs, which are both visible with sufficient magnification and transmitted illumination and contrast with many other nematode taxa. Caenorhabditis nematodes have a pointed tail, whereas some other nematodes have a round tail.</li>
	<li>Collect the Caenorhabditis nematodes under a dissecting microscope in as little liquid as possible using a 20-100 &#181;L pipette. Transfer the collected nematodes directly to 1-3 mL of sterile M9-T in a sterile 3 cm Petri dish for washing the worms to remove non-attached microbes (step 3.3) or, alternatively, transfer individual worms onto a plate with nematode growth medium (NGM) to establish a worm population (step 3.4).</li>
	<li>Wash the nematodes to remove microbes from the outside of the nematode. 
	NOTE: This protocol enriches for gut bacteria but does not completely eliminate bacteria sticking to the worm cuticle.
	<ol>
		<li>Incubate the nematodes for 10-15 min in M9-T.</li>
		<li>Pipette the nematodes in as little liquid as possible into 1-3 mL of fresh M9-T in a new sterile 3 cm Petri dish.</li>
		<li>Repeat the incubation and transfer the nematodes to fresh M9-T two more times. 
		NOTE: The following steps can be done either with individual worms or with worm populations. The worms can now be used for the characterization of C. elegans and associated microbes, as well as the isolation of bacteria (steps 4 and 5). Alternatively, they can be transferred individually to NGM plates to establish a worm population (step 3.4).</li>
	</ol>
	</li>
	<li>To obtain a worm population, pipette an individual nematode to a NGM plate. 
	NOTE: Only hermaphroditic nematodes such as C. elegans or C. briggsae are able to produce offspring from single worms. However, single worms of other species may still produce offspring if they were already mated.
	<ol>
		<li>Naturally isolated nematodes usually contain bacteria in their gut, which they shed onto the NGM plates, where these bacteria grow and are available as food for C. elegans. Do not add separate food organisms like the standard laboratory food organism, E. coli strain OP50. 
		NOTE: Rearing worms on plates influences the composition of the associated bacterial community, yet the composition is still comparable to that of the natural C. elegans isolates6,7.</li>
		<li>Allow the nematodes to proliferate for up to 10 days at the appropriate temperature (e.g., 15-20 &#176;C for temperate locations). Freeze these nematodes (step 3.5) or use them for the characterization of C. elegans and associated microbes as well as the&#160;isolation of microbes (steps 4 and 5).</li>
	</ol>
	</li>
	<li>Freezing nematodes for long-term storage
	<ol>
		<li>Leave the nematodes on plates until the food bacteria have disappeared, and there are mainly small larval stages on the plates. Wash the worms off the plates in 1.5 mL of S-buffer.</li>
		<li>Mix 500 &#181;L of worm-containing S-buffer thoroughly with 500 &#181;L of 30% (v/v) glycerol in S-buffer in a sterile 2 mL tube. Freeze the tubes promptly at -80 &#176;C for long-term storage, otherwise the glycerol may harm the nematodes.</li>
	</ol>
	</li>
</ol>
4. Preparation of the worms for molecular identification of C. elegans and microbes
<ol>
	<li>For unbiased identification of nematode-associated microbes, prepare a 96-well plate with three sterile 1 mm beads, 19.5 &#181;L of PCR-buffer, and 0.5 &#181;L of Proteinase K (20 mg/mL) per well. Pipette an individual, washed nematode to each well, transferring as little liquid as possible.</li>
	<li>Worm populations can also be used. For this, wash the worms from the plates with M9-buffer and transfer ~300 &#181;L of worm-containing M9-buffer to 2 mL tubes with 10-15 beads.</li>
	<li>Break up the nematodes using a bead homogenizer (e.g., bead-beating for 3 min at 30 Hz). Centrifuge the plate or tubes briefly to get the liquid to the bottom (e.g., for 10 s at 8000 x g at room temperature [RT]).</li>
	<li>Identification of C. elegans
	<ol>
		<li>Isolate the DNA of individual nematodes by heating the samples in a PCR cycler for 1 h at 50 &#176;C and 15 min at 95 &#176;C. Isolate the DNA of worm populations using any isolation method of choice (example protocols of different isolation methods using commercial kits7,9). Freeze the DNA at -20 &#176;C for long-term storage.</li>
		<li>For the identification of C. elegans, use the DNA and the primer pair nlp30-F (Table 1, 5&#39;-ACACATACAACTGATCACTCA-3&#39;) and nlp30-R (Table 1, 5&#39;-TACTTTCCCCATCCGTATC-3&#39;) in a PCR, following the instructions of a Taq supplier of choice.</li>
		<li>Use the following PCR conditions: initial denaturation step at 95 &#176;C for 2 min, followed by 35 cycles of 95 &#176;C for 45 s, 55 &#176;C for 30 s, 72 &#176;C for 1 min, and a final elongation step at 72 &#176;C for 5 min. C. elegans produces a 154 bp PCR product.</li>
	</ol>
	</li>
	<li>Characterize the nematode-associated bacteria via 16S amplicon sequencing of the V3-V4 region, using the isolated DNA.
	<ol>
		<li>Prepare a 16S library with the 16S primers of choice and follow the library preparation kit protocol. One option is to use the primers 341F (Table 1, 5&#39;-CCTACGGGNGGCWGCAG-3&#39;) and 806R (Table 1, 5&#39;-GACTACHVGGGTATCTAATCC-3&#39;) covering the V3-V4 region of the 16S rRNA gene, which results in sequences that can be classified with standard databases with good resolution7. 
		NOTE: The amount of input DNA is critical in this step. DNA acquired from single worms is going to be much less than that obtained from worm populations. For single worms, it might be necessary to increase the amount of input DNA or to increase the amount of PCR cycles7.</li>
		<li>Libraries can be sequenced on a sequencing platform using a suitable sequencing kit. 
		NOTE: Here, the MiSeq platform is used with a suitable MiSeq Reagent Kit. The reagents are improved constantly and should be chosen to the newest standards.</li>
	</ol>
	</li>
</ol>
5. Isolation and cultivation of nematode-associated bacteria (Figure 2)
<ol>
	<li>To isolate bacteria, prepare a 96-well plate with three sterile 1 mm beads, 20 &#181;L of M9-buffer per well, and pipette an individual, washed nematode to each well, transferring as little liquid as possible. 
