Bacterial 16s rRNA gene amplicon data (V3-V4) and qPCR data

Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless, divergence in microbiome composition among related groups arises. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider Stegodyphus dumicola. We simulated initiation of new groups and compared variation in microbiome composition among and within groups. Theory predicts a decrease in beta diversity with increasing group size, and we found that single founders harboured the highest diversity. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Consistent host-symbiont relationships in the species must then be maintained by other processes. Individual founders harboured higher relative abundances of non-core symbionts some of which are possible pathogens, compared with founders in small groups. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.

Methods
Bacterial 16S rRNA amplicon data of the V3-V4 region. 

qPCR of bacterial 16S rRNA gene copies normalized to spider gene copies.