Unraveling the secret of interactions between viruses and bacteria in man-made environments

Viruses in man-made environments cause public health concerns, but are generally less studied than bacteria. A recent study by environmental scientists from Hong Kong City University (CityU) provided the first evidence of frequent interactions between viruses and bacteria in artificial environments. She discovered that viruses have the potential to help host bacteria adapt and survive in nutrient-depleted artificial environments through a unique gene insertion.

By understanding these virus-bacteria interactions and identifying the possible spread of antibiotic resistance genes, the research team hopes their latest findings can help derive effective control strategies to minimize human exposure to harmful microorganisms.

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 artificial environments, including buildings, public spaces, transportation and infrastructure, have been poorly understood.

“As more and more of the global population lives in urban areas, the importance of hygiene in man-made environments is growing, especially indoor ones, as indoor occupants are constantly exposed to different microorganisms, which have public health implications. However, most previous studies of man-made environments have overlooked viruses,” he said Professor Patrick Lee Kwan-Hon at CityU’s School of Energy and Environment (SEE), which led the study.

“Therefore, in our study, we comprehensively studied viruses in man-made environments and identified many new molecular mechanisms in which viruses and bacteria interact with each other. These findings are important not only for basic microbial science, but also for the management of man-made environments to protect the health of residents,’ added Professor Lee.

In the study, researchers collected 738 samples from different types of man-made environments, including public structures and residences, in Hong Kong. They collected the samples mainly from the surfaces of the residents’ handrails, bollards, floors, posts, doorknobs and skin. Then they used the metagenomic sequencing technique for the analysis.

The analysis has led to many interesting discoveries. First, the data showed that viruses are integral members of microbial communities in man-made environments. Among these, bacteriophages, a kind of virus that infects and replicates within bacteria, are found on various surfaces in man-made environments. The team also identified many viruses distinct from those found in other ecosystems.

Second, the team found evidence of viruses inserting genes that control a specific step in a metabolic pathway and even the entire metabolic pathway into bacterial hosts. This suggests that viruses could help bacteria adapt and coevolve to survive in nutrient-depleted artificial environments.

The study also found several new immune systems against viruses in bacteria and small proteins in viruses that can evade the bacteria’s immune systems. These results suggest that hosts of viruses and bacteria frequently interact with each other in man-made environments and that each hosts mechanisms to defend against each other.

They also detected antibiotic resistance genes (ARGs) in viruses on human skin and on frequently touched interior surfaces. These ARG-carrying viruses could infect bacterial hosts and ARGs could be horizontally transferred between bacterial species. Therefore, the role played by viruses in artificial environments in the development of antibiotic resistance in bacteria is crucial and deserves further investigation.

‘Our study shows that the diversity, composition, metabolic functions and lifestyle of viruses vary, depending on the conditions of each human-made environment,’ said Professor Lee. “Therefore, it is important to develop customized control strategies to minimize human exposure to harmful microorganisms and better protect the health of residents. Our findings can contribute to this goal by improving the fundamental understanding of the complex virus-bacteria interactions in man-made environments.”

The results were published in the scientific journal Nature communications under the title “Highly host-bound viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution”.

The first author is Miss Du Shicong, PhD student in SEE, and the corresponding author is Professor Lee. Other team members include Professor Alvin Lai Chi Keung, Professor Chan Chak Keung AND Dr. Tong Xinzhaoto SEE, e Professor Christopher E. Masonby Weill Cornell Medicine.

The research is supported by the Research Grants Council’s Research Impact Fund and the Hong Kong General Research Fund.

https://www.cityu.edu.hk/research/stories/2023/07/06/unveiling-secret-viruses-bacteria-interactions-man-made-environments