	NOTE: Alternatively, worm populations can be washed from the plates with M9-buffer and ~300 &#181;L of worm-containing M9-buffer can be transferred to 2 mL tubes with 10-15 beads. In all cases, the worms should come from a culture that was identified to be C. elegans using steps 4.1-4.4.</li>
	<li>Break up the nematodes using a bead homogenizer (e.g., bead-beating for 3 min at 30 Hz). Centrifuge the plate or tubes briefly to get the liquid to the bottom (e.g., for 10 s at 8000 x g at RT). 
	NOTE: The usage of this method led to the isolation of bacterial taxa similar to those revealed by 16S rDNA amplicon sequencing7, suggesting that the described bead-beating leaves most bacterial cells intact.</li>
	<li>Collect the supernatant, serially dilute it at 1:10, and plate up to 100 &#181;L onto 9 cm agar plates.
	<ol>
		<li>To ensure that most bacteria can be cultivated, use a variety of alternative media with different nutrient compositions, including diluted trypticase soy agar (TSA, 1:10 dilution), MacConkey agar, Sabouraud glucose agar, potato dextrose agar, or yeast peptone dextrose agar.</li>
	</ol>
	</li>
	<li>Incubate the plates at the average temperature conditions of the sampling location (e.g., temperatures between 15-20 &#176;C for temperate locations) for 24-48 h.</li>
	<li>Use the standard three-streak technique and a sterile loop to obtain pure bacterial cultures (Figure 2).
	<ol>
		<li>Pick a single colony from a plate using a sterile loop or toothpick and streak it out onto a new agar plate containing the same agar medium as used for purification. Make sure to use only roughly 1/3 of the plate.</li>
		<li>Either use a new sterile loop or sterilize a reusable loop and drag it through the first streak to create a second streak on another 1/3 of the same plate.</li>
		<li>Repeat this step by dragging a sterile loop through the second streak.</li>
		<li>Incubate the plate at the same growth conditions used for isolation. This technique must result in single colonies growing in the area of the third streak. 
		NOTE: It might be necessary to repeat the purification step multiple times as natural isolates tend to form biofilms and/or aggregates.</li>
	</ol>
	</li>
	<li>Grow the pure colonies in a liquid medium (of the same type as the agar medium) using the same temperature and growth time as above (step 5.4)</li>
	<li>Prepare bacteria stocks by adding 300 &#181;L of the bacterial culture to 200 &#181;L of 86% (v/v) glycerol (in the respective growth medium, e.g., TSB) and pipette up and down to mix properly. Alternatively, prepare DMSO stocks by mixing 50 &#181;L of bacterial culture with 50 &#181;L of 7% (v/v) DMSO. Freeze at -80 &#176;C for long-term storage.</li>
	<li>Characterizing bacteria using sequencing of the full 16S ribosomal RNA gene
	<ol>
		<li>Extract the bacterial DNA from pure liquid cultures using a suitable technique (e.g., a DNA extraction kit; from experience, a CTAB-based extraction protocol works very well22).</li>
		<li>Amplify the 16S rRNA gene using the primers 27F (Table 1, 5&#39;-GAGAGTTTGATCCTGGCTCAG-3&#39;) and 1495R (Table 1, 5&#39;-CTACGGCTACCTTGTTACGA -3&#39;)28 and the following PCR conditions: 95 &#176;C, 2 min, 22x (95 &#176;C, 30 s; 55 &#176;C, 30 s; 72 &#176;C, 100 s), and a final extension period at 72 &#176;C, 5 min.</li>
		<li>In order to acquire the full sequences, additionally use two internal sequencing primers, such as 701F (Table 1, 5&#39;-GTGTAGCGGTGAAATGCG-3&#39;) and 785R (Table 1, 5&#39;-GGATTAGATACCCTGGTAGTCC-3&#39;)6.</li>
	</ol>
	</li>
</ol>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/64249/64249fig2v2.jpg" /> 
Figure 2: Species identification and isolation of individual bacteria. Individual nematodes are broken up using a bead homogenizer, and DNA is isolated for species determination via PCR or sequencing. Alternatively, the broken-up nematode material is serially diluted and plated onto growth medium plates. Plates are incubated until bacterial colonies appear, and single colonies are streaked to new plates to obtain pure cultures. Single colonies of the pure cultures are used to grow liquid bacterial cultures for the preparation of bacterial stocks for long-term storage at -80 &#176;C. Figure created with BioRender.com. <a href="https://www.jove.com/files/ftp_upload/64249/64249fig2v2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+C.+elegans+and+related+nematodes.">Isolation of C. elegans and related nematodes.</a> WormBook. , 1-19 (2014).</li><li>Weisburg, W. G., Barns, S. M., Pelletier, D. A., Lane, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=16S+ribosomal+DNA+amplification+for+phylogenetic+study.">16S ribosomal DNA amplification for phylogenetic study.</a> Journal of Bacteriology. 173 (2), 697-703 (1991).</li><li>Brenner, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+genetics+of+Caenorhabditis+elegans.">The genetics of Caenorhabditis elegans.</a> Genetics. 77 (1), 71-94 (1974).</li><li>Crombie, T. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Local+adaptation+and+spatiotemporal+patterns+of+genetic+diversity+revealed+by+repeated+sampling+of+Caenorhabditis+elegans+across+the+Hawaiian+Islands.">Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands.</a> Molecular Ecology. 31 (8), 2327-2347 (2022).</li><li>Haber, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolutionary+history+of+Caenorhabditis+elegans+inferred+from+microsatellites:+Evidence+for+spatial+and+temporal+genetic+differentiation+and+the+occurrence+of+outbreeding.">Evolutionary history of Caenorhabditis elegans inferred from microsatellites: Evidence for spatial and temporal genetic differentiation and the occurrence of outbreeding.</a> Molecular Biology and Evolution. 22 (1), 160-173 (2004).</li><li>Watson, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolic+network+rewiring+of+propionate+flux+compensates+vitamin+B12+deficiency+in+C.+elegans.">Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.</a> eLife. 5, 17670 (2016).</li></ol>

