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.