Substrate and Species Identity Shape Bacterial Communities Within Myxomycete Fruiting Bodies

Myxomycete fruiting bodies are closely associated with bacteria, but the mechanisms shaping the bacterial communities remain unclear. We compared bacterial communities in fruiting bodies of four myxomycete species and their paired wood substrates using 16S rRNA gene amplicon sequencing. We detected 9732 bacterial ASVs across all 60 samples. Fruiting bodies and paired substrates shared 89% of ASV‐associated reads, but fruiting bodies showed significantly lower bacterial diversity and were enriched in Proteobacteria‐related lineages, especially Gammaproteobacteria, Burkholderiales, Burkholderiaceae, and Burkholderia – Caballeronia – Paraburkholderia . The bacterial community composition differed significantly between fruiting bodies and substrates ( p  < 0.001), and host species identity also significantly explained the variation in fruiting body bacterial communities ( R ²  = 0.149, p  = 0.001). The bacterial community assembly differed between habitats, with substrate communities dominated by homogeneous selection (82%), whereas fruiting body communities were shaped by a more balanced combination of homogeneous selection (40%), heterogeneous selection (4%), dispersal limitation (43%), and drift (13%). Overall, myxomycetes do not simply inherit substrate bacteria, but potentially restructure substrate‐derived communities through host‐associated ecological processes.