Kitchen-scale connectivity dominates bacterial and fungal communities across sink surfaces

Background Built environments function as hubs of microbial exchange, and kitchens serve as key sites for interaction between occupants and physical surfaces. Understanding how spatial connectivity and regional variation influence bacterial and fungal colonization on kitchen surfaces is relevant to the protection of human health and food safety. Here, we applied long-read 16S rRNA and ITS amplicon sequencing to samples collected from countertops, drain holes, and faucet spouts (n = 123) in 41 residential kitchens across two counties in North Carolina, USA to quantify variation in microbial community structure across multiple spatial scales. Results We found lower taxonomic resolution for bacteria than for fungi, with species-level assignments representing ~ 30% of bacterial reads and ~ 88% of fungal reads. Community structure was driven primarily by kitchen identity (45% of bacterial and 37% of fungal variation), with ZIP code, surface type and county each explaining smaller, yet significant, proportions of the observed variation. Countertops exhibited the highest bacterial and fungal diversity, whereas drain holes and faucet spouts were dominated by taxa including Pseudomonas , Acinetobacter , Penicillium , and Candida . Targeted taxonomic screening identified Stenotrophomonas maltophilia , Acinetobacter junii , Aspergillus fumigatus , and Penicillium brevicompactum , indicating that sink surfaces can harbor opportunistic taxa associated with infections in immunocompromised individuals. Conclusions Our findings demonstrate that kitchen identity signatures dominate microbial community structure, with moisture-retaining surfaces acting as key niches. This multi-scale structuring supports the framework that indoor microbiomes are seeded by outdoor inputs but structured by human occupancy.