Disinfectants Foster the Growth of Novel Microbial Strains in Urban Settings

A recent study in the journal Microbiome has uncovered new strains of microbes that have evolved to utilize the scarce resources found in cities. This reveals that daily habits are altering the composition of microorganisms in indoor environments.

Built environments offer distinct conditions that set them apart from natural and engineered habitats. Areas with many buildings are low in the traditional nutrients and essential resources microbes need for survival, so these built environments have a unique microbiome.”

Dr. Xinzhao Tong, Assistant Professor, Xi’an Jiaotong-Liverpool University (XJTLU)

“Our use of cleaning and other manufactured products creates a unique setting that puts selective pressures on microbes, which they must adapt to or be eliminated, but the mechanisms by which microbes adapt and survive in built environments are poorly understood,” Dr. Tong explains.

City Dwellers

The researchers gathered 738 samples from various built environments in Hong Kong, such as subways, homes, public spaces, piers, and human skin. They utilized shotgun metagenomic sequencing to examine the genetic makeup of the microbes and determine how they have adapted to the demanding conditions of urban areas.

The team discovered 363 previously unknown microbial strains that reside on the human skin and in the surroundings. Some of these strains' genomes contained genes that allow them to metabolize man-made products found in cities, using them as sources of carbon and energy. Notably, they identified a strain from the Candidatus phylum Eremiobacterota, which had only been observed in Antarctic desert soil before.

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. Microbes possessing enhanced capabilities to utilize limited resources and tolerate manufactured products, such as disinfectants and metals, out-compete non-resistant strains, enhancing their survival and even evolution within built environments. They could, therefore, pose health risks if they are pathogenic.”

Dr. Xinzhao Tong, Assistant Professor, Xi’an Jiaotong-Liverpool University (XJTLU)

The research team discovered 11 distinct, previously uncharacterized strains of Micrococcus luteus. Although these strains are generally non-pathogenic, they can lead to opportunistic infections in individuals with weakened immune systems.

“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%,” notes Dr Tong.

A Balancing Act

The researchers also characterized two new strains of Patescibacteria, commonly referred to as "nanobacteria" due to their small genomes, which lack numerous genes required for generating their own resources.

Some strains of Patescibacteria are considered parasitic as they rely on bacterial hosts to supply their nutrients. However, in this study, the researchers found that one of the nanobacteria strains, recovered from human skin, contains genes for the biosynthesis of carotenoids and ubiquinone. These antioxidant compounds are vital to humans, and we typically acquire them, especially carotenoids, through our diets, suggesting a possible mutualistic relationship between bacteria and us as their hosts.”

Dr. Xinzhao Tong, Assistant Professor, Xi’an Jiaotong-Liverpool University (XJTLU)

This improved comprehension of microbial metabolic functions in constructed environments aids in formulating strategies to establish a healthy indoor microbial ecosystem for human coexistence.

The team is currently exploring the transmission and evolution of resistance in pathogenic microbes within intensive care units subjected to rigorous disinfectant practices. Their goal is to enhance infection control measures and bolster the safety of clinical settings for both healthcare workers and patients.