We declare that we have no conflict of interest.

The nematode Caenorhabditis elegans is one of the most intensively studied model organisms in biological research. It was introduced by Sydney Brenner in the 1960s, originally for understanding the development and the function of the nervous system29. Since then, C. elegans has become a powerful model for studying fundamental processes across all biological disciplines, including behavioral biology, neurobiology, aging, evolutionary biology, cell biology, developmental biology, and immunology. Its success is based on a unique combination of advantageous properties, including a short generation time of approximately 3 days, ease of cultivation, transparent body (permitting efficient phenotyping), survival of freezing, efficient sterilization and developmental synchronization, and also efficient methods for genetic manipulation by mutagenesis, CRISPR-Cas, or RNAi. Today, C. elegans is studied in approximately 1,500 laboratories worldwide. When Sydney Brenner first established C. elegans as a model system in the laboratory, he grew the bacterivore nematode on the Gram-negative bacterium Escherichia coli OP50 as a food source. Ever since, C. elegans has been maintained in monoxenic culture on E. coli OP50 in laboratories all over the world29. Moreover, C. elegans populations are habitually synchronized or de-contaminated by a bleaching procedure that is only survived by sterile eggs and no associated microbe. It is thus easy to generate sterile animals that then can be exposed to individual bacteria under highly controlled conditions. However, as a result of these standardized C. elegans laboratory maintenance protocols, almost all studies on C. elegans biology were done in the absence of its naturally associated bacteria. In fact, information on the diversity of naturally associated microorganisms was only published in 20164,5,6, and the exact diversity of associated microbes is still not fully explored.
The described methods will help to further characterize the diversity of microbes which are associated with C. elegans in nature. These microbes are likely important determinants of the nematode&#39;s life history and should thus be an essential resource for future work with this worm. The described methods are an updated version of the only previously published methods for isolating microbes from natural C. elegans samples collected directly from the field6,7. The protocol takes advantage of the fact that C. elegans inhabits decomposing plant matter in nature. Such rotting material is rich in microbes, which serve as food for C. elegans and are likely to fulfill other functions, such as immune protection (i.e., protection against pathogens)5,6,11,13,14. The first key step is thus to obtain suitable substrates for worm isolation. Suitability may depend on the time of the year; in Northern Germany, C. elegans is primarily found from September until November2. This is the time when fruits like apples or pears become available and start rotting on the ground. The exact time is likely to vary among geographic regions23,24,25,30. Any plant material appears suitable for C. elegans, as long as it shows a high degree of decomposition and thus bears a rich microbial community-except for material dominated by fungi, which often are pathogenic to C. elegans1. Moreover, C. elegans is usually particularly common when general humidity is not too low2. To date, systematic information is lacking on whether Caenorhabditis nematodes vary in abundance in plant material from industrial versus organic farming or surface versus deeper layer of detritus or dependence on rain or not.
Once the samples have been collected and transferred to the lab, worms need to be &#34;lured&#34; out of their substrates. This has been achieved with a couple of different approaches, for example, by worm extraction through Baermann funnels31 or the placement of samples on an agar plate containing the E. coli laboratory food as an attractant in the middle27. In our experience, the protocol described here is generally faster and more efficient. It is based on the idea that the substrate samples are submerged in a liquid or viscous solution, which efficiently forces the worms out of the substrate and up to the surface of the liquid, from where they can be easily collected. The viscosity of the medium is not absolutely needed, but it slows down the movement of the worms and thus may make it easier to collect them. The efficient collection of worms is facilitated when the liquid is added carefully to the substrate, thereby avoiding solubilization of any humous substances, which can darken the liquid and may make it difficult to see the nematodes.
The next challenge is to identify C. elegans. Some morphological features can help to distinguish Caneorhabditis worms from other nematodes27, yet are insufficient for precise species identification. Rotting plant matter often contains other similar-looking nematodes, including congeneric species, such as C. briggsae or C. remanei2,6,23,25, which are impossible to distinguish at first sight. Therefore, C. elegans can best and most reliably be identified with the help of diagnostic PCR using species-specific primers2,6,7, as described in the protocol. In this context, it can be useful to establish a proliferating population of the isolated natural C. elegans in the lab, for example, on standard NGM plates. The natural C. elegans usually bring along associated bacteria, which are shedded onto the NGM plates, where the bacteria usually grow, subsequently serving as food for the worms6,7. Although the exact composition of the associated microbes changes during C. elegans proliferation on plates, it is still comparable to that of immediately characterized natural nematode samples6,7, and thus is a useful compromise that allows the isolation of both C. elegans and the associated microbes.
Once C. elegans is successfully identified, then the nematodes or the associated substrate samples can be used for the isolation and characterization of the associated microbes. To ensure that the microbes are truly associated with C. elegans in nature, it is of prime importance to avoid contaminations across all steps of the protocols. Collection of compost and fruit samples in the field should be done with particular care by the researcher, using sterilized material. All processing of material in the laboratory must ensure a high level of hygiene and again sterilized plastic ware and buffers. To reduce the contamination risk, all laboratory work should ideally be performed in a separate laboratory room, which is exclusively dedicated to the isolation of the microbes. As an alternative, all work with open plates, tubes, or other containers should be done in a laminar flow cabinet. To assess the contamination risk, appropriate control samples (e.g., without samples or without worms) should be processed in parallel. Moreover, a variety of different media could be used to ensure that all different types of bacteria with their different growth requirements can be cultivated and isolated. Nevertheless, previous work indicated that all thus far isolated bacteria, which are associated with natural C. elegans isolates, readily grow on NGM and TSA plates. Thus, it may be sufficient to focus on these media.
The isolated and characterized microbes will contribute to an improved understanding of the natural history of C. elegans. More importantly, to date, it is not well understood how C. elegans responds to its naturally associated microbes, which molecular processes are involved, and which functions mediate the worm&#39;s interaction with its microbial associates. One of the main exceptions is the comprehensive work by the Walhout group on the interaction between C. elegans and Comamonas DA 1877. It revealed vitamin B12 as a central metabolite provided by the bacterium, which influences worm gene expression, fertility, lifespan, and development15,16,17. The Walhout group further demonstrated that the vitamin B12 effect on fertility and development depends on the methionine/S-Adenosylmethionine cycle and is influenced by several transcription factors, such as the nuclear hormone receptor NHR-2315,16,17. Moreover, bacterial vitamin B12 contributes to the breakdown of the potentially toxic short-chain fatty acid propionate acid, which in the absence of vitamin B12 can be compensated through metabolic network rewiring, apparently through the production of 3-hydroxypropionate16,32. A different example is the neuro-modulatory effect of Providencia, discovered by the Sengupta lab, where bacterial tyramine is converted by the C. elegans tyramine &#946;-hydroxylase to octopamine, which subsequently influences worm behavior through its interaction with the OCTR-1 octopamine receptor in specific sensory neurons18. Yet another example is immune protection, which is provided by various bacteria, especially those of the genus Pseudomonas. This occurs either through the production of antimicrobial compounds or through an indirect effect, possibly via the activation of specific host responses6,11,14. Additional microbes and especially the use of naturally associated microbial communities will help to obtain a more realistic understanding of the biology of this model nematode.

