In this Research Communication we investigate potential correlations between key bacterial groups and nutrient removal efficiency in an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating synthetic dairy processing wastewater. Reactor aeration rates of 06 and 04 litre per minute (LPM) were applied to an 8 l laboratory scale system and the relative impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies compared. Aeration at 06 LPM over several sludge retention times (SRTs) resulted in approximately 92% removal efficiencies for both PO4-P and NH4-N. Biomass samples subjected to next-generation sequencing (NGS), 16S rRNA profiling revealed a concomitant enrichment of Polaromonas under 06 LPM conditions, up to 50% relative abundance within the reactor biomass. The subsequent shift in reactor aeration to 04 LPM, over a period of 3 SRTs, resulted in markedly reduced nutrient removal efficiencies for PO4-P (50%) and NH4-N (45%). An 857% reduction in the genus level relative abundance of Polaromonas was observed under 04 LPM aeration conditions over the same period.