Gut and Internal Nest Wall Microbiomes Are Compartmentalized Within Colonies of Neotropical Termitidae

Termites host complex microbial communities in the digestive tract, while microbial communities in their nests remain less well characterized. Here, we reanalyzed previously generated V4 16S ribosomal RNA (rRNA) gene amplicon data from 19 colony-matched gut and internal nest wall pairs (38 samples) representing eight Neotropical Termitidae species. We asked whether the two compartments harbor consistently different bacterial and archaeal assemblages when colony identity is controlled. Alpha-diversity metrics showed no global compartment shift, whereas paired community-level analyses supported consistent compositional differentiation. Gut profiles were characterized by termite-associated lineages including Treponema, Tyzzerella and Candidatus Symbiothrix, whereas internal nest walls showed greater representation of Acidothermus, Conexibacter, Nocardioides, Candidatus Udaeobacter and Gryllotalpicola. Exploratory paired genus-level contrasts reinforced these patterns, and secondary analyses indicated additional host species-associated structure within each compartment. Because feeding guild and nest type are partially confounded with host identity, they were treated descriptively rather than as independent drivers. Together, these results show that gut and internal nest wall microbiomes are compositionally distinct within the same colonies, supporting spatial partitioning of termite-associated microbial communities while highlighting host-associated variation across Neotropical Termitidae.