In nature, C. elegans is commonly found in rotten plant matter, especially rotten fruits like apples or on compost heaps1. It is also associated with certain invertebrate hosts such as slugs and woodlice2,3. These habitats are rich in microbes, which not only serve as food for the worm, but may also form stable associations with it. Information on the diversity of naturally associated microorganisms was only published in 20164,5,6. Since then, these and only a few more recent studies have revealed that C. elegans is associated with a variety of bacteria and fungi, most commonly including bacteria of the genus Pseudomonas, Enterobacter, Ochrobactrum, Erwinia, Comamonas, Gluconobacter, and several others6,7,8. Several associated bacteria can stably colonize the worm gut, although not all6,9,10,11,12. They are likely to be of key importance for our understanding of C. elegans biology because they can provide nutrition, protect against pathogens and possibly other stressors, and affect central life-history traits such as reproductive rate, development, or behavioral responses.
As an example, naturally associated isolates of the genera Pseudomonas, Ochrobactrum, and also Enterobacter or Gluconobacter can protect the worm from pathogen infection and killing in distinct ways5,6,11,13,14. A specific isolate of the genus Comamonas influences nematode dietary response, development, lifespan, and fertility15,16,17. Providencia bacteria produce the neuromodulator tyramine and thereby modulate host nervous system activity and resulting behavioral responses18. A set of different naturally associated bacteria were demonstrated to affect population growth rate, fertility, and behavioral responses5,6,9,11,19.
To date, the exact diversity and consistency of the native C. elegans microbiota across habitats and geographic locations are not fully understood, and further associations between the worm and microbes from its environment remain to be uncovered. Several previous studies used bacterial strains isolated from some soil environment, natural C. elegans habitats, or from mesocosm experiments (i.e., lab-based environments that recreate natural habitats) with C. elegans laboratory strains4,5,20. Even though these studies obtained new insights into the influence of microbes on specific nematode traits (e.g., nematode metabolism21), the relevance of these interactions for C. elegans biology in nature is unclear. Therefore, this manuscript describes the methods to directly isolate C. elegans from nature and to isolate and subsequently characterize the naturally associated microbes from both single worms and groups of worms. The described methods are an updated and improved version of the procedures used previously for the isolation and characterization of natural C. elegans and its native microbiota2,6,7. Considering that C. elegans is widely found in decomposing plant matter across the globe (especially in rotting fruits, temperate regions, and in autumn)1,2,22,23,24,25, this protocol can be applied by any lab whenever there is interest in relating C. elegans traits to naturally associated microbes and thus a more naturally relevant context. The latter is pivotal for a full understanding of the nematode&#39;s biology because it is known from a diversity of other host systems that the associated microbiota can affect diverse life history characteristics26, an aspect which is currently largely neglected in the multitude of C. elegans studies across almost all life science disciplines.

