1. Microbiome studies in Platyhelminthes have predominantly focused on a limited number of taxa, overlooking the vast diversity of turbellarian hosts. Here, we aimed to expand our understanding of microbial associations in a selection of free-living representatives of Rhabdocoela, a group of turbellarian flatworms that is very species rich and ecologically diverse. 2. Using 16S rRNA sequencing, we characterised the microbiomes of three species of Rhabdocoela, representing the two most speciose lineages within this taxon: Dalytyphloplanida and Kalyptorhynchia. The specimens were captured in the wild and obtained from marine or freshwater habitats. 3. The microbiomes of Gyratrix hermaphroditus (Kalyptorhynchia) and Mesostoma ehrenbergii (Dalytyphloplanida) were both dominated by Proteobacteria, while Phaenocora evelinae (Dalytyphloplanida) was predominantly associated with Cyanobacteria, more specifically Oxyphytobacteria (chloroplasts). 4. Based on the observed genera, our analysis revealed distinct microbial patterns, possibly associated with the habitat and lifestyle of the studied species. We could not exclude the presence of a phylosymbiotic signal as a limited core microbiome was present for each rhabdocoel species, although no set of bacteria common to all three rhabdocoel species was found. 5. This explorative study contributes to the expanding knowledge of invertebrate microbiomes, providing new insights into the microbial associations of a selection of turbellarians. The descriptive results presented here open up several promising avenues for future research, including the search for functional roles of turbellarian bacterial symbionts and exploring potential correlations between microbiome compositions, turbellarian phylogeny and environmental variables.
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