Comparative bacterial community profiling of hospital, community, and abattoir wastewater in Mbarara, Uganda, using 16S rRNA amplicon sequencing

Wastewater-based epidemiology provides a complementary approach to public-health and environmental surveillance, but comparative bacterial community data from different wastewater systems in Uganda remain limited. This study characterised bacterial communities in hospital-associated, community and abattoir wastewater lagoons in Mbarara, Uganda. Forty-five wastewater samples were collected weekly from 18 February to 18 March 2026 at the inlet, midpoint and outlet of the TASO, Kizuungu and Ruti lagoons. Bacterial communities were characterised using 16S rRNA gene amplicon sequencing. Sequence processing and diversity analyses used nf-core/ampliseq and QIIME 2, while functional potential was inferred using PICRUSt2. Sequencing identified 9,870 amplicon sequence variants. Bacterial community composition differed significantly among the three lagoons across Bray–Curtis, Jaccard, weighted UniFrac and unweighted UniFrac metrics, whereas alpha-diversity measures did not differ significantly. Of 13 bacterial genus-level groups examined for public-health relevance, Acinetobacter (q = 0.0013) and Enterobacter (q = 0.0248) differed significantly among lagoons after false-discovery-rate correction. Acinetobacter was relatively abundant in TASO and Ruti wastewater but less abundant in Kizuungu, while Enterobacter had its highest mean relative abundance in TASO. PICRUSt2 predicted broadly overlapping metabolic pathway profiles across the lagoons. The three lagoons harboured distinct bacterial community compositions despite comparable within-sample diversity. These findings establish baseline microbiome information for comparative wastewater surveillance in Mbarara and provide a foundation for further investigation of microbial patterns across additional wastewater systems.