<table><tbody><tr><td>COMSOL</td><td>COMSOL</td><td></td><td>multiphysics simulation software</td></tr></tbody></table>

isolation and characterization of the natural microbiota of the model nematode caenorhabditis elegans

The nematode Caenorhabditis elegans interacts with a large diversity of microorganisms in nature. In general, C. elegans is commonly found in rotten plant matter, especially rotten fruits like apples or on compost heaps. It is also associated with certain invertebrate hosts such as slugs and woodlice. These habitats are rich in microbes, which serve as food for C. elegans and which can also persistently colonize the nematode gut. To date, the exact diversity and consistency of the native C. elegans microbiota across habitats and geographic locations is not fully understood. Here, we describe a suitable approach for isolating C. elegans from nature and characterizing the microbiota of worms. Nematodes can be easily isolated from compost material, rotting apples, slugs, or attracted by placing apples on compost heaps. The prime time for finding C. elegans in the Northern Hemisphere is from September until November. Worms can be washed out of collected substrate material by immersing the substrate in buffer solution, followed by the collection of nematodes and their transfer onto nematode growth medium or PCR buffer for subsequent analysis. We further illustrate how the samples can be used to isolate and purify the worm-associated microorganisms and to process worms for 16S ribosomal RNA analysis of microbiota community composition. Overall, the described methods may stimulate new research on the characterization of the C. elegans microbiota across habitats and geographic locations, thereby helping to obtain a comprehensive understanding of the diversity and stability of the nematode's microbiota as a basis for future functional research.

The nematode C. elegans is frequently found in decomposing fruits, such as apples, and also compost samples. In Northern Germany, C. elegans as well as congeneric species (particularly C. remanei but also C. briggsae) are mainly found from September until November2. The nematodes are most commonly found in decomposing plant matter, especially rotting fruits such as apples or pears, and also compost, particularly material that shows a high grade of decomposition. The fruit and compost samples can be taken into the lab (Figure 3A,B), distributed in Petri dishes (Figure 3C,D), and subsequently submerged in a liquid or viscous medium to force the worms to leave the substrate material and swim to the medium&#39;s surface (Figure 3E,F). Thereafter, the worms can be collected, transferred onto agar plates or microcentrifuge tubes, and the species identity determined using diagnostic PCRs2,6,7,22.
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/64249/64249fig03.jpg" /> 
Figure 3: Preparation of apples for isolation of nematodes. (A,B) Nematodes can be isolated from environmental samples like compost or rotten fruits and additionally be attracted by placing apples on compost. (C,D) The samples are divided, and small pieces are placed in a Petri dish. (E,F) Viscous medium is added to the samples, which usually leads to nematodes leaving the substrate material and swimming to the surface of the medium. <a href="https://www.jove.com/files/ftp_upload/64249/64249fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
PCR using the C. elegans specific primers nlp30-F and nlp30-R results in a PCR product of 154 bp length for C. elegans and no product for other nematodes (Figure 4). To confirm the successful performance of the PCR, DNA of a laboratory strain such as N2 should be run as positive control concurrently with the DNA of the isolated nematodes. Small amounts of biological material, such as small larval stages, can result in weak PCR bands (Figure 4A). The visibility of the PCR bands can be improved by using more DNA in the PCR (note that this will minimize the amount of DNA left for bacterial 16S rDNA amplicon sequencing, e.g., 2 &#181;L of DNA instead of 1 &#181;L), by applying a larger amount of the PCR product to the gel (e.g., 10-15 &#181;L), or by increasing the number of PCR cycles. In comparison to single worms, worm populations consisting of at least 50 worms usually yield a larger amount of DNA, and the bands in the electrophoresis gel are clearly visible (Figure 4B).
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/64249/64249fig04.jpg" /> 
Figure 4: PCR product of C. elegans-specific PCR. (A,B) The C. elegans-specific primers nlp30-F and nlp30-R produce a PCR product of 154 bp length. As an example, PCRs were performed on (A) single worms and (B) worm populations (e.g., 300-500 individuals), all isolated with the described protocol from rotting plant matter from the compost of the Botanical Garden in Kiel, Germany. (A) DNA of single worms and, in particular, of small larval stages often results in weak PCR bands. (B) DNA isolated from worm populations (e.g., 300-500 individuals) results in clearer bands. DNA of C. elegans N2 was used as positive control (+), no template was used as negative control (-). The smears below PCR bands are gel artifacts. <a href="https://www.jove.com/files/ftp_upload/64249/64249fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The microbes, which are associated with C. elegans, can be isolated from worms and also the worm-containing substrate samples. Microbe isolation follows general microbiology standards, including isolation of pure cultures from agar plates, their growth in liquid media, and their subsequent characterization (e.g., using the sequences of the 16S ribosomal RNA gene for bacteria). It is critical that the microbes are isolated as pure single colonies from plates, using standard microbiology procedures (Figure 5). This is important because some of the C. elegans-associated bacteria can form biofilms and/or easily aggregate, resulting in multi-species cultures (Figure 5C,D). The purity of the isolated bacterial cultures can be confirmed through the sequences of the 16S rRNA gene, as done for previously isolated C. elegans-associated microbes6,7. The obtained microbes can subsequently be used in experiments with C. elegans.
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/64249/64249fig05.jpg" /> 
Figure 5: Bacterial isolates on agar plates. Individual bacterial isolates are streaked out onto agar plates, in this case, tryptic soy agar (TSA) plates, showing as examples an isolate of (A) Pseudomonas lurida, (B) Pseudomonas fluorescens, and an example with several bacterial species, shown as an (C) overview of the entire plate and (D) magnification of a section of this plate, in which distinct colony types are visible. <a href="https://www.jove.com/files/ftp_upload/64249/64249fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Table 1: List of primers used in this study <a href="https://www.jove.com/files/ftp_upload/64249/Table_1.xlsx" target="_blank">Please click here to download this Table.</a>

Watch this Scientific Journal Video about Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans at JoVE.com

Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans

Caenorhabditis elegans is one of the main model species in biology, yet almost all research is performed in the absence of its naturally associated microbes. The methods described here will help to improve our understanding of the diversity of associated microbes as a basis for future functional C. elegans research.

Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans

The nematode Caenorhabditis elegans interacts with a large diversity of microorganisms in nature. In general, C. elegans is commonly found in rotten plant ...

isolation-characterization-natural-microbiota-model-nematode

Nanyang Technological University

Research

JoVE Journal

Biology

2.9K Views.  University of Kiel. Caenorhabditis elegans is one of the main model species in biology, yet almost all research is performed in the absence of its naturally associated microbes. The methods described here will help to improve our understanding of the diversity of associated microbes as a basis for future functional C. elegans research.

Video: Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans

The Nematode Caenorhabditis Elegans - A Versatile In Vivo Model to Study Host-microbe Interactions

We demonstrate a method using Caenorhabditis elegans as a model host to study microbial interaction. Microbes are introduced via the diet making the intestine the primary location for disease. The nematode intestine structurally and functionally mimics mammalian intestines and is transparent making it amenable to microscopic study of colonization. Here we show that pathogens can cause disease and death. We are able to identify microbial mutants that show altered virulence. Its conserved innate response to biotic stresses makes C. elegans an excellent system to probe facets of host innate immune interactions. We show that hosts with mutations in the dual oxidase gene cannot produce reactive oxygen species and are unable to resist microbial insult. We further demonstrate the versatility of the presented survival assay by showing that it can be used to study the effects of inhibitors of microbial growth. This assay may also be used to discover fungal virulence factors as targets for the development of novel antifungal agents, as well as provide an opportunity to further uncover host-microbe interactions. The design of this assay lends itself well to high throughput whole-genome screens, while the ability to cryo-preserve worms for future use makes it a cost-effective and attractive whole animal model to study.

The Nematode Caenorhabditis Elegans - A Versatile In Vivo Model to Study Host-microbe Interactions

Here, we present the nematode Caenorhabditis elegans as a versatile host model to study microbial interaction.

We demonstrate a method using Caenorhabditis elegans as a model host to study microbial interaction. Microbes are introduced via the diet making the ...

Genetics

Rapid Isolation of Wild Nematodes by Baermann Funnel

Beyond being robust experimental model organisms, Caenorhabditis elegans and its relatives are also real animals that live in nature. Studies of wild nematodes in their natural environments are valuable for understanding many aspects of biology, including the selective regimes in which distinctive genomic and phenotypic characters evolve, the genetic basis for complex trait variation, and the natural genetic diversity fundamental to all animal populations. This manuscript describes a simple and efficient method for extracting nematodes from their natural substrates, including rotting fruits, flowers, fungi, leaf litter, and soil. The Baermann funnel method, a classical nematology technique, selectively isolates active nematodes from their substrates. Because it recovers nearly all active worms from the sample, the Baermann funnel technique allows for the recovery of rare and slow-growing genotypes that co-occur with abundant and fast-growing genotypes, which might be missed in extraction methods that involve multiple generations of reproduction. The technique is also well suited to addressing metagenetic, population-genetic, and ecological questions. It captures the entire population in a sample simultaneously, allowing an unbiased view of the natural distribution of ages, sexes, and genotypes. The protocol allows for deployment at scale in the field, rapidly converting substrates into worm plates, and the authors have validated it through fieldwork on multiple continents.

This protocol outlines a method for efficiently extracting live nematodes from natural substrates in the field.

Beyond being robust experimental model organisms, Caenorhabditis elegans and its relatives are also real animals that live in nature. Studies of wild ...

Isolation of Specific Neuron Populations from Roundworm Caenorhabditis elegans

During the aging process, many cells accumulate high levels of damage leading to cellular dysfunction, which underlies many geriatric and pathological conditions. Post-mitotic neurons represent a major cell type affected by aging. Although multiple mammalian models of neuronal aging exist, they are challenging and expensive to establish. The roundworm Caenorhabditis elegans is a powerful model to study neuronal aging, as these animals have short lifespan, an available robust genetic toolbox, and well-cataloged nervous system. The method presented herein allows for seamless isolation of specific cells based on the expression of a transgenic green fluorescent protein (GFP). Transgenic animal lines expressing GFP under distinct, cell type-specific promoters are digested to remove the outer cuticle and gently mechanically disrupted to produce slurry containing various cell types. The cells of interest are then separated from non-target cells through fluorescence-activated cell sorting, or by anti-GFP-coupled magnetic beads. The isolated cells can then be cultured for a limited time or immediately used for cell-specific ex vivo analyses such as transcriptional analysis by real time quantitative PCR. Thus, this protocol allows for rapid and robust analysis of cell-specific responses within different neuronal populations in C. elegans.

Isolation of Specific Neuron Populations from Roundworm Caenorhabditis elegans

Here, we present a protocol for simple isolation of specific groups of live neuronal cells expressing green fluorescent protein from transgenic Caenorhabditis elegans lines. This method enables a variety of ex vivo studies focused on specific neurons and has the capacity to isolate cells for further short-term culturing.

During the aging process, many cells accumulate high levels of damage leading to cellular dysfunction, which underlies many geriatric and pathological ...

