City microbes that survive on disinfectants, nothing

After the recent pandemic, our use of disinfectants has increased, but are our efforts to create sterile urban environments counterproductive?

A new study published in the journal Microbiome has identified new strains of microbes that have adapted to use the limited resources available in cities and has shown that our daily behavior is changing the composition of microorganisms in indoor environments.

“Built environments offer different conditions that differentiate them from natural and engineered habitats,” says Dr Xinzhao Tong, assistant professor at Xi’an Jiaotong-Liverpool University (XJTLU), China, and lead author of the study.

“Areas with many buildings have few traditional nutrients and essential resources that microbes need to survive, so these built environments have a unique microbiome.

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

Inhabitants of the city

The researchers collected 738 samples from various built environments including subways, residences, public facilities, docks and human skin in Hong Kong. They then used shotgun metagenomic sequencing to analyze the genomic content of the microbes and understand how they have adapted to the harsh urban conditions.

The team identified 363 previously unidentified microbial strains that live on our skin and in the environment around us. Some of the genomes of these strains contained genes to metabolize the manufactured goods found in cities and use them as sources of carbon and energy. This includes the discovery of a Candidatus phylum Eremiobacterota strain, previously only reported in Antarctic desert soil.

Dr Tong says: “The genome of this new strain of Eremiobacterota allows it to metabolize ammonium ions found in cleaning products. The strain also has genes for alcohol and aldehyde dehydrogenases to break down the ‘residual alcohol found in common disinfectants.

“Microbes that have enhanced abilities to use limited resources and tolerate manufactured products, such as disinfectants and metals, outcompete non-resistant strains, improving their survival and even evolution in built environments. Therefore, they could pose risks to to health if they are pathogenic”.

The team identified 11 unique and previously uncharacterized strains of Micrococcus luteus, normally non-pathogenic but capable of causing opportunistic infections in immunocompromised individuals.

“The problem of their adaptation to our behavior becomes especially critical in clinical settings where hospitals serve as hot spots for various pathogens that cause hospital-acquired infections (HAIs). HAIs pose a significant threat, especially in intensive care units where mortality rates can be as high as 30%,” says Dr Tong.

A balancing act

The researchers also characterized two new strains of Patescibacteria, known as “nanobacteria” because they have tiny genomes that don’t contain many genes to produce their own resources.

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

This improved understanding of microbial metabolic functions within built environments helps develop strategies to create a healthy indoor ecosystem of microbes to live alongside.

The team is now investigating the transmission and evolution of resistance in pathogenic microbes in intensive care units that are exposed to strict and extensive disinfection practices. They hope to improve infection control practices and increase the safety of clinical settings for healthcare workers and patients.