Model organisms play a crucial role in advancing our current understanding of biology. However, we often overlook the importance of considering their ecology to comprehend their biology fully. In this context, we examine the microbiomes of two common model organisms— the nematode Caenorhabditis and the larvae of the fruit fly Drosophila— which share the same natural habitat and thereby potentially the same resource, i.e. bacteria.

Taking samples from a compost heap from September to December reveals that Caenorhabditis and Drosophila larvae coexist on rotten apples, sharing most and specifically abundant members of theirmicrobiome. However, certain ASVs are enriched in the respective sample types. Additionally, microbiomes from both hosts cluster separately in a PCoA. Laboratory compost experiments corroborate the observations and reveal that the presence of Drosophila negatively impacts worm population size. Digging deeper, a complex interaction network emerges: Drosophila larvae can ingest eggs and larval stages of the worm, sometimes releasing live worms after gut passage. Conversely, the presence of L4 and adult worms accelerates the fly's development, indicating a stress response likely triggered by resource competition. Notably, dead fly larvae become a food source for the nematode. Worms seemingly enter fly larvae corpses through the mouth opening, proliferating both inside and outside the deceased body.

In summary, our studies reveal a complex relationship of dual nature between Drosophila and Caenorhabditis in their shared habitat. Drosophila feeds on specific worm stages, while smaller worms survive gut passage, dispersing across the habitat, potentially finding new resources, including dead fly larvae. Competition for resources might result in fly larvae entering pupation earlier for survival, creating an opportunity for the worm population to increase.