Developmental Biology

Selective Cleaning of Wild Caenorhabditis Nematodes to Enrich for Intestinal Microbiome Bacteria

Caenorhabditis elegans (C. elegans)&#160;has proven to be an excellent model for studying host-microbe interactions and the microbiome, especially in the context of the intestines. Recently, ecological sampling of wild Caenorhabditis nematodes has discovered a diverse array of associated microbes, including bacteria, viruses, fungi, and microsporidia. Many of these microbes have interesting colonization or infection phenotypes that warrant further study, but they are often unculturable. This protocol presents a method to enrich the desired intestinal microbes in C. elegans and related nematodes and reduce the presence of the many contaminating microbes adhering to the cuticle. This protocol involves forcing animals into the dauer stage of development and using a series of antibiotic and detergent washes to remove external contamination. As dauer animals have physiological changes that protect nematodes from harsh environmental conditions, any intestinal microbes will be protected from these conditions. But, for enrichment to work, the microbe of interest must be maintained when animals develop into dauers. When the animals leave the dauer stage, they are singly propagated into individual lines. F1 populations are then selected for desired microbes or infection phenotypes and against visible contamination. These methods will allow researchers to enrich unculturable microbes in the intestinal lumen, which make up part of the natural microbiome of C. elegans and intracellular intestinal pathogens. These microbes can then be studied for colonization or infection phenotypes and their effects on the host fitness.

Selective Cleaning of Wild Caenorhabditis Nematodes to Enrich for Intestinal Microbiome Bacteria

Wild Caenorhabditis nematodes are associated with many microbes, often in the gut lumen or infecting the intestine. This protocol details a method to enrich unculturable microbes colonizing the intestine, taking advantage of the resistance of the dauer cuticle.

Caenorhabditis elegans (C. elegans)&#160;has proven to be an excellent model for studying host-microbe interactions and the microbiome, especially in the ...

Immunology and Infection

RNA Fluorescence in situ Hybridization (FISH) to Visualize Microbial Colonization and Infection in Caenorhabditis elegans Intestines

The intestines of wild Caenorhabditis nematodes are inhabited by a variety of microorganisms, including gut microbiome bacteria and pathogens, such as microsporidia and viruses. Because of the similarities between Caenorhabditis elegans and mammalian intestinal cells, as well as the power of the C. elegans system, this host has emerged as a model system to study host intestine-microbe interactions in vivo. While it is possible to observe some aspects of these interactions with bright-field microscopy, it is difficult to accurately classify microbes and characterize the extent of colonization or infection without more precise tools. RNA fluorescence in situ hybridization (FISH) can be used as a tool to identify and visualize microbes in nematodes from the wild or to experimentally characterize and quantify infection in nematodes infected with microbes in the lab. FISH probes, labeling the highly abundant small subunit ribosomal RNA, produce a bright signal for bacteria and microsporidian cells. Probes designed to target conserved regions of ribosomal RNA common to many species can detect a broad range of microbes, whereas targeting divergent regions of the ribosomal RNA is useful for narrower detection. Similarly, probes can be designed to label viral RNA. A protocol for RNA FISH staining with either paraformaldehyde (PFA) or acetone fixation is presented. PFA fixation is ideal for nematodes associated with bacteria, microsporidia, and viruses, whereas acetone fixation is necessary for the visualization of microsporida spores. Animals were first washed and fixed in paraformaldehyde or acetone. After fixation, FISH probes were incubated with samples to allow for the hybridization of probes to the desired target. The animals were again washed and then examined on microscope slides or using automated approaches. Overall, this FISH protocol enables detection, identification, and quantification of the microbes that inhabit the C. elegans intestine, including microbes for which there are no genetic tools available.

RNA Fluorescence in situ Hybridization FISH to Visualize Microbial Colonization and Infection in Caenorhabditis elegans Intestines

Intestinal microbes, including extracellular bacteria and intracellular pathogens like the Orsay virus and microsporidia (fungi), are often associated with wild Caenorhabditis nematodes. This article presents a protocol for detecting and quantifying microbes that colonize and/or infect C. elegans nematodes, and for measuring pathogen load after controlled infections in the lab.

The intestines of wild Caenorhabditis nematodes are inhabited by a variety of microorganisms, including gut microbiome bacteria and pathogens, such as ...

A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes

Caenorhabditis elegans is one of the major model organisms in biology, but only recently have researchers focused on its natural ecology. The relative sparsity of information about C. elegans in its natural context comes from the challenges involved in the identification of the small nematode in nature. Despite these challenges, an increasing focus on the ecology of C. elegans has caused a wealth of new information regarding its life outside of the laboratory. The intensified search for C. elegans in nature has contributed to the discovery of many new Caenorhabditis species and revealed that congeneric nematodes frequently cohabitate in the wild, where they feed on microbial blooms associated with rotting plant material. The identification of new species has also revealed that the androdioecious mating system of males and self-fertilizing hermaphrodites has evolved three times independently within Caenorhabditis. The other two selfing species, C. briggsae and C. tropicalis, share the experimental advantages of C. elegans and have enabled comparative studies into the mechanistic basis of important traits, including self-fertilization. Despite these advances, much remains to be learned about the ecology and natural diversity of these important species. For example, we still lack functional information for many of their genes, which might only be attained through an understanding of their natural ecology. To facilitate ecological research of selfing Caenorhabditis nematodes, we developed a highly scalable method to collect nematodes from the wild. Our method makes use of mobile data collection platforms, cloud-based databases, and the R software environment to enhance researchers&#39; ability to collect nematodes from the wild, record associated ecological data, and identify wild nematodes using molecular barcodes.

A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes

This protocol can be used to perform large-scale ecological surveys of selfing Caenorhabditis nematodes. The primary advantage of this method is the efficient organization and analysis of ecological and molecular data associated with the nematodes collected from nature.

Caenorhabditis elegans is one of the major model organisms in biology, but only recently have researchers focused on its natural ecology. The relative ...

