Every surface tells a story. Just as every person carries a unique fingerprint, every place has an invisible identity written in the microbes that settle there. In Singapore’s hawker centres, routine wipe-downs are meant to reset the scene for the next diner. Yet distinct microbial ecosystems persist on these surfaces, shaped by food, people and place.
“The constant presence of nutrient-rich food residues creates a fertile substrate that can support potentially benign and clinically relevant microbes,” said Jonathan Teo, a Researcher at the A*STAR Genome Institute of Singapore (A*STAR GIS).
Despite serving millions daily, food centres have remained a surveillance blind spot. This gap motivated the team, led by A*STAR GIS Associate Director Niranjan Nagarajan, to characterise microbiomes at food centres across the city-state. They collaborated with Kyaw Thu Aung’s team as well as researchers from the National Environment Agency, Singapore and the Singapore Food Agency.
To disentangle microbial inputs from human contact, food handling and the surrounding environment, the researchers sampled table surfaces from 16 of Singapore’s food centres at two timepoints, three years apart. The researchers then performed shotgun metagenomics, a technique of sequencing the DNA from a microbial community to uncover both species identities and their ecological functions, supported by machine learning analysis.
While food-related DNA from fish, meat and vegetables explained nearly half of the microbial variation between locations, the analysis identified 22 microbial species that distinguished individual food centres with over 80 percent accuracy. These biological fingerprints proved stable at several food centres, persisting for more than three years despite disruptions from the COVID-19 pandemic and changes in going-out behaviours.
“We believe the local environment is the dominant driver of these persistent microbial signatures,” said Nagarajan. “Unlike people or food offerings, which change daily, the physical features—surfaces, ventilation and microclimate—change much more slowly.”
The metagenomics survey also detected typical bacteria of interest in clinical settings, such as Klebsiella pneumoniae, Acinetobacter baumannii and Enterobacter species. According to the researchers, this bacterial presence reflects environmental background signals associated with nutrient-rich public spaces, rather than evidence of any immediate health concerns.
One unexpected discovery was the enrichment of genes conferring resistance to colistin, a last-resort antibiotic. This reflects a low-level baseline likely introduced through global food chains or travel, the team noted, allowing the resistance genes to linger in the area despite local bans on the drug.
“These environments are relevant for understanding how nutrient-rich settings shape microbial growth, persistence and transmission,” Teo said. Together, these findings provide a reference point for microbial ecosystems in communal dining spaces, highlighting the importance of continued environmental surveillance efforts both locally and globally.
The A*STAR-affiliated researchers contributing to this research are from the A*STAR Genome Institute of Singapore (A*STAR GIS).
