Research finds that viruses and bacteria frequently interact in artificial environments

Viruses in man-made environments raise public health concerns but are generally less studied than bacteria. A recent study led by environmental scientists at the City University of Hong Kong (CityU) provided the first evidence of frequent interactions between viruses and bacteria in man-made environments. It turns out that viruses can potentially help host bacteria adapt and survive in nutrient-depleted engineered environments through unique gene insertions.

By understanding the interactions between these viruses and bacteria and identifying the potential spread of antibiotic resistance genes, the research team hopes the latest findings will help minimize human exposure to harmful microbes. We hope that it will help in deriving effective control strategies.

Virus-host interactions are central to the ecology and evolution of microbial communities in diverse ecosystems. However, the immune mechanisms of infection and virus-host interactions that occur in man-made environments such as buildings, public spaces, transportation and infrastructure are poorly understood.

“With an increasing number of the world’s population living in urban areas, indoor residents are constantly exposed to a wide variety of microorganisms that affect public health, increasing the importance of hygiene in man-made environments, especially indoor environments. Viruses have been overlooked in previous research on engineered environments,” said Professor Patrick Lee Kwanhong of the School of Energy and Environment (SEE) at City University, who led the study.

“Therefore, in our study, we comprehensively surveyed viruses in artificial environments and identified many new molecular mechanisms by which viruses and bacteria interact. , is also important for the management of microbial “artificial environments to protect the health of the population,” added Professor Lee.

For this study, researchers collected 738 samples from different types of man-made environments, including public buildings and residences in Hong Kong. They collected samples primarily from handrails, bollards, floors, poles, doorknob surfaces, and residents’ skin. Next, metagenomic sequencing technology was used for analysis.

The analysis yielded many interesting findings. First, the data showed that viruses are integral members of microbial communities in man-made environments. Among them, bacteriophages are a type of virus that infects and replicates within bacteria and are present on various surfaces in artificial environments. The research team also identified many viruses that differed from viruses in other ecosystems.

Second, the researchers found evidence that the virus inserts genes into the bacterial host that control specific steps, or even entire metabolic pathways. This suggests that viruses may help adapt and co-evolve to help bacteria survive in nutrient-depleted artificial environments.

The study also discovered a diverse and novel immune system against viruses within bacteria and a small protein within viruses that can evade the bacterial immune system. These results suggest that viral and bacterial hosts frequently interact in artificial environments and that each has mechanisms to defend against the other.

Antibiotic resistance genes (ARGs) were also detected in viruses on human skin and frequently touched indoor surfaces. Viruses harboring these ARGs can infect bacterial hosts, and ARGs can be horizontally transferred between bacterial species. Therefore, the role of viruses in engineered environments in the development of bacterial antibiotic resistance is critical and warrants further investigation.

“Our study shows that viral diversity, composition, metabolic function and lifestyle change according to the conditions of their engineered environments,” said Professor Lee. “Therefore, it is important to develop customized control strategies to minimize human exposure to harmful microbes and better protect the health of the population. We can contribute to this goal by enhancing our fundamental understanding of the complex viral-bacterial interactions.”

The research results were published in a scientific journal Nature Communications Entitled “Highly host-associated viruses in constructed environments possess habitat-dependent diversity and functions for potential virus-host co-evolution.”

The first author is SEE PhD student Miss Du Shicong and the corresponding author is Professor Lee. Other team members include Prof. Alvin Lai Chi-Keung, Prof. Chan Chak-Keung, Dr. Tong Xinzhao from SEE, and Prof. Christopher E. Mason from Weill Cornell Medicine.

This work was supported by the Research Grants Council’s Research Impact Fund and the Hong Kong General Research Fund.