Virus–host links in the different habitats of built environments. Image: Du et al, Nature Communications

Indoor viruses show habitat-specific diversity

7 July 2023

New research from the City University of Hong Kong shows that viruses in built environments, like homes and offices, show diversity linked to specific habitats and potential to evolve with hosts

In-depth studies of viruses in built environments such as homes and offices are less common compared to bacteria. This research delves into the viromes or viral communities found across 11 different habitats within four types of built environments, ranging from low to high occupancy. The study discovered that the diversity, composition, metabolic functions, and lifestyles of these viromes are influenced by their specific habitats.

Species of the Caudoviricetes virus family were found in abundance on surfaces within these built environments, some of which are unique compared to those found in other settings. Interestingly, genes that confer resistance to antimicrobials were detected in viruses present on frequently touched surfaces and on human skin.

In a possible sign of co-evolution between viruses and their hosts, the study found varied CRISPR/Cas immunity systems in bacterial hosts, and their corresponding anti-CRISPR proteins in the viruses. There’s also evidence of viruses possibly assisting host adaptation in specific habitats, identified through unique gene insertions.

This research sheds light on how virus-host interactions frequently occur in built environments and how integral viruses are to the microbiomes of these settings.

Viruses are key players in many ecosystems, balancing crucial roles in health and environmental dynamics. Human-built environments like homes and offices are rich in diverse microorganisms, with viruses often overlooked in studies typically focused on bacteria and fungi. Yet, viruses are prevalent in built environments, with estimates suggesting approximately 10^5 virus particles per cubic meter. Despite built environments' oligotrophic conditions, which are generally unfavorable for microbial life, a diverse array of viruses, including those associated with epidemics (like SARS-CoV-2 and yellow fever virus), are found in microbial communities on surfaces and in the air of built environments.

Previous studies on viromes in public buildings have been restricted in their spatial scope and sample types, often missing out on the relationships between viruses and their bacterial hosts. However, recent global-scale research utilizing bulk metagenomic sequencing has shown that viruses are ubiquitous on public surfaces within built environments.

Interactions between viruses and their hosts are pivotal to the evolution and ecology of microbiomes across ecosystems. Innovative bioinformatic tools can now precisely predict associations between metagenome-derived viruses and potential bacterial hosts, considering factors like matching molecular signals (e.g., CRISPR spacer, integrated genome, and tRNA) and k-mer frequency consistency. Phages, viruses that infect bacteria, utilize various life cycle strategies and transmission methods, playing essential roles in global nutrient cycling and mediating bacterial species competition.

Annotation of the high-quality viral genomes recovered from metagenomes collected from built environments. Image: Du et al, Nature Communications

While phages drive rapid bacterial genetic and phenotypic changes, bacteria also evolve defense mechanisms against phage attacks. Bacteria's arsenal includes the versatile CRISPR/Cas systems, a topic of intense recent study. Counteracting these defenses, phages have developed anti-CRISPR (Acr) proteins to neutralize bacterial Cas nucleases during infection. This strategic back-and-forth can even lead to some bacterial lineages losing their CRISPR/Cas systems due to long-term phage inhibition.

Although CRISPR/Cas systems are known to exist in surface microbiomes in urban environments, much remains unknown about the dynamics of these systems and virus-host interactions in built environments. To address these gaps, this study analyzed 738 bulk metagenomes from a variety of habitats across different built environments in Hong Kong. The findings suggest a strong correlation between the abundance of bacterial populations in built environments and their resident viruses, supporting the idea that viruses assist bacterial hosts in adapting to specific environmental conditions in built environments. This research provides strong evidence that viruses are integral members of built environment microbiomes, highlighting the need for a deeper understanding of these interactions for effective health and environmental management.

The research was led by Professor Patrick Lee Kwan-Hon from the School of Energy and Environment, City University of Hong Kong (CityU). The first author of the paper is Ms Du Shicong, a PhD student. Other key contributors include Professor Alvin Lai Chi-Keung, Professor Chan Chak-Keung, and Dr Tong Xinzhao from CityU, and Professor Christopher E. Mason from Weill Cornell Medicine. The findings were published in Nature Communications.