High-Throughput Screening of Microbial Isolates with Impact on Caenorhabditis elegans Health

With its small size, short lifespan, and easy genetics, Caenorhabditis elegans offers a convenient platform to study the impact of microbial isolates on host physiology. It also fluoresces in blue when dying, providing a convenient means of pinpointing death. This property has been exploited to develop high-throughput label-free C. elegans survival assays (LFASS). These involve time-lapse fluorescence recording of worm populations set in multiwell plates, from which population median time of death can be derived. The present study adopts the LFASS approach to screen multiple microbial isolates at once for the effects on C. elegans susceptibility to severe heat and oxidative stresses. Such microbial screening pipeline, which can notably be used to prescreen probiotics, using severe stress resistance as a proxy for host health is reported here. The protocol describes how to grow both C. elegans gut microbiota isolate collections and synchronous worm populations in multiwell arrays before combining them for the assays. The example provided covers the testing of 47 bacterial isolates and one control strain on two worm strains, in two stress assays in parallel. However, the approach pipeline is readily scalable and applicable to the screening of many other modalities. Thus, it provides a versatile setup to rapidly survey a multiparametric landscape of biological and biochemical conditions that impact C. elegans health.

High-Throughput Screening of Microbial Isolates with Impact on Caenorhabditis elegans Health

Gut microbes may positively or negatively impact the health of their host via specific or conserved mechanisms. Caenorhabditis elegans is a convenient platform to screen for such microbes. The present protocol describes high-throughput screening of 48 bacterial isolates for impact on nematode stress resistance, used as a proxy for worm health.

With its small size, short lifespan, and easy genetics, Caenorhabditis elegans offers a convenient platform to study the impact of microbial isolates on ...

Using Single-Worm Data to Quantify Heterogeneity in Caenorhabditis elegans-Bacterial Interactions

The nematode Caenorhabditis elegans is a model system for host-microbe and host-microbiome interactions. Many studies to date use batch digests rather than individual worm samples to quantify bacterial load in this organism. Here it is argued that the large inter-individual variability seen in bacterial colonization of the C. elegans intestine is informative, and that batch digest methods discard information that is important for accurate comparison across conditions. As describing the variation inherent to these samples requires large numbers of individuals, a convenient 96-well plate protocol for disruption and colony plating of individual worms is established.

Using Single-Worm Data to Quantify Heterogeneity in Caenorhabditis elegans-Bacterial Interactions

This protocol describes a 96-well disruption of individual bacterially colonized Caenorhabditis elegans following cold paralysis and surface bleaching&#160;to remove external bacteria. The resulting suspension is plated on agar plates to allow accurate, medium-throughput quantification of bacterial load in large numbers of individual worms.

The nematode Caenorhabditis elegans is a model system for host-microbe and host-microbiome interactions. Many studies to date use batch digests rather ...

Hand Dissection of Caenorhabditis elegans Intestines

Comprised of only 20 cells, the Caenorhabditis elegans intestine&#160;is the nexus of many life-supporting functions, including digestion, metabolism, aging, immunity, and environmental response. Critical interactions between the C. elegans host and its environment converge within the intestine, where gut microbiota concentrate. Therefore, the ability to isolate intestine tissue away from the rest of the worm is necessary to assess intestine-specific processes. This protocol describes a method for hand dissecting adult C. elegans intestines. The procedure can be performed in fluorescently labeled strains for ease or training purposes. Once the technique is perfected, intestines can be collected from unlabeled worms of any genotype. This microdissection approach allows for the simultaneous capture of host intestinal tissue and gut microbiota, a benefit to many microbiome studies. As such, downstream applications for the intestinal preparations generated by this protocol can include but are not limited to RNA isolation from intestinal cells and DNA isolation from captured microbiota. Overall, hand dissection of C. elegans intestines affords a simple and robust method to investigate critical aspects of intestine biology.

Hand Dissection of Caenorhabditis elegans Intestines

The present protocol describes a procedure for isolating intestines from adult Caenorhabditis elegans nematode worms by hand for input in genomics, proteomics, microbiome, or other assays.

Comprised of only 20 cells, the Caenorhabditis elegans intestine&#160;is the nexus of many life-supporting functions, including digestion, metabolism, ...

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans

The nematode Caenorhabditis elegans is emerging as a useful model for studying the molecular mechanisms underlying interactions between hosts and their gut microbiomes. While experiments with well-characterized bacteria or defined bacterial communities can facilitate the analysis of molecular mechanisms, studying nematodes in their natural microbial context is essential for exploring the diversity of such mechanisms. At the same time, the isolation of worms from the wild is not always feasible, and, even when possible, sampling from the wild restricts the use of the genetic toolkit otherwise available for C. elegans research. The following protocol describes a method for microbiome studies utilizing compost microcosms for the in-lab&#160;growth in microbially diverse and natural-like environments.
Locally sourced soil can be enriched with produce to diversify the microbial communities in which worms are raised and from which they are harvested, washed, and surface-sterilized for subsequent analyses. Representative experiments demonstrate the ability to modulate the microbial community in a common soil by enriching it with different produce and further demonstrate that worms raised in these distinct environments assemble similar gut microbiomes distinct from their respective environments, supporting the notion of a species-specific core gut microbiome. Overall, compost microcosms provide natural-like in-lab environments for microbiome research as an alternative to synthetic microbial communities or to the isolation of wild nematodes.

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans

Compost microcosms bring the microbial diversity found in nature into the laboratory to facilitate microbiome research in Caenorhabditis elegans. Provided here are protocols for setting up microcosm experiments, with the experiments demonstrating the ability to modulate environmental microbial diversity to explore the relationships between environmental microbial diversity and worm gut microbiome composition.

The nematode Caenorhabditis elegans is emerging as a useful model for studying the molecular mechanisms underlying interactions between hosts and their ...

Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans

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High-Throughput Screening of Microbial Isolates with Impact on Caenorhabditis elegans Health

Using Single-Worm Data to Quantify Heterogeneity in Caenorhabditis elegans-Bacterial Interactions

Hand Dissection of Caenorhabditis elegans Intestines

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans