Raw counts, biomass measurements and 16S metabarcoding sequences with metadata file.

The datasets originate from controlled laboratory experiments investigating microbiome-mediated effects on community assembly and priority effects between two freshwater zooplankton species, Daphnia magna and Daphnia pulicaria. The experiments manipulated host arrival order and supplementation with host-conditioned medium to assess reciprocal effects between host community assembly and free-living bacterioplankton communities.Specifically, this item includes:Raw zooplankton count data and corresponding biomass estimates for D. magna and D. pulicaria across all experimental treatments and replicates16S rRNA gene metabarcoding data (Illumina MiSeq, V3–V4 region) characterizing bacterioplankton communities from host-conditioned medium monocultures and experimental aquariaAssociated metadata files for the sequences including pertinent information such as treatments, inoculation order, conditioned medium fractions, and sample identifiersSupplementary material (appendix) containing additional methodological details and supporting analysesThese data enable full reproducibility of the analyses presented in the manuscript and can be reused for comparative studies on priority effects, host–microbiome interactions, and microbial community assembly in freshwater systems.