Li Deng

RESEARCH FOCUS

Virus in Nature and Health

The Deng’s lab takes an integrated approach to investigate microbes and viruses interactions by combining microcosm experiments, employing ecological relevant models, with culture-independent methods and high-throughput metagenomics. Our research focus is on virus interactions in the human body (especially lung) and in the environment (especially groundwater).

Viruses, especially (bacterio)phages (viruses infecting bacteria), typically outnumber microbial cells by ~10-fold in aquatic systems, recasting them more recently from environmentally insignificant to the most abundant biological entities on Earth. Viruses are now considered ubiquitous players that impact microbial communities through mortality and horizontal gene transfer to modulate microbial metabolism. During the past years diverse phenomena critical to the biology of microbes has been described to be driven by viruses, especially with respect to rapid environmental changes. The view that viruses are “only” parasites is no longer valid but rather that they are able to transfer and store genetic information of their hosts and influence biogeochemical cycles in ecosystems. Consequently, biogeochemical processes in microbial ecosystems and their potential for novel niche adaptation in response to changing environmental conditions can be understood only when this large dynamic gene pool carried by lytic and temporary viruses is recognized.

Methods developed

Bioinformatic toolbox

Despite growing interest in recent years, studying the virome remains a challenging endeavor due to several reasons, including the scarcity of viral genomic material (compared to microbial and human nucleic acid fraction), small genome sizes of viruses and their low abundance in some cases. In a microbial community only 2–5% of the total DNA is generally of viral origin. Additionally, no conserved gene regions applicable for all viral types have been identified so far. Moreover, many viruses have not been characterized yet and are not included in viral databases. These facts impede straightforward contig assemblages as well as functional annotation of viral genomes and metagenomes.

We built a human virome protein cluster (HVPC) database in order to improve and facilitate functional annotation and characterization of human viromes. This Human Viral Metagenomic Database for Diversity and Function Annotation constitutes of 12 terabases in total, more than 6 Million open reading frames (ORFs), and 927K function clusters. Further improvements such as using machine learning tools (random forest ad neural networks/deep learning) to identify host of viruses using signals including CRISPR, prophages, k-mer, etc. are currently on-going.