Urban environments, defined by their dense infrastructure and human activity, may be influencing the evolution of microorganisms that inhabit them. A recent study published in Microbiome uncovers how microbes adapt to limited resources in cities, particularly in the face of frequent disinfection practices, which has altered the composition of indoor microbial communities.
"Built environments offer distinct conditions that set them apart from natural and engineered habitats," says Xinzhao Tong, an assistant professor at Xi’an Jiaotong-Liverpool University (XJTLU) and lead author of the study. He explains that microbes must either adapt to these unique conditions or face elimination.
Investigating Microbial Life in Urban Spaces
To explore how microbes are adapting to urban environments, the research team collected 738 samples from various locations in Hong Kong, including subway systems, residential areas, public facilities, piers, and human skin. They employed shotgun metagenomic sequencing to analyze the genomic content of the microbes and gain insight into their survival mechanisms in such challenging environments.
The study identified 363 previously unknown microbial strains that thrive in both the environment and on human skin. Many of these strains possess genes that enable them to metabolize manufactured compounds prevalent in cities. Among these was a strain of Candidatus Eremiobacterota, a phylum previously associated only with Antarctic desert soil.
“The genome of this novel strain of Eremiobacterota enables it to metabolize ammonium ions found in cleaning products. The strain also has genes for alcohol and aldehyde dehydrogenases to break down residual alcohol found in common disinfectants,” Tong notes. This ability to use manufactured chemicals as energy sources may give certain microbes a competitive advantage in urban spaces. However, this raises concerns over potential health risks, especially if these microbes are pathogenic.
Pathogens in Urban Microbiomes
The study's findings included 11 previously uncharacterized strains of Micrococcus luteus, a typically non-pathogenic microbe that can cause opportunistic infections in immunocompromised individuals. These strains demonstrate how the selective pressures exerted by urban environments and human behavior, such as frequent use of disinfectants, may encourage the evolution of microbes that are more resistant and harder to eliminate.
“The issue of their adaptation to our behavior becomes particularly critical in clinical settings where hospitals serve as hotspots for diverse pathogens that cause hospital-acquired infections (HAIs). HAIs pose a significant threat, particularly in intensive care units where mortality rates can reach up to 30%,” emphasized Tong.
Nanobacteria and Mutualistic Relationships
The research also revealed two novel strains of Patescibacteria, tiny microbes with small genomes that typically rely on other bacteria for survival. However, one of the strains recovered from human skin exhibited genes involved in producing carotenoids and ubiquinone—compounds beneficial to human health. Carotenoids, typically acquired through diet, are known for their antioxidant properties.
These findings suggest a potential mutualistic relationship between humans and the microbes living on their skin. Tong points out that understanding these relationships is crucial for developing strategies that promote healthy indoor microbial ecosystems. The research team is now focused on investigating the transmission of resistant pathogenic microbes in clinical settings like intensive care units. These environments, where disinfectants are used extensively, present an ideal context for studying how microbial resistance evolves.
Publication Details
Tong, X., Luo, D., Leung, M.H.Y. et al. Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments. Microbiome 12, 198 (2024). https://doi.org/10.1186/s40168-024-01926-6